Engineering Proteins

Key Words

ENGINEERING PROTEINS

Acid derivatives / Compounds with functional groups based on carboxylic acid (-COOH ) see table p300 in Chemical Ideas e.g.
Ester –COOR, Acyl chloride –COCl, Amide -CONH2
Acid anhydride -(CO)2O
Active site / The region in an enzyme into which the substrate binds before it reacts with it.
Amino acid / An organic molecule that contains both an –NH2 group and a –COOH group
Base pairs / Pairs of bases that fit neatly together thus placing groups in just the right positions for hydrogen bonds to form. These can be seen in the DNA double helix.
Bifunctional Compounds / Compounds which have two functional groups e.g. amino acids have -NH2 and -COOH.
Chiral / A carbon centre within a molecule surrounded by four different groupings of atoms (=> non-superimposable mirror images).
Closed system / One where no chemicals can enter or leave e.g. a stoppered flask.
Codons &
Anti-codons / Codons are the different combinations of triplet codes that define a particular amino acid. Anti-codons allow tRNA molecules to recognise and bind onto the codons on mRNA, e.g. G & C recognise one another and so do U & A.
D or L-optical isomers / The two mirror image forms of an enantiomer – one rotates plane polarised light to the right (dextro-rotatory) while the other rotates it to the left (laevo-rotatory).
Denatured / A term used to describe the destruction of the active sites in a protein caused by the loss of shape when the tertiary structure is broken.
DNA / Deoxyribonucleic acid
Dynamic equilibrium / A reversible reaction in which forward and reverse reactions proceed simultaneously but there is no overall change in any of the concentrations.
Equilibrium constant / A constant calculated for a reversible reaction, as follows:
For the reaction aA + bB  cC + dD
The equilibrium constant is: Kc = CcDd / AaBb
First order reaction (enzymes) / One in which the reaction rate is directly proportional to the substrate concentration.
Gene / A DNA segment responsible for a particular protein (DNA codes for RNA which, in turn codes for proteins)
Genome / The full set of all the genes of an organism.
Half-life / The time taken for half of a particular reagent in a reaction to become used up.
Helix/sheet / Hydrogen bonding causes regular folding or twisting of protein chains. The helix is a tight coil of protein chain while extended chains can be bonded into a sheet.
Hydrogen bonding / A particularly strong type of intermolecular force of attraction in which highly polar N-H, O-H, or F-H bonds in molecules cause very strong dipole-dipole attraction between molecules.
Initial rate / The rate of a chemical reaction at the start.
Instantaneous dipole -induced dipole / A type of intermolecular attraction in which temporary dipoles in one molecule induces a dipole in a neighbouring molecule and then attracts it.
Insulin / A hormone produced in the pancreas that controls the uptake of glucose and some other sugars by our cells.
Intermediates / Chemicals formed in the middle of a reaction mechanism
Macroscopic scale / The scale that we as humans are used to – test tubes and flasks!
Mechanism / The series of separate steps that make up a reaction.
Microscopic scale / Individual molecule scale
mRNA / Messengerribonucleic acid. It carries the code for protein synthesis.
NMR / Nuclear magnetic resonance – a type of spectroscopy in which the number and type of grouping that hydrogen nuclei exist in within a molecule can be determined.
Optical isomers (enantiomers) / Mirror image molecules (ones that are non-superimposable).
Order of reaction / The power to which the concentration of a reactant in a rate equation must be raised.
Overall order / The sum of the separate orders in a rate equation.
Polypeptide / A polymer containing up to 40 amino acid residues joined by peptide links.
Position of equilibrium / The term that describes the relative concentrations of products to reactants in an equilibrium
Primary structure (of a protein) / The order of amino acids in the protein.
Quaternary structure / The joining of insulin monomers into a hexamer
Rate determining step / The slowest step of the separate steps that make up a mechanism.
Rate equation / An equation which links the rate of a reaction to the initial concentrations of the reactants:
e.g. for the reaction: A + B  products
the rate equation is: rate = k AmBn
where m is the order of reaction with respect to A and n is the order of reaction with respect to B.
Ribosome / A cell’s catalyst for protein production.
RNA / Ribonucleic acid
Secondary structure / The coiling of parts of the protein chain into a helix or the formation of a region of sheet
Steady state / This can occur in an open system where the concentrations of products and reactants in a series of reactions remains constant i.e. there is no overall change.
Substrate / A molecule that reacts with a particular enzyme.
Tertiary structure / The overall shape of a protein – the folding of the secondary structure into an insulin monomer.
Triplet code / A code consisting of a combination of three bases (from U,C,A,G) that tells a cell which amino acids to use to build a protein
tRNA / Transfer ribonucleic acid – collects an amino acid and takes it into the mRNA strand.
Zero order reaction (enzymes) / One in which the reaction rate does not depend on the substrate concentration.
Zwitterion / An ion containing both positively and negatively charged groups.