Protein Structure, Ligand Binding And Conformational Change Flashcards
What are proteins
Polymers of amino acid monomers
How are amino acids linked
Peptide bonds to form polypeptides
What do a,ion acids share and not share
Have the same basic structure but differing r groups present
What do different r groups have
Different size, shape, charge, hydrogen bonding capacity, chemical reactivity
How are amino acids classified
According to r groups basic, acidic, polar and hydrophobic groups
What does the wide range of functions carried out by proteins result in
The diversity of amino acid R groups
What is the primary structure
Sequence in which the amino acids are synthesised into the polypeptide
What results in a secondary structure
Hydrogen bonding along the backbone of the protein strand
What do secondary structures have
Alpha helices
Parallel or antiparellel beta pleated sheets
Turns
LEARN HOW TO LABEL SECONDSRY STRUCTURE
What’s a tertiary structure
The polypeptide folds into a tertiary structure. This conformation is stabilised by interactions betweeen R groups
Give examples of R groups
Hydrophobic interactions
Ionic bonds
LDFs
Hydrogen bonds
What’s a quaternary structure
Exists in proteins with two or more connected polypeptide subunits. It describes the spatial arrangement of the subunits
What’s a prosthetic group
Non protein unit tightly bound to a protein necessary for its function e.g in the molecule haemoglobin
What’s haemoglobin definition
Iron containing oxygen transporting protein present in the red blood cells of almost all vertebrates
What is the ability of haemoglobin to bind to oxygen dependant on
Non protein haem group
What influences interactions of R groups
Temperature and ph
What happens when temperature is increase in R group
Disrupts the interactions that hold the protein shape. The protein begins to unfold, eventually becoming denatured
What happens to R groups as Ph increases or decreases
As ph increases or decreases from the optimum the normal ionic interactions between charged groups are lost which gradually changes conformation of the protein until it becomes denatured
What’s a ligand definition
A substance that can bind to a protein
What can R groups do that are not involved in protein folding
Allow binding to ligands
What do bonding sites of R groups have when binding to ligand
Complementary shape and chemistry to ligand
What happens as the ligand binds to the protein binding site
The conformation of the protein changes. This change I’m conformation causes functional change in the protein
What’s allosteric definition
Interactions which occur between spatially distinct sites
What does the binding of a substrate molecule of one active site of an allosteric enzyme do
Increases the affinity of the other active sites for binding subsequent substrate molecules
What can the activity of allosteric enzymes do
Vary greatly with small changes in substrate concentrations
What do many allosteric proteins have
Multiple subunits which means they have a quaternary structure
What do allosteric proteins with multiple subunits do
Show cooperatively In binding which changes in binding at one subunit alter the affinity of the remaining subunits
What sites do allosteric enzymes have
Active site and allosteric site
What do modulators do
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 positive and negative modulators do
Positive modulators increase the enzymes affinity for the substrate
Negative modulators decrease the enzymes affinity
Give examples if negative and positive modulators
Negative-inhibition
Positive-activation
What shows cooperatively
The binding and release of oxygen in haemoglobin
What does changes if oxygen at one subunit do
Alter the affinity of the remaining subunits for oxygen
What is the binding of oxygen to haemoglobin affected by
Ph and temperature
Describe the effect of ph in binding of oxygen to haemoglobin
Decrease-decreases the affinity for oxygen
Increase-increases affinity for oxygen
Describe the effect of temperature on binding of oxygen to haemoglobin
Decrease- increases affinity for oxygen
Increase-decreases affix y for oxygen
What can an addition of removal of a phosphate cause
Reversible conformational changes in proteins, this is a common form of post translation modification
What do protein kinases to
Catalyse the transfer of a phosphate group to other proteins
What is transferred to a specific R group of proteins
Terminal phosphate or ATP
What catalyses the reverse reaction of phosphate
Protein phosphates
What does phosphorylation do
Brings about conformational changes which can affect a proteins activity
What happens to proteins in phosphorylation
Some are activated others are inhibited
What does adding a phosphate group do
Adds negative charges
What is disrupted in unphosphorylated proteins
Ionic interactions
