1.2(c) - Protein Structure, Ligand Binding and Conformational Change Flashcards
Describe the structure of amino acids
Amino acids have the same basic structure however have different R groups. R groups of amino acids vary in size, shape, charge, hydrogen bonding capacity and chemical reactivity
How do amino acids form polypeptides?
Amino acids are linked by peptide bonds to form polypeptide chains
Name the different amino acid R groups
Basic (positively charged), acidic (negatively charged), polar and hydrophobic
How do proteins have such a wide range of functions?
The diversity of R groups
What is the primary structure of proteins?
The sequence in which amino acids are synthesised to form a polypeptide chain
What is the secondary structure of proteins?
Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure including alpha helices, beta-pleated sheets and turns
What is the tertiary structure of a protein?
The final folded shape of the protein. It is stabilised by interactions between R groups including, hydrophobic interactions, ionic bonds, LDFs, hydrogen bonds and disulfide bridges
What are disulfide bridges?
Covalent bonds between R groups containing sulfur
What is the quaternary structure of protein?
Exists is proteins with two or more connected polypeptide subunits. It describes the spatial arrangement of the subunits
What is a prosthetic group and give an example
ts a non-protein unit tightly bound to a protein which is necessary for its function
The ability of haemoglobin to bind to oxygen is dependent upon the the non-protein haem group
What effect does increasing the temperature have on R groups?
What effect does increasing the temperature have on R groups?
What effect does pH have on R groups?
The charges on acidic and basic R groups are affected. 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
Define a ligand
A ligand is a substance that can bind to a protein
What can R groups not involved in protein folding do?
They can allow binding to ligands
Describe what happens when a ligand binds
When a ligand binds to a protein-binding site the conformation of the protein changes. This change in conformation can cause functional changes in the protein
Describe the structure of a binding site
The binding site will have a complementary shape to the ligand
What happens when a substrate molecule binds to one active site of an allosteric and why is it important?
It increases the affinity of the other active sites for binding of subsequent substrate molecules
Its important because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration
What is cooperativity?
Changes in binding at one subunit alters the affinity for the remaining subunits
What is the second site on an allosteric enzyme called?
An allosteric site
What is the role a positive or negative modulator?
A positive modulator increases the enzyme’s affinity for the substrate whilst a negative modulator reduces the enzyme’s affinity
What happens when a modulator binds?
Following binding of a modulator, the conformation of the enzyme changes and this alters the affinity of the active site for the substrate
What do modulators do?
Once bound to the allosteric site they regulate the activity of the enzyme
How does the binding and release of oxygen in haemoglobin show cooperativity?
Changes in binding of oxygen at one subunit alters the affinity of the remaining subunits for oxygen
What influence does temperature have on the binding of oxygen?
An increase in temperature lowers the affinity of haemoglobin for oxygen so the binding of oxygen is reduced. This promotes increased oxygen delivery to tissue
