(i) Amino acid sequence determines protein structure

• Proteins are polymers of amino acid monomers

• Amino acids are linked by peptide bonds to form polypeptides

  • Recognise the chemical structure of a peptide bond from a diagram.

• Amino acids have the same basic structure, differing only in the R group present

  • R groups of amino acids vary in size, shape, charge, hydrogen bonding capacity and chemical reactivity.

• Amino acids are classified according to their R groups: basic (positively charged); acidic (negatively charged); polar; hydrophobic

  • Classify amino acids according to the R group present.

  • Names and structures of individual amino acids are not required.

• The wide range of functions carried out by proteins results from the diversity of R groups

• The primary structure is the sequence in which the amino acids are synthesised into the polypeptide

• Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure — alpha helices, parallel or anti-parallel beta-pleated sheets, or turns

• The polypeptide folds into a tertiary structure

• This conformation is stabilised by interactions between R groups: hydrophobic interactions; ionic bonds; London dispersion forces; hydrogen bonds; disulfide bridges

  • Disulfide bridges are covalent bonds between R groups containing sulfur.

• Quaternary structure exists in proteins with two or more connected polypeptide subunits

  • Quaternary structure describes the spatial arrangement of the subunits.

• A prosthetic group is a non-protein unit tightly bound to a protein and necessary for its function

  • The ability of haemoglobin to bind oxygen is dependent upon the non-protein haem group.

• Interactions of the R groups can be influenced by temperature and pH

  • Increasing temperature disrupts the interactions that hold the protein in shape; the protein begins to unfold, eventually becoming denatured. 

  • The charges on acidic and basic R groups are affected by pH. 

  • As pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured.

(ii) Ligand binding changes the conformation of a protein

• A ligand is a substance that can bind to a protein

• R groups not involved in protein folding can allow binding to ligands

• Binding sites will have complementary shape and chemistry to the ligand

• As a ligand binds to a protein-binding site the conformation of the protein changes

• This change in conformation causes a functional change in the protein

• Allosteric interactions occur between spatially distinct sites.

  • The binding of a substrate molecule to one active site of an allosteric enzyme increases the affinity of the other active sites for binding of subsequent substrate molecules.

  • This is of biological importance because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration.

• Many allosteric proteins consist of multiple subunits (have quaternary structure)

• Allosteric proteins with multiple subunits show co-operativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits

• Allosteric enzymes contain a second type of site, called an allosteric site

• Modulators regulate the activity of the enzyme when they bind to the allosteric site

• Following binding of a modulator, the conformation of the enzyme changes and this alters the affinity of the active site for the substrate

  • Positive modulators increase the enzyme’s affinity for the substrate, whereas negative modulators reduce the enzyme’s affinity.

• The binding and release of oxygen in haemoglobin shows co-operativity

  • Changes in binding of oxygen at one subunit alter the affinity of the remaining subunits for oxygen.

• The influence and physiological importance of temperature and pH on the binding of oxygen

• A decrease in pH or an increase in temperature lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced. 

• Reduced pH and increased temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue.

  • Effects of DPG are not required

(iii) Reversible binding of phosphate and the control of conformation

• The addition or removal of phosphate can cause reversible conformational change in proteins

• This is a common form of post-translational modification

• Protein kinases catalyse the transfer of a phosphate group to other proteins

• The terminal phosphate of ATP is transferred to specific R groups

• Protein phosphatases catalyse the reverse reaction

• Phosphorylation brings about conformational changes, which can affect a protein’s activity

• The activity of many cellular proteins, such as enzymes and receptors, is regulated in this way

• Some proteins are activated by phosphorylation while others are inhibited

  • Adding a phosphate group adds negative charges. 

  • Ionic interactions in the unphosphorylated protein can be disrupted and new ones created.