1.2.3 protein structure, ligand binding, conformational change Flashcards
what determines protein structure
amino acid sequence
what are proteins
polymers of amino acid monomers
what are amino acids linked with to form polypeptides
peptide bonds
do amino acids have the same basic structure
yes
how do amino acid structures differ
the R group present
how do R groups of amino acids vary
- size
- shape
- charge
- hydrogen bonding capacity
- chemical reactivity
how are amino acids classified
according to their R groups
what are the different amino acid classifications
- basic (positively charged)
- acidic (negatively charged)
- polar
- hydrophobic
what does the diversity of the R groups of amino acids result in
the amino acids having a wide range of functions carried out by their proteins
what is the primary structure
the sequence in which the amino acids are synthesised into the polypeptide
what results in the secondary structure
hydrogen bonding along the backbone of the protein strand results in regions of secondary structure
what are examples of the secondary structures
- alpha helices
- parallel beta-pleated sheets
- anti-parallel beta-pleated sheets
- turns
what does the polypeptide structure fold into
tertiary structure
what stabilizes the tertiary structure (give examples)
interactions between R groups
- hydrophobic interactions
- ionic bonds
- london dispersion forces
- hydrogen bonds
- disulfide bridges
what are disulfide bridges
covalent bonds between R groups containing sulfur
when does a quaternary structure exist
in proteins with two or more connected polypeptide subunits
what is a quaternary structure
the spatial arrangement of the subunits
what is a prosthetic group
a non protein unit tightly bound to a protein and necessary for its function
what is the ability of haemoglobin to bind oxygen dependent on
the non protein haem group
what can influence the interactions of the R groups
- temperature
- pH
what happens to proteins when you increase the temperature
- the increased temperature disrupts the interactions that hold the protein in shape
- the protein begins to unfold, eventually becoming denatured
what can pH affect in relation to proteins
the charges on acidic and basic R groups
why does pH affect the charges on acidic and basic R groups
- 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
what does ligand binding change
the conformation of a protein
what is a ligand
a substance that can bind to a protein
which R groups can allow binding to ligands
those that are not involved in protein folding
why can ligands attach to binding sites
they have complementary shape and chemistry to the ligand
what happens as a ligand binds to a protein-binding site
the conformation of the protein changes
what does protein conformation cause
a functional change in the protein
where do allosteric interactions occur
between spatially distinct sites
what does the binding of a substrate molecule to one active site of an allosteric enzyme cause
an increase in the affinity of the other active sites for binding of subsequent substrate molecules
why is the binding of substrate molecules to one active site of an allosteric enzyme of biological importance
the activity of the allosteric enzymes can vary greatly with small changes in substrate concentration
what do many allosteric proteins consist of? and what does this mean for their structure?
multiple subunits, so they have a quaternary structure
what does cooperativity in binding mean (when looking at allosteric proteins with quaternary structures)
changes in binding at one subunit alter the affinity of the remaining subunits
what is the name of the other site on allosteric enzymes
allosteric site
what do modulators do
they regulate the activity of the enzyme when they bind to the allosteric site
what happens following 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 modulators do
they increase the enzymes affinity for the substrate
what do negative modulators do
they reduce the enzymes affinity for the substrate
what does the binding and release of oxygen in haemoglobin show
cooperativity
what does the change in binding of oxygen at one subunit alter
the affinity of the remaining subunits for oxygen
does temperature and pH have an influence on the binding of oxygen
yes
what lowers the affinity of haemoglobin for oxygen, therefore causing a reduction in the binding of oxygen
- decrease in pH
- increase in temperature
what reduces the binding of oxygen to haemoglobin, promoting increased oxygen delivery to tissue?
- reduced pH
- increased temperature
what can the addition or removal of a phosphate cause
reversible conformational change in proteins
is phosphorylation a form of post translational modification
yes
what do protein kinases do
they catalyse the transfer of a phosphate group to other proteins
where is the terminal phosphate of ATP transferred to
specific R groups
what do protein phosphotases do
catalyses the reverse reaction of phosphorylation (removes, rather than adds)
what does phosphorylation bring about
conformational changes, which can affect a proteins activity
how is the activity of many cellular proteins, such as enzymes and receptors, regulated?
through phosphorylation
is it true that all proteins are activated by phosphorylation
no. some are inhibited
does adding a phosphate group add negative or positive charges
negative
can ionic interactions in the unphosphorylated protein remain undisrupted
no, they can get disrupted and new ones will then get created
