Organic 13: Biochemistry

A species that has both a positive and negative charge on different parts of the molecule

Due to the strong ionic attraction between opposite charges on zwitterions

Central chiral carbon surrounded by hydrogen, carboxylic acid group, variable group, and amine group

Glycine Because glycine’s variable group is hydrogen, which means there are only three different groups around the central carbon All other amino acids are optically active but only one enantiomer is present in nature

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In strongly acidic conditions, the lone pair on NH2 accepts a proton to form an NH3+ ion (is protonated)

In strongly alkaline conditions, the -OH group loses a hydrogen ion (is deprotonated) to form an OH- ion

The bond formed after condensation reaction between two amino acids

The fixed sequence of amino acids in the polypeptide chain It is relatively stable due to covalent bonding

The initial folding of a polypeptide chain into either an alpha helix or a beta-pleated sheet due to hydrogen bonding Hydrogen bonds are much weaker than covalent bonds so the secondary structure is more easily disrupted

Further folding into a three-dimensional shape held in place by hydrogen bonding, ionic bonding, and disulfide bridges

With hydrochloric acid of concentration 6moldm-3 for about 24 hours This hydrolyses all peptide linkages

By refluxing the protein in 6moldm-3 hydrochloric acid to break the amide linkages (hydrolysis) resulting in a mixture of all the individual amino acids

• Add a small spot containing the mixture of amino acids about 1cm up the plate • Place the plate in a tank containing a suitable solvent, and put a lid on it (this allows the solvent vapours to carry the amino acids up the stationary phase) • The affinity for the mobile and stationary phase depends on the intermolecular forces that act between the amino acid and each phase • Mark the solvent front (how far the solvent was carried up the stationary phase) • Spray the plate with ninhydrin, which reacts with amino acids to form a purple compound, OR shine ultra-violet light onto the plate to see how far the amino acids were carried • Calculate the Rf value (distance moved by spot/distance moved by solvent)

Protein-based catalysts that speed up the rate of reactions Usually globular proteins with active sites where the reaction occurs

The reacting molecule fits precisely into the active site and is held in the precise orientation necessary to react

The reacting molecule must bond to the active site temporarily by intermolecular forces (i.e. van Der Waals) These forces allow electrons to move within the substrate to lower the activation energy for the reaction

The active site of an enzyme is selective to individual enantiomers Because the substrate molecule must have a 3D structure that can bind precisely to the active site

Changes in pH Changes in temperature (Too much deviation from optimum)

Where a molecule with a similar shape/tertiary structure to the substrate can be used to block the active site to prevent enzyme-substrate complexes from forming

Penicillin Inhibits the enzymes responsible for controlling the building of cell walls in bacteria

Computer modelling techniques can be used to predict the shape of proteins before they have been synthesised So can therefore predict their properties

Phosphate 2-Deoxyribose Organic base

Adenine, Thymine, Cytosine, Guanine