THEORY

Question 1

(a) (i) amino acid chemistry:
• the general structure of amino acids
• proteins as condensation polymers formed from amino acid monomers
• the formation and hydrolysis of the peptide link between amino acid residues in proteins
• experiments involving the hydrolysis of peptides

Answer 1

• Proteins = naturally occuring condensation polymers
  
  • made from amino acids (monomers)
    
    • amino acid monomers in a protein chain that have lost the elements of water in forming a peptide are called amino acid residues
  • joined by peptide links/bonds (secondary amide links)
    
    • when amino group of one amino acid reacts with carboxylic acid group of another (condensation reaction, so water eliminated)
  • two amino acids joined together = dipeptide
  • three = tripeptide
  • more = polypeptide chain
• To break polypeptide into amino acids –> hydrolyse it
  
  • Hydrolysis reaction = addition of water
  • by heating with conc acid or conc alkali
  • e.g. heat under reflux with conc HCl to hydrolyse amide C-N bond (forms ammonium salts of amino acids), then neutralised using base
  • living organisms –> hydrolyse proteins by enzymes instead of conc acid/alkali

Question 2

(b) the primary, secondary and tertiary structure of proteins; the role of intermolecular bonds in determining the secondary and tertiary structures, and hence the properties of proteins

Answer 2

• Primary structure:
  
  • sequence in which amino acids (residues) are joined together in the polypeptide chain
• Secondary structure:
  
  • folding of the primary sequence into an α-helix or a β-pleated sheet
  • held together by hydrogen bonds between -NH groups on one peptide link and -C=O groups of another peptide link
• Tertiary structure:
  
  • further folding of the secondary structure
  • has a 3D shape
  • id-id bonds form between non-polar side chains
  • h-bonding forms between polar side chains
  • ionic bonds form
  • covalent bonds form (disulfide bridges)

Question 3

(c) (i) DNA and RNA as condensation polymers formed from nucleotides, which are monomers having three components (phosphate, sugar and base):
the phosphate units join by condensation with deoxyribose or ribose to form the phosphate–sugar backbone in DNA and RNA
Monomers of DNA and RNA are given on the Data Sheet.

Answer 3

• DNA (deoxyribonucleic acid) = contains genetic information of a living organism
  
  • polymer made from monomers (DNA nucleotides)
    
    • phosphate group
    • pentose (five carbon) sugar, deoxyribose
    • base (adenine (A), guanine (G), cytosine (C), thymine (T). )
• RNA (ribonucleic acid)
  
  • polymer made from monomers (RNA nucleotides)
    
    • phosphate group
    • pentose (five carbon) sugar, ribose
    • base (adenine (A), guanine (G), cytosine (C), uracil (U). )
• Phosphate-sugar backbone (long single chain of alternating sugar-phosphate groups)
  
  • formed by condensation polymerisation of phosphate group on one nucleotide and sugar of another
  • when phosphate + sugar react, water = lost and phosphate-ester link formed
  • phosphate-sugar backbone of RNA is the same except sugar is ribose not deoxyribose

Question 4

(c) (ii) DNA and RNA as condensation polymers formed from nucleotides, which are monomers having three components (phosphate, sugar and base):
the four bases present in DNA and RNA join by condensation with the deoxyribose in the phosphate–sugar backbone

Answer 4

• DNA and RNA bases join to the sugar by a condensation reaction
• the -OH group of the sugar reacts with the NH group on the base
  
  • H₂O is eliminated
• In RNA the sugar is ribose (bases; A,U,C,G)
• In DNA the sugar is deoxyribose (bases; A,T,C,G)

Question 5

(c) (iii) DNA and RNA as condensation polymers formed from nucleotides, which are monomers having three components (phosphate, sugar and base):
two strands of DNA form a double-helix structure through base pairing

Answer 5

• Nucleotides join together to form a polynucleotide chain
• DNA is made of two polynucleotide strands that are complementary to each other
• The two strands spiral together to form a double helix structure
• complementary base pairing between bases
  
  • ​held together by hydrogen bonds
    
    • A pairs with T (2 h-bonds)
    • G pairs with C (3 h-bonds)

Question 6

(g) the characteristics of enzyme catalysis, including: specificity, temperature sensitivity, pH sensitivity, competitive inhibition; explanation of these characteristics of enzyme catalysis in terms of a three-dimensional active site (part of the tertiary structure)

Answer 6

• Enzymes are biological catalysts
  
  • catalyse many reactions in living organisms
  • speed up chemical reactions by providing an alternative pathway of lower E_a (activation enthalpy)
• Have highly specific tertiary structures (3D) and active sites (part of the tertiary structure) which complementary to specific substrate molecules
• Lock and Key model
  
  • temporary weak bonds form between substrate and R groups of the enzymes amino acids, active site (e.g. hydrogen bonds, id-id forces)
    
    • Binding causes other bonds within substrate to weaken (breaking substrate up into smaller products)
    • or alters shape of substrate so that substrates brought closer together to react (making larger product)
    • Product(s) leave enzyme, enzyme = unchanged
• Sensitive to pH:
  
  • Optimum pH = pH at which rate of reaction is maximum
    
    • usually at 7, but stomach enzymes have acidic optimum pH’s
  • In too low/high pH’s:
  • Ionic bonds that hold the specific shape of the active site break, changing the tertiary structure (active site no longer complementary to the substrate)
  • Enzyme becomes denatured, stops functioning properly (can no longer catalyse reaction effectively)
• Sensitive to temperature:
  
  • Optimum temperature = temperature at which rate of reaction is maximum
  • Before optimum; as temperature increases so does enzyme activitity, due to more molecules having enough kinetic energy to collide and successfully react
  • If temperature = too high;
  • weak dipole-dipole bonds and hydrogen bonds that hold the specific shape of the active site break, changing the tertiary structure (active site no longer complementary to the substrate)
  • Enzyme becomes denatured, stops functioning properly (can no longer catalyse reaction effectively)
• Competitive inhibition:
  
  • Molecules with a similar shape to substrate
  • fit (reversibly) into the active site but cannot be catalysed = competitive inhibitors
  • Block active site so substrate cannot bind
  • Compete with substrate molecules for the active site

Question 7

(h) the acidic nature of carboxylic acids, and their reaction with metals, alkalis and carbonates

Answer 7

• Carboxylic acids = weak acids (partially dissociate)
  
  • dissociate into carboxylate ions and H⁺ ions
• Strong enough acids to react/be neutralised, with strong alkalis (alkali = solube/aqueous base) to form salts and water (Phenols also react with strong bases to form salts and water, alcohols do not)
• Carboxylic acids react with carbonates
  
  • forms salt, carbon dioxide and water
  • reaction produces fizz (because of CO₂ production)
  • acid-base reaction, where the carbonate ion, CO₃^2-_(aq) acts as the base
  • Phenols and Alcohols do not have a great enough conc of H⁺ so do not react with carbonates (no fizz)
• Carboxylic acids react with reactive metals
  
  • forms salt and hydrogen gas
  • redox reaction
  • phenols and alcohols also react with reactive metals in this way

Question 8

(i) the acid–base properties of amino acids and their existence as zwitterions
• test-tube experiments involving amino acids

Answer 8

• Amino acids = amphoteric (have both acidic + basic properties)
  
  • bifunctional (contain two functional groups)
• Zwitterions:
  
  • An overall neutral molecule that has both positively and negatively charged groups in different parts of the molecule
  • form because functional groups interact with each other; proton-donating -COOH and proton accepting -NH₂ groups react with each other
  • act as a buffer (solution that resists changes in pH with addition of small amounts of acid/alkali)
    
    • in alkali: OH^- + H₃N^+_CHRCOO^- –> H₂O + H₂N^+_CHRCOO^-
    • in acid: H₃O⁺ + H₃N^+_CHRCOO^- –> H₂O + H₃N^+_CHRCOOH
  • aqueous solution of amino acids = mostly zwitterions
  • amino acids = very soluble in water (because effectively ionic)
  • neutral in solution unless extra COOH and NH₂ functional groups present in R groups
• AMINO ACIDS: Exist in 3 different ionic forms depending on the pH of the solution

Question 9

(j) the basic nature of the amino group; the reaction of amines with acids
In terms of a lone pair on the nitrogen accepting a proton to give a cation.

Answer 9

Amino acids:

• Amino group -NH₂ is basic
  
  • form salts with acids (like amines)
• Test for amines =
  
  • turns piece of damp red litmus paper blue
  • and react with small amount of an acyl chloride
    
    • if amine = present, white fumes of hydrogen chloride gas formed
• Properties of amines –> due to lone pair (similar to ammonia)
  
  • soluble in water (form H-bonds)
    
    • amines with small alkyl chains = more soluble than with larger alkyl chains
  • acts a base
• Amines act as bases:
  
  • Amines act as bases because donate lone pair and accept protons and form a cation (postively charged ion)
  • Lone pair on the nitrogen of the amine can form a dative covalent bond with a H⁺ ion
    
    • e.g. CH₃NH_2(aq) + H₂O_(l) –> CH₃NH₃⁺_(aq) + OH^-_​(aq)​
    • methylammonium ion
  • presence of OH^- makes solution alkaline (solutions of amines = alkaline)
• Amines can also neutralise acids
  
  • product = ammonium salt
  • the H₃O⁺ (H⁺) are much better proton donors than water, reaction goes to completion and amine loses its strong smell (large amines smell very fishy, small amines, more volatile (gaseous) smell slightly fishy similar to ammonia)
  • general overall equation is; RNH₂ + HX –> RNH₃⁺X^-
  • ionic equation; RNH_2(aq) + H₃O⁺_(aq) –> RNH₃⁺_(aq) + H₂O_(l)

Question 10

(a) (ii) amino acid chemistry:
techniques and procedures for paper chromatography

Answer 10

• Paper chromatography can be used to identify individual amino acids present in a peptide
  
  • peptide = hydrolysed under reflux
  • products compared with known samples of pure amino acids
• Carrying out chromatography:
  
  • Chromatography relies on different organic compounds having different affinities for a solvent, so will travel at different rates
  • Spot concentrated spots of the sample and reference samples on a pencil base line, 1cm from the bottom of the paper
    
    • pencil used because it will not run with the solvent
  • Suspend the paper in a beaker of the solvent (the solvent level should be below the spots)
  • Place a watch glass over the beaker to prevent evaporation of solvent
  • Remove paper from the beaker when the solvent is near the top
  • Mark where the solvent has reached (solvent front) and allow plate to dry
  • most organic compounds = colourless, so spots need to be located using either ninhydrin spray, iodine vapour or UV light
  • Find and compare the Rf values (with spots of known samples, or if chromatography carried out under standard conditions, compare with table of known Rf values)
    
    • Rf = (distance travelled by spot/distance travelled by solvent)

Question 11

(e) (i) molecular recognition (the structure and action of a given pharmacologically active material) in terms of:
the pharmacophore and groups that modify it

Answer 11

• Pharmocophore = part of a medicine that gives it, its pharmacological effect
• can be modified by changing functional groups attatched to them to make medicine more effective or to reduce side-effects

Question 12

(e) (ii) molecular recognition (the structure and action of a given pharmacologically active material) in terms of:
its interaction with receptor sites

Answer 12

• Pharmacophores:
  
  • interact with receptor sites by forming weak interactions (H-bonding, metal coordination, ionic bonds, and dipole-dipole bonds)

Question 13

(e) (iii) molecular recognition (the structure and action of a given pharmacologically active material) in terms of:
the ways that species interact in three dimensions (size, shape, bond formation, orientation)

Answer 13

• Pharmacophores need to have a specific complementary shape to fit into receptors
• Functional groups form temporary weak interactions with receptor
• Orientation - if pharmacphore has an E/Z isomer, then only one will fit

Question 14

(m) the hydrolysis of esters and amides by both aqueous acids and alkalis, including salt formation where appropriate
• the hydrolysis of an ester or amide e.g. nylon

Answer 14

• Hydrolysis (Large molecule broken into two small molecules with addition of water)
• Amides:
  
  • Acid hydrolysis: amide heated with moderately concentrated sulfuric or hydrochloric acid
  • Acid acts as catalyst and also forms a cation with ammonia
    
    • products of acid hydrolysis of primary amides = carboxylic acid, ammonium cation (and corresponding amine salt e.g. NH₄⁺Cl^- if HCl was used as catalyst)
    • primary amide acid hydrolysis:
      
      • CH₃CONH₂ + H₂O + H⁺ (catalyst) –> CH₃COOH + NH₄⁺ (and NH₄⁺Cl^-)
    • if secondary amide = hydrolysed, carboxylic acid and primary amine salt formed
      
      • CH₃CONHCH₃ + H₂O + H⁺ (catalyst) –> CH₃COOH + CH₃NH₃⁺ (CH₃NH₃⁺Cl^-)
  • Alkaline hydrolysis: amide heated with moderately concentrated alkali (e.g. NaOH)
    
    • if NaOH used; alkaline hydrolysis of primary amide: carboxylate ion + ammonia gas formed
      
      • CH₃CONH₂ + OH^- –> CH₃COO^- (and CH₃COO^-Na⁺) + NH_3(g)
    • NaOH used; alkaline hydrolysis of secondary amide: carboxylate ion + amine formed
      
      • CH₃CONHCH₃ + OH^- –> CH₃COO^- (and CH₃COO^-Na⁺) + CH₃NH₂
• In both acid + akaline hydrolysis of amides, C-N bond broken
• Esters:
  
  • Acid hydrolysis:
    
    • products = carboxylic acid (before COO) and alcohol (after COO) acids acts a catalyst
    • conditions + reagents = reflux ester with dilute hydrochloric/sulfuric acid
    • reversible reaction so excess water has to be added to increase yield of products (equilibrium shifts to right)
  • Alkaline hydrolysis:
    
    • refluxed with dilute alkali; sodium hydroxide usually used
    • products = carboxylate salt (before COO) and alcohol (after COO)
    • irreversible reaction so preferred over acid hydrolysis because goes to completion
      
      • C₂H₅COOCH₃ + (Na⁺)OH^- –> C₂H₅COO^-(Na⁺) + CH₃OH

Question 15

(n) the reactions of acyl chlorides with amines and alcohols

Answer 15

• Acyl chlorides react vigorously with amines
  
  • produce secondary amides and HCl
  • RCOCl + R’NH₂ –> RCONHR’ + HCl
  • happens at room temperature
• Acy chlorides react vigorously with alcoholds
  
  • produce esters and HCl
  • RCOCl + R’OH –> RCOOR’ + HCl
  • happens at room temperature
• In both reaction Cl has been substituted by an oxygen or nitrogen group and hydrogen chloride fumes given off
  
  • both are nucleophilic substitution reactions
  • both are condensation reactions
• Test for acyl chlorides:
  
  • Slowly add alcohol to sample
  • If cloudy fumes given off that turn a piece of damp blue litmus paper red, then acyl chloride present

Question 16

(f) the shape of the rate versus substrate concentration curve for an enzyme-catalysed reaction; techniques and procedures for experiments involving enzymes
At low concentrations of substrate the order with respect to the substrate is one, at higher concentrations of substrate the order with respect to the substrate is zero.
• kinetics experiments involving enzymes

Answer 16

• When the substrate concentration = low enough
• not all enzyme active sites bound to a substrate
  
  • limiting factor = substrate concentration
• rate determining step = E + S –> ES
  
  • rate = dependent on how quickly enzyme substrate complexes forming
• rate of reaction is first order with respect to substrate and directly proportional to substrate concentration
• if substrate concentration = high enough
• all enzyme active sites will be bound to a substrate molecule (enzyme active sites = saturated)
• when substrate concentration increased further no more ESC’s can be formed
  
  • limiting factor = enzyme active sites (enzyme concentration)
• rate determing step = EP –> E + P
  
  • how quickly enzyme can release product from enzyme product complex
• if rate of reaction = zero order with respect to substrate

Experiments measuring rates:

• Gas syringe: measuring volume of gas produced at regular time intervals using gas syringe
• Mass balance: if reaction produces a gas (except H₂), measure mass of reactans and calculate mass lost at regular time intervals using mass balance
• Titrations: take samples at regular intervals and use titrations to find concentration of a substrate/product in solution

Experiments studying rates:

• Independent variable:
  
  • temperature
  • pH
  • substrate concentration

Question 17

(q) (i) optical isomerism:
diagrams to represent optical stereoisomers of molecules

Answer 17

• Locate the chiral carbon
  
  • Carbon with four different groups attached
• Draw an enantiomer in a tetrahedral shape with chiral carbon at its centre
• Other enantiomer = mirror image

Question 18

(q) (ii) optical isomerism:
the use of the term chiral as applied to a molecule and identifying carbon atoms that are chiral centres in molecules

Answer 18

• A chiral (centre) carbon atom is a carbon which has four different groups attached to it
• Molecules with one chiral carbon have two isomers (optical isomers, called enantiomers –> type of stereoisomerism)
• Amino acids (apart form glycine) all have chiral carbons

Question 19

(q) (iii) optical isomerism:
enantiomers as non-superimposable mirror image molecules

Answer 19

• Enantiomers = non-superimposable
  
  • isomers are mirror images of each other
  • if a molecule can be superimposed it doesnt have optical isomers and called achiral
• proteins in the human body only built from one enantiomer of each amino acid
• Enantiomers behave identically in testube reactions
  
  • most physical properties = same
  • e.g. melting point, density, solubility
  • fit into different receptors, may smell/taste different

Question 20

(d) the significance of hydrogen bonding in the pairing of bases in DNA and relation to the replication of genetic information; how DNA encodes for RNA which codes for an amino acid sequence in a protein
Some triplet base codes are given on the Data Sheet.

Answer 20

• Hydrogen bonding:
  
  • Adenine, (A) pairs with thymine, (T)/uracil, (U)
    
    • 2 H-bonds
  • Guanine, (G) pairs with cytosine, (C)
    
    • 3 H-bonds
  • hydrogen bond forms between a hydrogen in a polar bond (H attached to highly electronegative N/O/F) and a lone pair of electrons (on a N/O/F)
• DNA replication:
  
  • Before cell division, DNA replicates
  • Hydrogen bonds = break, and DNA double helix starts to split into two single strands
  • Free nucleotides complementary base pair to the exposed bases on each strand of DNA
  • DNA polymerase joins new nucleotides to form polynucleotide chain
  • Two copies of DNA formed, indentical to original molecule (each new strand contains one parent and one new strand)

Protein synthesis:

• Transcription:
  
  • section (relating to one protein) of the DNA double helix unzips
    
    • single strand acts as a template
  • Free RNA nucleotides complementary base pair to exposed DNA bases
  • RNA polymerase joins RNA nucleotides together, forming a strand of mRNA
  • DNA double helix reforms (unaltered)
  • mRNA (exists as a single polynucleotide strand) = small enough to leave cell nucleus
• Translation:

Question 21

(l) the formulae for the following functional groups: primary amide, secondary amide

Answer 21

Question 22

(k) the formulae and systematic nomenclature of members of the following homologous series: carboxylic acids, phenols, acyl chlorides, acid anhydrides, esters, aldehydes, ketones, diols, dicarboxylic acids, primary amines, diamines; naming nylon structures
The structures of nylon-6,6 nylon-6,10 and nylon-6

Answer 22

• Naming:
  
  • acyl chlorides;
    
    • (named like carboxylic acids, except -ic acid replaced with -oyl chloride)
      
      • ethanoyl chloride
  • amines;
    
    • smaller primary amines = R group added to suffix -amine
      
      • e.g. methylamine, ethylamine
    • longer amines = amino added as prefix
      
      • e.g. 2-aminopropane
  • diamines;

Question 24

(o) the differences between addition and condensation polymerisation

Answer 24

• Condensation polymerisation:
  
  • monomers react together to give longer chain polymer and a small stable molecule (water or hydrogen chloride)
    
    • form condensation polymers (polyesters + polyamides)
    • usually two different monomers
    • monomers must have at least 2 functional groups to produce condensation polymer
    • main polymer chain = unreactive
• Addition polymerisation
  
  • monomers join together to give addition polymer only
  • formed from alkenes (one type of monomer)
  • double bond open up and join together to make addition polymer
    
    • diamines + dicarboxylic acids = polyamide
    • diols + carboxylic acids = polyesters
    • reactivity = links between monomers; amide links/ester links can be hydrolysed under acidic/alkaline conditions to break down polymer into original monomers