Chemistry: Polymers and Life

A copy of the data sheet can be found here.

a Amino acids:

Test yourself
• Amino acids contain at least one amino (-NH₂) group and one carboxylic acid (C=OOH) group
• 2-amino acids (or alpha-amino acids / α-amino acids) have the NH₂ group attached to the carbon next to the COOH group. The general formula is H2N-CHR-COOH:
  
• There are 20 amino acids which are part of proteins, with full names like glycine. These names are shortened to 3 letters (Gly, Ala, Val etc)
• All amino acids are solids, with high (over 500 K) melting points
• They share some properties of amines and carboxylic acids

Peptides:

• Reacting two amino acids will cause them to release a water molecule (this is a condensation reaction). A bond then forms between the carbon from the COOH group (the OH has been broken off to create the water molecule) and the nitrogen from the NH₂ group (a H has also been broken off), as shown below:
  
• The -CONH- (in blue above) is called the peptide link
• The above dipeptide is made from Ala and Gly. These are written from left to right (with the NH₂ group (N-terminal) on the left and COOH group (C-terminal) on the right) without spaces - GlyAla
• These amino acids joined with -CONH- links are known as amino acid residues, as they have lost the elements of water
• With three amino acid residues, it's called a tripeptide. A relatively short chain is called a polypeptide
• A chain of many amino acids is known as a protein

Hydrolysis of proteins:

• Hydrolysing the peptide link releases the amino acids
• This is done by heating with a medium-concentration acid/alkali
• In organisms, enzymes are used as the catalyst
• Chromatography can then be used to find which amino acids are present

Paper chromatography:

• Thin layer and paper chromatography are used to separate organic compounds
• TLC uses a silica plate, and paper chromatography uses chromatography paper
  Steps:
  1) Draw a pencil line about 1 cm from the bottom of the paper. Spot on the sample and reference samples onto this line (e.g. pure amino acid samples if detecting the compounds making up a polypeptide/protein)
  2) Suspend the plate in a beaker containing the solvent. Cover the beaker with a watch glass to saturate the air inside with the solvent
  3) Once the solvent reaches the top, remove the paper and let it dry
  4) Spots can be located with iodine, ninhydrin or UV. Now s (the distance travelled by the spot divided by the distance moved by the solvent) can be calculated and analysed

b Protein structures:

Test yourself
• The primary structure is the sequence of amino acids in the chain
• Peptide links form hydrogen bonds with each other - and the structure formed is known as the protein's secondary structure. The most common types are alpha-helix and beta-pleated sheet
• Additional bonds may also form between groups of amino acid residues, folding and coiling the protein. This is its tertiary structure. Tertiary structure can affect the properties of the protein (e.g. changing the shape of the active site in an enzyme)

Bonds creating these structures:

• Charged side groups have ionic interactions bonding them together
• Some groups can hydrogen bond together (e.g. -OH)
• A disulfide bond/disulfide bridge can form between -SH groups on the Cys amino acid
• There are also instantaneous dipole-induced dipole bonds between groups

c, d DNA:

Test yourself
• DNA is made from nucleotide monomers, containing:
  - A phosphate group
  - A sugar (deoxyribose)
  - A base: adenine, thymine, cytosine or guanine (A, T, C or G)
  (all of these structures and their names are given in the data sheet)
• Each phosphate group bonds to a sugar group, creating a phosphate-sugar backbone

RNA:

• RNA acts as a messenger between the DNA and ribosomes, where protein synthesis takes place
• It's very similar to DNA, except:
  - with ribose instead of deoxyribose as the sugar
  - with uracil instead of thymine

Bonding within DNA:

• Two polynucleotide strands form a double-helix structure, held together by hydrogen bonds between the bases
  - These hydrogen bonds form between A and T (with 2 hydrogen bonds), and C and G (with 3 hydrogen bonds), complimentary base pairing
  - Any other pairing would have two repelling partial charges close together, so they wouldn't bond
• The phosphate-sugar backbone is formed with condensation polymerisation, a water molecule is lost (from an OH group in the phosphate and H in the CH₂OH group in the sugar). This is where the link forms. This process is the same in RNA
• Bases also form condensation polymers with the backbone by bonding to the sugar, replacing the OH to form water. The additional H comes from the NH group in the base

Genetic code:

• Every protein synthesised in the body is coded for by a gene, a section of DNA
• Each amino acid is coded for by three bases, base triplets or codons
• This means that there are 4³ = 64 possible combinations, so some amino acids are coded for by multiple combinations
  - There are also 'stop' codons and a 'start'
• Only the order of amino acid residues is needed, as this also determines the secondary and tertiary structure

Note:

Both the textbook and CGP revision guide contain information on mRNA, tRNA, translation, transcription, etc. This is not required knowledge in the new course and was likely mistakenly copied over to the new books (the majority of their content was just republished from the old texts).

You may also see questions on the development of DNA models in old past papers, this has also been removed in this new course.

Everything you need to know is on this page.

e Receptors:

Test yourself
• Most cells in the body contain receptor sites which can bond to chemicals that fit
• The pharmacophore is the part of a drug which fits into receptor sites. Other parts of a drug can often be changed to reduce side effects or increase its effectiveness
• Therefore, drugs need to have a specific size, shape, orientation, and groups which create the required bonds (e.g. dipole-dipole, hydrogen and ionic). Also, only one optical isomer will often fit, or both will have different effects (which is why many drugs are available as both racemic (both optical isomers) mixes and isolated isomers)

f, g Enzymes:

Test yourself
• Enzymes are proteins (or mostly a protein) which act as biological catalysts
• A substrate is a molecule that enzymes catalyse
• The active site of an enzyme is the part which the substrate fits into. It's part of the protein's tertiary structure
• Most enzymes only work on one substrate; they have high specificity - other substrates won't fit. This can be visualised with the lock and key model
• The substrate is held in place with temporary bonds such as hydrogen bonds while it reacts

Optimal conditions for enzymes:

• All enzymes have an optimal pH and temperature
• If the temperature is too low, the reaction is too slow due to low kinetic energy
• If temperature is too high, or the pH isn't optimal, the active site will change shape due to tertiary structure changes - it denatures

Competitive inhibition:

• Competitive inhibitors can fit inside and bond to the active site, but do not react
• This prevents the substrate from utilising the enzyme
• Many drugs are competitive enzyme inhibitors

Reaction rates:

• If a first-order reaction is not catalysed by an enzyme, rate will increase as substrate concentration increases
• If this reaction is catalysed by an enzyme, it is first order up to a certain substrate concentration - after that it becomes zero-order. This is because, after this point, there are more substrate molecules than enzymes, so all active sites are occupied at any one time
  

Techniques and procedures:

• By adjusting conditions (e.g. pH, temperature, substrate concentration) and measuring the rate with one of the methods described in OZ(f), you can prove the optimal conditions above experimentally

h Carboxylic acids:

Test yourself
• Carboxylic acids contain a -COOH group, which is always at the end of the chain
• Only a small amount of a carboxylic acid is ionised at any time, so it's a weak acid
• The carboxylic acid, e.g. ethanoic acid, dissociates with water to form a carboxylate ion (ethanoate in this example) and an oxonium ion (the old name, hydronium ion is still sometimes used):
  CH₃COOH(l) + H₂O(l) ⇌ CH₃COO^-(aq) + H₃O⁺(aq) (full equation)
  CH₃COOH(aq) ⇌ CH₃COO^-(aq) + H⁺(aq) (ionic equation)

  With aqueous alkalis:

• Carboxylic acids react with aqueous alkalis to form a salt and H₂O, much like dilute HCl(aq) would:
  CH₃COOH(aq) + NaOH(aq) → CH₃COONa(aq) + H₂O(l) (full equation)
  H⁺(aq) + OH^-(aq) → H₂O(l) (ionic equation)

  With carbonates:

• Carboxylic acids form H₂O, CO₂ and a salt when reacted with a carbonate; the carbonate is the base:
  2CH₃COOH(aq) + Na₂CO₃(s) → 2CH₃COONa(aq) + H₂O(l) + CO₂(g) (full equation)
  2H⁺(aq) + CO₃^2-(aq) → H₂O(l) + CO₂(g) (ionic equation)
• For group 1 metal carbonates, the general equation is 2RCOOH(aq) + M₂CO₃(s) → 2RCOOM(aq) + H₂O(l) + CO₂(g)
• For group 2 metal carbonates, the general equation is 2RCOOH(aq) + MCO₃(s) → M(RCOO)₂(aq) + H₂O(l) + CO₂(g)
• Alcohols and phenols don't react with carbonates like this - they don't have a high enough H⁺(aq) concentration

  With metals:

• Carboxylic acids also form salts with metals in a redox reaction, e.g.:
  Mg(aq) + 2CH₃COOH(aq) → Mg(CH₃COO)₂(aq) + H₂(g)
• For group 1 metals, the general equation is 2RCOOH(aq) + 2M(s) → 2RCOOM(aq) + H₂(g)
• For group 2 metals, the general equation is 2RCOOH(aq) + M(s) → M(RCOO)₂(aq) + H₂(g)

i Zwitterions:

Test yourself
• The amine and carboxylic acid groups in amino acids can react with each other, forming a compound with both negatively charged groups and positively charged groups (zwitterions), such as H₃N⁺-CHR-COO^-
• A solid or aqueous amino acid sample will mostly contain zwitterions

Amino acids in varying pHs:

• If hydroxide ions, OH^-, are added to a solution of amino acid zwitterions, a H⁺ is removed from the H₃N⁺ group, bonding with the OH^- to form H₂O. This will make the pH decrease towards neutral - the zwitterions act as a buffer solution by resisting the change in pH
• Similarly, if H⁺ ions are added, they are picked up by the COO^-, increasing the pH back towards neutral
• At a certain pH (which is different for every amino acid), zwitterions have no overall charge

j Amines:

Test yourself
• An amine is like ammonia, but with one or more of the hydrogens replaced by a carbon chain
• The NH₂ is called the amino group
• Amines have a strong fishy smell. This is more prevalent with longer-chained amines

Amine solubility:

• Amines are soluble in water because the lone pair on the nitrogen forms hydrogen bonds with the water
• Longer-chain amines are less soluble in water. This is because the long chain needs to force itself between water molecules which are hydrogen bonded together; the enthalpy to break the water hydrogen bonds exceeds the enthalpy of formation of the new hydrogen bonds

Amines as bases:

• The lone pair on the nitrogen is also responsible for amines acting as bases - it is used to form a dative covalent bond with H⁺ ions in an acid to form a cation (positive ion)
• Because the amine is accepting a H⁺, it is considered a base
• For example:
  CH₃NH₂(aq) + H₃O⁺(aq) → CH₃NH₃⁺(aq) + H₂O(l)
  (H₃O⁺ is the source of H⁺ ions in water; H⁺ cannot exist on their own in solution)

k Organic functional groups:

Test yourself
• See the WM module for more details on some of these groups. As WM is also required for the A2 exams, the required WM content for this module is not included here

Carboxylic acids:

• Name carboxylic acids from the alkane (without the final e) and 'oic acid', e.g. ethanoic acid is a carboxylic acid with 2 carbon atoms (CH₃COOH)
• For branched-chain carboxylic acids, add a prefix as with naming alkanes, e.g. 2-methylbutanoic acid
• If 2 COOH groups are on the molecule, it is named with the full alkane name (including the e) and 'dioic acid', e.g. ethanedioic acid, which is two COOH groups joined by a single bond
• With a benzene ring, the chain part of the carboxylic acid is written as benzene or benzo (e.g. benzenecarboxylic acid or benzocarboxylic acid)

Phenols:

• Phenol is C₆H₅OH
• Write any other groups as a prefix, e.g. 2-methylphenol. The -OH is in position 1, so the 2-methyl means that the methyl group is one carbon along from the OH

Acyl chlorides:

• Acyl chlorides are derivatives of carboxylic acids, but with a Cl instead of OH (an acyl group is R-C=O, and a Cl will bond to the remaining electron around the C)
• They are named similarly to carboxylic acids, but with oyl chloride instead of oic acid, such as ethanoyl chloride (CH₃COCl)

Acid anhydrides:

• Acid anhydrides are made from two carboxylic acids with a H₂O molecule removed - the OH from one and H from the other's alcohol group
• To name them, take the name of the parent acid, and replace acid with anhydride, e.g. ethanoic anhydride

Esters:

• Esters are named from the alcohol and acid used to make them (in that order), with the ending -oate, for example, ethyl ethanoate (ethanol and ethanoic acid)
• Remember that the carbon in the C=O from the acid is counted when naming the acid part

Aldehydes:

• Aldehydes have the suffix -al, e.g. propanal which has 3 carbons total (including the one inside CHO group), CH₃CH₂CHO

Ketones:

• Ketones have the suffix -one, e.g. pentan-2-one. The number indicates the position of the carbonyl (C=O) group.

Diols:

• Diols contain two -OH groups
• They are named after the alkane they are attached to, with the suffix diol and two numbers to indicate the positions of each OH group; e.g. ethane-1,2-diol (two carbons atoms, an OH at each end, HOCH₂CH₂OH)

Primary amines:

• A primary amine is an amine with one alkyl group
• For primary amines with 1-2 carbon atoms, the names methylamine and ethylamine can be used. This doesn't work for amines with more than 2 carbon atoms because the location of the NH₂ group must be specified
• Therefore, use a prefix of n-amino, where n is the carbon which the NH₂ group is on. For example: 2-aminopropane is CH₃CH(NH₂)CH₃

Diamines:

• Diamines have two NH₂ groups
• They are named similarly to primary amines, but with two numbers if there are more than 2 carbon atoms. For example: ethanediamine or 1,3-diaminopropane

Nylon structures:

• Nylons from two monomers (a diamine and a dicarboxylic acid) have the name nylon-a,b, where a is the number of carbon atoms in the diamine, and b is the number of carbons in the dicarboxylic acid
• Nylons from a single monomer (with an amine group on one end and carboxylic acid group on the other) have one number representing the number of carbon atoms, n, in the single monomer - nylon-n

l Amides:

Test yourself
• An amide is like a carboxylic acid - but with the OH replaced by a NH₂. Therefore the amide group is -CONH₂
• Primary amides are amides where the nitrogen atom is bonded to one carbon and two hydrogen atoms. The general formula is:
  
• Secondary amides have the nitrogen bonded to two carbon atoms and one hydrogen. The general formula is:
  

m Hydrolysis:

Test yourself
• Hydrolysis is a reaction with water (or dilute acid/hydroxide ions). Water on its own is often too slow, so catalysis by a dilute acid/alkali reduces reaction time

Acid hydrolysis of an ester:

• Hydrolysing an ester under reflux, with a dilute acid catalyst, produces the carboxylic acid and alcohol which make up the ester
• These reactions are written with H⁺ above the reversible arrow, and with the ester and water as the reactants
• Since this reaction is reversible, an excess of water is required for complete hydrolysis (to push the equilibrium to the right)

Alkali hydrolysis of an ester:

• The ester is heated under reflux with a dilute alkali solution, e.g. NaOH(aq)
• With this method, the reaction is one-way and the products are easy to separate; the alcohol can be distilled off
• The alcohol which makes up the ester is produced, as well as a sodium salt - the H on the carboxylic acid is replaced by Na (e.g. ethanoic acid → sodium ethanoate)
• Alkali hydrolysis of an ester is usually written as
  CH₃CH₂COOCH₃ + NaOH → CH₃CH₂COONa + CH₃OH
• After distilling off the alcohol, the carboxylic acid can be obtained by adding a strong dilute acid and then it can be distilled off

Acid hydrolysis of an amide:

• When heated with a dilute hydrochloric acid, the carboxylic acid and ammonium chloride is formed, e.g.:
  CH₃CONH₂ + H₂O + HCl → CH₃COOH + NH₄⁺Cl^-
• A secondary amide would produce a salt of a primary amine (e.g. CH₃NH₂⁺Cl^-) instead of ammonium chloride

Alkali hydrolysis of an amide:

• Ammonia gas is given off, leaving a salt, e.g.:
  CH₃CONH₂ + NaOH → CH₃COONa + NH₃
• With a secondary amide, an amine will be produced instead of ammonia

n Reactions of acyl chlorides:

Test yourself
• An amine and an acyl chloride react at room temperature to form a secondary amide and HCl(g)
• An alcohol and an acyl chloride react at room temperature to form an ester and HCl(g)
• These are both condensation reactions, as a small molecule, HCl, is produced
• These reactions are also nucleophilic substitution reactions

Testing for an acyl chloride:

• Add an alcohol to an acyl chloride. If damp blue litmus paper is turned red by the released HCl (cloudy white gas), it's an acyl chloride

o, p Polymerisation:

Test yourself
• Polymers are named with the prefix poly and brackets around the monomer - e.g. poly(chloroethene)

Addition polymerisation:

• Addition polymers are formed from alkene monomers - the double bond opens up and the carbon on the end bonds with a carbon from the next monomer

Condensation polymerisation:

• Condensation polymers usually contain two different monomers, each with two different functional groups (or two of the same functional group). The two monomers react together to form a link, and a small molecule is released - proteins and polypeptides are an example of condensation polymers
  - Polyamides are from dicarboxylic acids and diamines
  - Polyesters are from dicarboxylic acids and diols
• The repeat unit for a condensation polymer is the two monomers drawn bonded together
• The structural formula is [repeat unit]
• A condensation polymer can also be formed from a single monomer if it contains two different functional groups which can react together - e.g. a molecule with a carboxylic acid group and an alcohol group
• Unlike addition polymers, condensation polymers can be easily broken down by hydrolysing

q Optical isomerism:

Test yourself
• Chiral/asymmetric carbon atoms have four different groups attached
• The chiral centre of a molecule is the carbon atom which has the four different groups
• When identifying the chiral centre, remember to look at the groups attached to each carbon atom and not just the atoms it's directly bonded to

Enantiomers:

• With four different groups around the carbon, if the groups are rearranged, a completely different molecule will be formed. These molecules are called optical isomers (due to their effect on plane-polarised light) or enantiomers
• Enantiomers cannot be superimposed as shown below - all non-superimposable isomers are enantiomers
  
• The two optical isomers are named with the prefix D and L (we don't need to know which is which for this course)

Drawing optical isomers:

• Draw the groups around the chiral centre in a tetrahedral shape with its mirror image optical isomer next to it, i.e.
  
• If a molecule has two chiral centres, draw mirror images for each chiral centre separately, and then one showing the mirror images for both chiral centres

r Mass spectrometry losses:

Test yourself
• Sometimes fragments do not show in mass spectra, due to:
  - being too unstable to reach the detector
  - being uncharged (e.g. a radical), as a molecule usually splits into a charged ion and an uncharged radical when it fragments
• The 'lost' fragments' mass can be calculated by looking at the differences between peaks

High-resolution mass spectrometry:

• Often, a peak could represent several fragments with the same mass to the nearest whole number. However, to 4 decimal places, the exact number of each atom can be calculated from the M⁺ peak as atomic masses are never integers (due to isotopes)

s NMR spectroscopy:

Test yourself
• NMR (Nuclear Magnetic Resonance) has two common types:
  - carbon-13 (¹³C) NMR to determine the number/types of carbon environments
  - proton (¹H) NMR to determine the number of hydrogen atoms and their environments

¹³C NMR:

• Nuclei are shielded from magnetic fields by their electrons
• Atoms it's bonded to (its environment) will affect this shielding
• The absorption difference is measured in ¹³C NMR
• For example, ethane has one carbon environment repeated twice (two CH₃ groups). 1-chlorobutane has four carbon environments because the electronegative Cl affects the two CH₂ groups differently due to distance
• Absorption difference is measured compared to a substance called TMS, chemical shift () (measured in )
  - Therefore, TMS has a chemical shift of 0
  - TMS is used because:
     - it has just one carbon environment
     - it's very volatile (easy to remove)
     - it's non-toxic
     - it's inert

Interpreting ¹³C NMR:

• The number of peaks (excluding the peak at , TMS) shows the number of carbon environments
• The data sheet (linked at the top of this page) shows the range of shifts for different groups

¹H NMR:

• Each peak is often split into multiple peaks called multiplets, due to hydrogen atoms bonded to a carbon next to the environment responsible for the peak. This effect is called spin-spin coupling
• If there are n hydrogens in the neighbouring carbon environment(s), there will be n + 1 peaks. This is called the n + 1 rule
• You do not need to know the science behind this for A Level

Interpreting ¹H NMR:

• The number of peaks (excluding the peak at , TMS) shows the number of hydrogen environments
• The data sheet shows the range of shifts for different groups bonded to the hydrogen
• The ratio of areas under each peak shows the ratio of hydrogen atoms (i.e. a peak twice as high as another contains twice as many hydrogen atoms). This relative area is often shown as a number above each peak, or as a horizontal line (integration trace)