Protein function Flashcards
what determines a proteins 3D structure?
its primary structure
what is the structure of myglobin?
tertiary structure
what is the structure of hemoglobin?
quaternary structure
where does hemoglobin bind to and where is it released?
binds to O2 in the lungs and is released in tissues
where does myoglobin bind to? what is it’s function?
binds to O2 in muscles
-O2 reserve during exercise
-facilitates O2 diffusion in muscle tissue
-stores O2 in aquatic animals
what is the relationship between protein function and ability to bind?
the function of many proteins depends on their ability to bind other small molecules (ligands) reversibly
what does a high Kd signify?
a low affinity
what does a low Kd signify?
a high affinity
what is the relationship between ligand-protein complex and the [ligand] and [protein]?
the affinity of Y for X greatly influences the extent to which the (XY) complex is formed, regardless of the concentrations of X or Y. Higher affinity results in a greater proportion of complex formation, while lower affinity leads to less complex formation.
which numbers show a higher affinity? which ones show lower?
1 and 2- higher
3 and 4- lower
what is Kd ?
It’s a measure of the affinity of a ligand for its receptor. In other words, it represents the concentration of a ligand at which half of the available binding sites on the receptor are occupied by the ligand
which ligand will have a higher Kd? what would the binding curve look like?
Kd (z) will be higher due to its lower affinity
what helices is the heme group between for myoglobin?
between helices E and F
what are the structural differences between hemoglobin and myoglobin?
hemoglobin - quaternary structure
myoglobin - tertiary structure
what is the structure of heme?
-circular and planar
-Fe2+ ring between four N atoms
is heme hydrophobic or polar?
largely hydrophobic with 2 polar charged groups
what state must the Fe atom be inside the heme group?
Fe must be maintained as Fe2+
what position is the O2 at in regards to heme?
6th
what position is the Histidine at in regards to the heme group?
5th
what interactions are important for the heme to fit in the bidning pocket?
hydrophobic interactions
what positions is the heme group at?
1-4
what forces hold the hemoglobin porphyrin ring in place?
hydrophobic interactions and coordination bond between Fe2+ and a His (F8 or proximal)
what is the function of the proximal His?
1) bind heme into heme-binding pocket
2) prevent oxidation of iron atom
what is the proximal His reffered to as?
His F8
what is the distal His reffered to as?
His E7
what is the function of the Distal His (His E7)?
1) increases O2 binding affinity
2) lowers affinity of other molecules (CO)
3) creates increased specificity for O2
-anchors heme and doesn’t interact with Fe2+ at all
what is the realtionship between reactions and affinity?
favourable rxn’s - increase affinity
unfavourable rxn’s - decrease affinty
-in this example CO is blocked by the distal His in order to prevent binding
what is the difference on the dissociation curve of myoglobin vs hemoglobin?
-higher affinity of O2 to bind to myoglobin
-sigmoidal shape for hemoglobin
what subunits does hemoglobin have?
2 alpha
2 beta
what does a hyperbolic curve indicate about affinity?
is tells us that affinity is constant
-Kd doesnt change
-myoglobin
what does a sigmoidal curve tell us about affinity?
it tells us that binding affinity is cooperative
-ligand affinity changes as more ligands bind
-hemoglobin
what structural changes allow for Hb to change its affinity for O2?
change in tense vs relaxed state
-tense has low affinity
-relaxed has high affinity
what residues is the His group located between in the T state (deoxyhemoglobin)?
Between Thr and Pro
what residues is the His group located between in the R state (oxyhemoglobin)?
between 2 Thr groups
explain the differences between the T and R state of hemoglobin in regards to its affinity, O2 binding and central cavity size
what does an activator do to affinity?
increases binding affinity
-positive effector
what kind of effector is O2 to Hb?
homoallosteric activator
what events occur in O2 binding?
1) O2 binds to a subunit
2) Fe2+ moves into plane of heme
-His F8 moves with Fe
-Helix F moves
3) Subunit interface change affects other subunits
-Helix F / His F8 / Fe2+ movement
-O2 binding site becomes high-affinity (R), oxygen binds more readily to other binding sites
what 2 molecules are allosteric effectors for Hb?
O2
-homoallosteric activator
BPG (2,3-bisphosphoglycerate)
-heteroallosteric inhibitor for O2
H+
-heteroallosteric inhibitor for O2
what is BPG essential for in regards to Hb?
BPG is small and highly negative, it is essential in formation of the T state
-negative allosteric effector of O2 binding
-increased [BPG] = decreased O2 binding
where does BPG bind to?
binds in the central cavity of deoxyhemoglobin (T-state)
what does BPG interact with in the binding cavity?
the (-) charges on BPG interact with the (+) charged groups on the protein
what affect does BPG have on protonation of side groups?
groups associated with BPG binding become protonated (Bohr effect)
-enhance BPG binding
-Reduce O2 binding
-subunit interface effected by new electrostatic interactions
explain the path of O2 transport by Hb
deoxyHb
-BPG bound; T-state —> Lungs bind O2 and Hb switches to R-state
-BPG not bound —>
peripheral tissues release O2
-BPG bound
what is the effect of salt bridges on Hb?
salt bridges stabilize the deoxy form (T-state) of Hb
-CO2 binds to the N-terminus of Hb, HbNH-COO-, this forms a salt bridge stabilizing the T state.
how does the substitution of Glu6 for Val affect O2 binding to Hb?
the binding of Val to the hydrophobic surface exposed between E and F helices during transition from T to R causes Hb molecules to aggregate into long polymers / fibres
how does affinity differ from fetal Hb, adult Hb and Mb?
adult Hb < Fetal Hb < Mb
