Detailed and comprehensive notes on unit 3.3.13 (amino acids, proteins & DNA) for AQA A level chemistry. Covers: amino acid structure and properties, zwitterions, amino acid nomenclature, protein structure, enzymes, DNA structure, DNA polymerisation / complementary base pairing and anti-cancer drug...
Amino Acids
Content:
• Amino acids have both acidic and basic properties, including the formation of zwitterions.
Skills:
• Draw the structures of amino acids as zwitterions and the ions formed from amino acids:
o In acid solution.
o In alkaline solution.
Proteins
Content:
• Proteins are sequences of amino acids joined by peptide links.
• The importance of hydrogen bonding and sulfur–sulfur bonds in proteins.
• The primary, secondary (α-helix and β–pleated sheets) and tertiary structure of proteins.
• Hydrolysis of the peptide link produces the constituent amino acids.
• Amino acids can be separated and identified by thin-layer chromatography.
• Amino acids can be located on a chromatogram using developing agents such as ninhydrin or
ultraviolet light and identified by their Rf values.
Skills:
• Draw the structure of a peptide formed from up to three amino acids.
• Draw the structure of the amino acids formed by hydrolysis of a peptide.
• Identify primary, secondary and tertiary structures in diagrams.
• Explain how these structures are maintained by hydrogen bonding and s–s bonds.
• Calculate Rf values from a chromatogram.
Enzymes
Content:
• Enzymes are proteins.
• The action of enzymes as catalysts, including the concept of a stereospecific active site that binds to
a substrate molecule.
• The principle of a drug acting as an enzyme inhibitor by blocking the active site.
• Computers can be used to help design such drugs.
Skills:
• Explain why a stereospecific active site can only bond to one enantiomeric form of a substrate or
drug.
,Specification
DNA
Content:
• The structures of the phosphate ion, 2-deoxyribose (a pentose sugar) and the four bases adenine,
cytosine, guanine and thymine are given in the Chemistry Data Booklet.
• A nucleotide is made up from a phosphate ion bonded to 2-deoxyribose which is in turn bonded to
one of the four bases adenine, cytosine, guanine and thymine.
• A single strand of DNA (deoxyribonucleic acid) is a polymer of nucleotides linked by covalent
bonds between the phosphate group of one nucleotide and the 2-deoxyribose of another nucleotide.
This results in a sugar-phosphate-sugar-phosphate polymer chain with bases attached to the sugars in
the chain.
• DNA exists as two complementary strands arranged in the form of a double helix.
Skills:
• Explain how hydrogen bonding between base pairs leads to the two complementary strands of DNA.
Action of Anti-Cancer Drugs
Content:
• The Pt(II) complex cisplatin is used as an anticancer drug.
• Cisplatin prevents DNA replication in cancer cells by a ligand replacement reaction with DNA in
which a bond is formed between platinum and a nitrogen atom on guanine.
• Appreciate that society needs to assess the balance between the benefits and the adverse effects of
drugs, such as the anticancer drug cisplatin.
Skills:
• Explain why cisplatin prevents DNA replication.
• Explain why such drugs can have adverse effects.
,Amino Acids
Structure
• An amino acid has an amine (-NH2) group, a carboxyl (-COOH)
group and an organic side chain (-R).
• In glycine, the R-group is hydrogen.
• Cysteine has a thiol (-SH) group in its side chain.
• Almost all natural amino acids are α-amino acids (or 2-amino
acids), where the –NH2 is attached to the α-carbon.
• There are 20 naturally occurring amino acids that differ only by their side chains.
• Some amino acids have extra amine and carboxylic acid groups in their side chain.
Zwitterions
• A zwitterion has both a positive charge (-NH3+) and negative charge (-COO-).
• Each amino acid has a unique isoelectric point – the pH at which the zwitterion exists.
• It varies between amino acids due to the effect of different R-groups.
• If an extra carboxylic acid or amine group is present in the side chain, then this group will also react
and change form in alkaline or acidic conditions.
Ionic Properties
• Amino acids form crystalline solids with high melting points that dissolve readily in water – they are
significantly polar in nature.
• In both solid and solution state, amino acids exist as the zwitterion form, where the H atom of the
COOH group protonates the basic amine group.
• There are strong ionic interactions between zwitterions (as opposed to the weaker hydrogen bonding
that would occur in the no charge form) which cause the high melting points.
, Amino Acids
Acid & Base Properties
• The amine group is basic and the carboxylic acid group is acidic – amino acids are amphoteric.
• Amphoteric: Able to act as both a base and an acid.
• However, amino acids are both weak acids and bases.
• Amino acids act as weak buffers
• They will only gradually change pH if small amounts of acid and alkali are added.
o E.g. +NH3CH2COO- + HCl ! Cl- +NH3CH2COOH
o E.g. +NH3CH2COO- + NaOH ! NH2CH2COO- Na+ + H2O
Optical Activity
• All amino acids, except glycine, have 4 different groups around
the α-carbon.
• This makes all other amino acids chiral, so they exhibit optical
activity and will rotate plane-polarised light.
• Only the L-isomers are found naturally.
Solubility
• Amino acids are generally soluble in water, as the charged regions of the zwitterion are attracted to
the δ+ hydrogen atoms or δ- oxygen atom of water.
Nomenclature
• The carbon atom in the carboxylic acid group will always be carbon-1.
• Carboxylic acids take priority when naming, so the suffix should be –
oic acid.
• The amine group will typically be on carbon-2; use the prefix amino-.
• For molecules with 2 carboxylic acid groups, the carbon chain in between the 2 carboxyl groups is
used as the longest chain and the suffix is –dioic acid.
• (Note: there should be an ‘e’ before the dioic acid, e.g. butanedioic acid and not butandioic acid)
Reactions
• The carboxylic acid and amine groups in amino acids can undergo the usual reactions of these
functional groups:
o Condensation reactions with other amino acids to form dipeptides and
polypeptides/polyamides (COOH and NH2 groups).
o Esterification reactions with alcohols in the presence of a strong acid catalyst (COOH
group).
o Nucleophilic addition-elimination reactions with acyl chlorides (NH2 group).
o Nucleophilic substitution reactions with haloalkanes (NH2 group).
o Acid / Base reactions (COOH or NH2 group).
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