U1 - Protein structure, ligand binding and conformational change Flashcards
What determines a proteins structure
An amino acid sequence
Proteins are _______ of amino acid _____
Proteins are polymers of amino acid monomers
What are amino acids linked by and what is a chain of amino acids called?
Amino acids are linked by peptide bonds to form polypeptides.
What do amino acid structures differ by?
They differ by R groups; size, shape, charge , hydrogen bonding capacity and chemical activity
What are the four amino acid R groups?
Basic ( positively charged )
Acidic ( negatively charged )
Hydrophilic ( Polar )
Hydrophobic ( Non - Polar )
What determines the functions of proteins ?
The diversity of amino acid R groups and structures.
What is the primary structure
The sequence in which the amino acids are synthesised into the polypeptide.
What results in secondary structure
Hydrogen bonding along the backbone of the protein strand.
Name the different types of secondary structure
Alpha Helices
Parallel or anti parallel beta pleated sheets
Turns
What stabilises a tertiary structure
By interactions between R groups; Hydrophobic interactions Ionic bonds London dispersion forces Hydrogen bonds Disulphide bridges
What are disulfide bridges
Disulfide bridges are covalent bonds between groups containing sulfur
What forms a Quaternary structure
A quaternary structure is when two or more polypeptide subunits connect
What describes a Quaternary structure
It describes the spatial arrangement of subunits.
what is a prosthetic group?
A prosthetic group is a non-protein unit tightly bound to a protein and necessary for its function.
What allows haemoglobin to bind oxygen
It is dependent upon the non-protein haem group.
What can influence interactions of the R groups
Temperature
pH
How does temperature effect the interactions of the R groups
Increasing temperature disrupts the interactions that hold the protein in shape, the protein unfolds and eventually becomes de-natured.
How does pH effect the interactions of the R groups
As pH increases or decreases from optimum, the normal ionic interactions between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured.
What is a ligand
A ligand is a substance that can bind to a protein
What are the other functions of R groups, excluding protein folding
They allow ligands to bind
How are binding sites welcoming to ligands
They will have complementary shape and chemistry to the ligand.
What happens to the protein-binding site when a ligand binds?
The conformation of the protein changes
what happens when the conformation of a protein is changed by a ligand
It causes a functional change in the protein
What is an allosteric site
An active site that is spatially distinct from the main active site of the enzyme
What happens to the affinity of active sites if a molecule binds to the allosteric site
The binding of a structure molecule to one active site of an allosteric enzyme increases the affinity of the other active sites for binding of subsequent substrate molecules.
Why are allosteric enzymes of biological importance
This is of biological importance because the activity of allosteric enzymes can vary greatly with the small changes in substrate concentrations.
Many allosteric proteins consist of multiple subunits (quaternary)
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What features do 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
What is the second site on the allosteric enzyme called?
Allosteric site
What do modulators do?
They regulate the activity of the enzyme when they bind to the allosteric site.
What happens after the binding of a modulator?
The conformation of the enzyme changes and this alters the affinity of the active site for the substrate
what do the different types of modulators do?
Positive modulators increase the enzymes affinity for the substrate, whereas negative modulators reduce the enzymes affinity.
What is the relation between co-operativity and release of oxygen in haemoglobin
Changes in binding of oxygen at one subunit alter the affinity of the remaining subunits for oxygen.
if one substrate binds it loosens off the other and then more bind.
What is 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.
