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Notes/Chemistry/Polymers, amino acids, proteins and DNA, and organic synthesis (A-level)
Notes · ChemistryUK · A-Levels

Polymers, amino acids, proteins and DNA, and organic synthesis (A-level)

This A-level-only topic brings organic chemistry together. It covers addition and condensation polymers and their disposal, the acid-base chemistry of amino acids and the structure of proteins and enzymes, the structure of DNA and the action of the anti-cancer drug cisplatin, and the design of multi-step synthetic routes by functional-group interconversion.

4 sections·~12 min reading time·3 competencies·Level Advanced 4

T·171717 / 18
Exam profile
AO1 · Recall polymer types, amino-acid, protein and DNA structure, and the standard synthetic transformationsAO2 · Draw repeat units and monomers, write hydrolysis and synthesis equations, and plan multi-step routesAO3 · Evaluate polymer disposal and deduce a synthetic route to a target molecule
Operators:statedrawdeduceexplainoutlineevaluate

basic level

This entire topic is A-level only (A2); it is not assessed at AS.

higher level

The full A-Level treats addition and condensation polymers, amino acids/proteins/DNA, the action of cisplatin, and multi-step organic synthesis, drawing on all the earlier organic chemistry.

Depth

Reading depth: In depth

Text

Text size: Standard

Contents · 4 sections▾
  1. Polymers, amino acids, proteins and DNA, and organic synthesis (A-level)
    • 01Addition and condensation polymers●
    • 02Amino acids, proteins and enzymes●
    • 03DNA and the action of cisplatin●
    • 04Organic synthesis and functional-group interconversion●
§ 01

Addition and condensation polymers#

●●●AdvancedLPAQA 7405 3.3.14.1LPDfE GCE Chemistry - polymers

Addition versus condensation polymers

Two types of polymerisationTable with 3 columns and 4 rows, Data: Feature · Addition · Condensation; Monomer · unsaturated (C=C) · two reactive groups each; Small molecule lost · none · water or HCl; Linkage · C-C backbone · ester or amide; Hydrolysed / biodegradable · no · yesFEATUREADDITIONCONDENSATIONMonomerunsaturated (C=C)two reactive groups eachSmall molecule lostnonewater or HClLinkageC-C backboneester or amideHydrolysed / biodegradablenoyes
Fig. 1Addition polymers lose nothing and resist hydrolysis; condensation polymers lose a small molecule and can be hydrolysed.

Key points

There are two types of polymerisation. Addition polymerisation (from the alkenes topic) joins unsaturated monomers with no loss of any atoms, so the polymer has the same empirical formula as the monomer. Condensation polymerisation joins monomers with the loss of a small molecule (usually water or hydrogen chloride) at each linkage. The two main condensation polymers are polyesters (linked by ester bonds) and polyamides (linked by amide bonds), each formed from monomers that have two reactive groups so the chain can grow at both ends.
A polyester is made from a dicarboxylic acid and a diol (or from a single monomer with both a -COOH and an -OH group); each ester linkage forms with the loss of a water molecule. Terylene (PET) is a familiar polyester. A polyamide is made from a dicarboxylic acid and a diamine; each amide linkage forms with the loss of water (or from an acyl dichloride and a diamine, losing HCl). Nylon (from a diacid and a diamine) and Kevlar are polyamides; proteins are natural polyamides.
To find the repeat unit of a condensation polymer, join the two monomers by the appropriate linkage (ester or amide), remove the small molecule, and show the bonds continuing through the brackets. Conversely, to find the monomers from a repeat unit, break each linkage and add back the atoms of the small molecule (add -OH and H- across a broken ester or amide bond) to recover the acid and the alcohol or amine.
The linkages in condensation polymers can be hydrolysed - broken by water (with acid or alkali) - back to the monomers, because the ester and amide bonds react with water. This makes many condensation polymers biodegradable, unlike addition polymers whose inert carbon backbone resists hydrolysis. This difference is central to evaluating polymer disposal: addition polymers persist and are hard to dispose of, whereas polyesters and polyamides can be broken down, and newer biodegradable polymers are designed to be hydrolysed in the environment.
n HOOC-R-COOH+n HO-R’-OH→[OC-R-COO-R’-O]n+2n H2On\,\text{HOOC-R-COOH} + n\,\text{HO-R'-OH} \rightarrow [\text{OC-R-COO-R'-O}]_n + 2n\,\text{H}_2\text{O}nHOOC-R-COOH+nHO-R’-OH→[OC-R-COO-R’-O]n​+2nH2​O

Polyester formation

A diacid and a diol condense, losing a water molecule at each ester linkage.

Worked example

Monomers from a polyamide

Nylon-6,6 has the repeat unit -[CO(CH2)4CO-NH(CH2)6NH]-. Identify the two monomers and the small molecule lost during its formation.

  1. 01Break the amide links

    Break each -CO-NH- bond and add back the atoms of water: -OH to the C=O side and H- to the N side.

  2. 02Identify the acid

    The -CO(CH2)4CO- part becomes the dicarboxylic acid HOOC(CH2)4COOH (hexanedioic acid).

  3. 03Identify the amine

    The -NH(CH2)6NH- part becomes the diamine H2N(CH2)6NH2 (hexane-1,6-diamine); water is lost at each linkage.

Result: The monomers are hexanedioic acid and hexane-1,6-diamine, with water lost at each amide linkage.

Exam focus

  • Draw the repeat unit of a polyester or polyamide from its monomers, showing the ester or amide linkage and the small molecule lost.
  • Deduce the monomers from a condensation polymer's repeat unit, and evaluate the disposal of addition versus condensation polymers.

Typical mistakes

  • Forgetting to remove the small molecule (water/HCl) when drawing a condensation repeat unit.
  • Claiming addition polymers are biodegradable - their inert C-C backbone resists hydrolysis.

Active revision

A polyester is made from benzene-1,4-dicarboxylic acid and ethane-1,2-diol. Draw the repeat unit and state the small molecule lost.

Active recall

Recall the key points — then reveal.

Sources: GCE AS and A level subject content for the sciences (Department for Education) · AQA A-level Chemistry 7405 specification (AQA)

§ 02

Amino acids, proteins and enzymes#

●●●AdvancedLPAQA 7405 3.3.15.1LPDfE GCE Chemistry - amino acids and proteins

An amino acid and its zwitterion

Amino acid formsmulti-panel figure, 2 panels, Data: neutral — Skeletal structure with 5 atoms and 4 bonds; zwitterion — Skeletal structure with 5 atoms and 4 bondsAmino acid formsCNH2COOHHRneutralCNH3+COO-HRzwitterion
Fig. 2At neutral pH the amino acid exists as a zwitterion: the -COOH has donated its proton to the -NH2, giving -NH3+ and -COO-.

Key points

An amino acid contains both an amino group (−NH2-\text{NH}_2−NH2​, basic) and a carboxylic acid group (−COOH-\text{COOH}−COOH, acidic) on the same molecule; the twenty that make up proteins are 2-amino acids, with both groups on the same carbon. Because they contain both an acid and a base, amino acids are amphoteric - they react with both acids and bases. In the solid and in solution near neutral pH they exist as a zwitterion, in which the acid group has donated a proton to the amino group, so the molecule carries both a positive −NH3+-\text{NH}_3^+−NH3+​ and a negative −COO−-\text{COO}^-−COO− but is overall neutral.
The charge on an amino acid depends on the pH. In acidic solution the extra H+\text{H}^+H+ protonates the carboxylate, so the amino acid is positively charged (−NH3+-\text{NH}_3^+−NH3+​, −COOH-\text{COOH}−COOH); in alkaline solution the amino group loses its proton, so it is negatively charged (−NH2-\text{NH}_2−NH2​, −COO−-\text{COO}^-−COO−). At one particular pH, the isoelectric point, the amino acid carries no net charge (the zwitterion), and this pH is characteristic of each amino acid.
Amino acids join by condensation to form proteins, which are natural polyamides (polypeptides). The amino group of one amino acid and the carboxyl group of the next condense, losing water and forming a peptide (amide) bond, −CO-NH--\text{CO-NH-}−CO-NH-. Proteins are described by levels of structure: the primary structure is the sequence of amino acids; the secondary structure (α\alphaα-helices and β\betaβ-pleated sheets) is held by hydrogen bonds; and the tertiary structure is the overall folded three-dimensional shape, held by hydrogen bonds, ionic interactions and disulfide bridges. Proteins are hydrolysed back to their amino acids by heating with acid.
Enzymes are proteins that act as biological catalysts, and their specificity comes from the precise three-dimensional shape of their active site, which fits only a particular substrate. Many drugs work by fitting into an enzyme's active site and blocking it (inhibition), and because the active site is chiral, usually only one enantiomer of a drug fits - a direct link to optical isomerism. When you draw an amino acid, show the zwitterion at neutral pH, and be able to draw the different charged forms at low and high pH.
H2N-CHR-COOH+H2N-CHR’-COOH→H2N-CHR-CO-NH-CHR’-COOH+H2O\text{H}_2\text{N-CHR-COOH} + \text{H}_2\text{N-CHR'-COOH} \rightarrow \text{H}_2\text{N-CHR-CO-NH-CHR'-COOH} + \text{H}_2\text{O}H2​N-CHR-COOH+H2​N-CHR’-COOH→H2​N-CHR-CO-NH-CHR’-COOH+H2​O

Peptide bond formation

Two amino acids condense, losing water and forming a peptide (amide) bond -CO-NH-.

Worked example

Charge on an amino acid with pH

Describe and explain the charge on a simple amino acid in strongly acidic, neutral and strongly alkaline solution.

  1. 01Acidic solution

    Excess H+ protonates the carboxylate, so the amino acid is positive: -NH3+ and -COOH.

  2. 02Neutral (isoelectric point)

    It exists as the zwitterion, -NH3+ and -COO-, with no overall charge.

  3. 03Alkaline solution

    The amino group loses its proton, so the amino acid is negative: -NH2 and -COO-.

Result: Positive at low pH, neutral zwitterion at the isoelectric point, and negative at high pH.

Exam focus

  • Draw the zwitterion and the charged forms of an amino acid at low, neutral and high pH, and define the isoelectric point.
  • Describe the levels of protein structure and the bonds holding each, and the hydrolysis of proteins to amino acids.

Typical mistakes

  • Drawing the neutral form at neutral pH instead of the zwitterion.
  • Confusing the bonds holding secondary structure (hydrogen bonds) with the primary structure (the covalent sequence).

Active revision

Draw the structure of the amino acid glycine (H2NCH2COOH\text{H}_2\text{NCH}_2\text{COOH}H2​NCH2​COOH) as it exists at (a) low pH, (b) its isoelectric point and (c) high pH.

Active recall

Recall the key points — then reveal.

Sources: AQA A-level Chemistry 7405 specification (AQA)

§ 03

DNA and the action of cisplatin#

●●●AdvancedLPAQA 7405 3.3.15.2LPDfE GCE Chemistry - DNA and cisplatin

The structure of cisplatin

cisplatin: two NH3 and two Cl in cis positionsSkeletal structure with 5 atoms and 4 bonds, Data: Pt, NH3, H3N, Cl, Cl, Pt–NH3, Pt–H3N, Pt–Cl, Pt–ClPtNH3H3NClCl
Fig. 3Cisplatin is the cis isomer of square-planar [Pt(NH3)2Cl2]; the two chlorides are later replaced by bonds to DNA.

Key points

DNA is a natural condensation polymer built from nucleotides, each made of a phosphate group, the sugar 2-deoxyribose, and one of four nitrogenous bases (adenine, thymine, guanine and cytosine). The nucleotides join through phosphodiester bonds between the phosphate of one and the sugar of the next, forming a long sugar-phosphate backbone with the bases projecting from it. This is the primary structure of DNA - the sequence of bases carries the genetic information.
Two DNA strands wind around each other in a double helix, held together by hydrogen bonds between complementary base pairs. The pairing is specific: adenine pairs with thymine (two hydrogen bonds) and guanine pairs with cytosine (three hydrogen bonds). This complementary base pairing means the two strands carry the same information and, when the strands separate, each acts as a template so that the DNA can be copied - the molecular basis of inheritance.
Cisplatin is a platinum complex used as an anti-cancer drug. It is the cis isomer of the square-planar complex [Pt(NH3)2Cl2]\text{[Pt(NH}_3)_2\text{Cl}_2\text{]}[Pt(NH3​)2​Cl2​]: a central platinum(II) ion with two ammonia ligands and two chloride ligands in adjacent (cis) positions. Its geometry is essential to its action - the trans isomer is far less effective, which is a striking illustration of how the arrangement of ligands in space determines biological activity.
Cisplatin works by binding to the DNA in cancer cells. The two chloride ligands are replaced (ligand substitution) by bonds to nitrogen atoms of guanine bases on the DNA, so the platinum forms a cross-link that changes the shape of the DNA and prevents the cell from replicating its DNA and dividing. This stops the cancer cells multiplying. Because it also affects healthy dividing cells, cisplatin has serious side effects, and its use must balance its benefit against these - an example of the risk-benefit judgements in medicinal chemistry.
Worked example

How cisplatin stops cancer cells dividing

Outline how cisplatin prevents cancer cells from dividing.

  1. 01Structure

    Cisplatin is the cis square-planar complex [Pt(NH3)2Cl2], with two labile chloride ligands.

  2. 02Binding to DNA

    The two chloride ligands are replaced (ligand substitution) by bonds to nitrogen atoms of guanine bases, forming a cross-link on the DNA.

  3. 03Effect

    This distorts the DNA so it cannot be replicated, so the cancer cell cannot divide and dies.

Result: Cisplatin binds to DNA by ligand substitution at guanine, cross-linking and distorting it so the cancer cell cannot replicate.

Exam focus

  • Describe the structure of a nucleotide, the sugar-phosphate backbone and the complementary base pairing (A-T, G-C) held by hydrogen bonds.
  • Explain how cisplatin binds to DNA by ligand substitution and why its cis geometry is essential.

Typical mistakes

  • Getting the base pairing wrong (adenine pairs with thymine, guanine with cytosine).
  • Confusing cisplatin with its far less effective trans isomer.

Active revision

Explain how cisplatin acts as an anti-cancer drug, referring to its structure, ligand substitution and its effect on DNA.

Active recall

Recall the key points — then reveal.

Sources: AQA A-level Chemistry 7405 specification (AQA)

§ 04

Organic synthesis and functional-group interconversion#

●●●AdvancedLPAQA 7405 3.3.16.1LPDfE GCE Chemistry - organic synthesis

A functional-group interconversion map

Aliphatic reaction mapGraph, alkene → alcohol, alcohol → halogenoalkane, halogenoalkane → nitrile, nitrile → amine, nitrile → carboxylic acid, alcohol → aldehyde, aldehyde → carboxylic acidalkenealcoholhalogenoalkanenitrileaminecarboxylic acidaldehydesteam / H+HXKCNreducehydrolyse[O], distil[O], reflux
Fig. 4Each arrow is a known transformation; a synthesis is a path through this map from the starting material to the target.

Key points

Organic synthesis is the design of a sequence of reactions to convert an available starting material into a desired target molecule. It draws together every reaction in the course: each step changes one functional group into another, so a route is a chain of functional-group interconversions. To plan a route, you need to know which reagents and conditions carry out each transformation - for example, an alkene to an alcohol (steam/acid catalyst), an alcohol to a halogenoalkane, a halogenoalkane to a nitrile (KCN\text{KCN}KCN), and a nitrile to an amine (reduction) or to a carboxylic acid (hydrolysis).
A useful strategy is to work backwards from the target (retrosynthesis): ask what could be converted into the target in one step, then what could make that, and so on back to the starting material. Along the way, note where a step changes the number of carbon atoms - adding cyanide (as CN−\text{CN}^-CN−) increases the chain by one carbon, which is often the key to a synthesis that lengthens the carbon skeleton.
Some target molecules are chiral, and a synthesis that passes through a planar intermediate (such as a carbonyl in a cyanide addition) produces a racemic mixture. This matters when a single enantiomer is required, as for many pharmaceuticals, because separating enantiomers is difficult. Recognising where a racemate would form, and why, is part of evaluating a synthetic route.
The skill assessed is choosing a sensible, correct sequence of reactions with the right reagents and conditions at each step, and being able to justify it. When you plan a synthesis, set out each step with its reagent, conditions and product, check that the functional groups transform as intended, and keep the route as short as practicable. A clear reaction map of the common interconversions is the most valuable revision aid for this.
Worked example

A synthesis that lengthens the chain

Devise a route to convert 1-bromopropane into butanoic acid (which has one more carbon), giving reagents for each step.

  1. 01Add a carbon with cyanide

    React 1-bromopropane with potassium cyanide (in ethanol/water) by nucleophilic substitution to form butanenitrile, CH3CH2CH2CN, gaining one carbon.

  2. 02Hydrolyse the nitrile

    Heat the nitrile under reflux with dilute acid (or alkali then acidify) to hydrolyse it to the carboxylic acid.

  3. 03Product

    This gives butanoic acid, CH3CH2CH2COOH, with four carbons.

Result: 1-bromopropane -> (KCN) butanenitrile -> (hydrolysis) butanoic acid, adding one carbon via the cyanide step.

Exam focus

  • Plan a multi-step synthesis, giving the reagent and conditions for each functional-group interconversion.
  • Identify where a step changes the number of carbon atoms (e.g. adding CN-) or would produce a racemate.

Typical mistakes

  • Choosing reagents that do not carry out the intended transformation, or a route that is longer than necessary.
  • Overlooking that a synthesis through a planar intermediate produces a racemic mixture.

Active revision

Devise a two-step synthesis of propylamine (CH3CH2CH2NH2\text{CH}_3\text{CH}_2\text{CH}_2\text{NH}_2CH3​CH2​CH2​NH2​) from bromoethane, giving the reagents and conditions.

Active recall

Recall the key points — then reveal.

Sources: AQA A-level Chemistry 7405 specification (AQA)

Contents

Section -- / 04

    • 01Addition and condensation polymers●
    • 02Amino acids, proteins and enzymes●
    • 03DNA and the action of cisplatin●
    • 04Organic synthesis and functional-group interconversion●

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Polymers, amino acids, proteins and DNA, and organic synthesis (A-level)

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References & sources

Sources

Department for Education

  • GCE AS and A level subject content for the sciences

AQA

  • AQA A-level Chemistry 7405 specification

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