Module 3 - Protein Function Flashcards
Describe the structural differences between myoglobin and haemoglobin
Hb is a tetramer of four subunit (or a dimer of two alpha-beta protomers), where each subunit is similar to myoglobin (only a single fold domain).
Explain the structural basis of oxygen binding to myoglobin and haemoglobin. How do they differ?
Oxygen binds to the Fe2+ of the heme group (specifically with the iron atom) of a subunit. The Fe atom is located in the plane of the porphyrin ring system, with two available binding sites, one for a histidine residue and the other for the O2. The binding of O2 to the subunit is an example of a protein-ligand interaction.
Hb and Mb differs as Hb has four subunits, while Mb has only one. The effect of the binding of O2 to the rest of the Hb subunits is not applicable to Mb,
Describe the structural basis for the transition between the low and high affinity states of Hb.
When oxygen binds with Hb, it triggers a conformational change from the tense (lower affinity for O2) to the relaxed (higher affinity) state. This change involves breaking salt bridges between the residues at the α1-β2 interface (carboxylic group from the C-terminus of beta subunit and lysine residue form alpha residue).
Compare and contrast different models for cooperative binding.
Concerted:
- all or none event
- all subunits are thought to be in the inactive T or the active R form
- successive binding of ligand to the inactive state makes the transition to active state more likely
Sequential:
- each subunit of the multimer can be in either the T or R form
- Change in conformation in one subunit induces a similar change induces a similar change in ADJACENT subunit
Describe the Bohr effect.
pH difference between lungs and metabolic tissues increase efficiency of the O2 transport (by lowering the affinity of Hb to O2)
Explain the effect of pH on Hb affinity for O2 in terms of amino acid and protein structure,
Actively metabolizing tissues generate CO2 and H+, lowering the pH of the blood near the tissues relative to the lungs (catalyzed by carbonic anhydrase). H+ are thought to bind to the N-terminus of the alpha-subunit, His HC3 of the beta-subunit, and other amino acids residue. In particular, the ion pair between the protonated His and Asp stabilises the T state of Hb, lowering the affinity of Hb to O2.
Describe how haemoglobin transport CO2.
20% of CO2 is exported in the form of carbamate on the amino terminal residues of each of the polypeptide subunits. The formation of a carbamate yields a proton that can contribute to the Bohr Effect. The carbamate forms additional salt bridges, stabilizing T state.
Describe how Hb binds BPG and explain why it is important for oxygen release.
BPG binds and stabilises the T state, which interact with positively charge amino acid residue lining the cavity. Note that BPG has 2 phosphate groups and 1 carboxylate group. By stabilizing the T state it lowers the affinity of Hb to the O2, hence allowing for a more efficient transport of O2.
Explain why higher concentration of BPG is advantageous at high altitude.
At high altitude, pO2 in the environment decreases so Hb is less saturated and O2 delivery is then decreases. With BPG, the affinity for O2 decreased, hence O2 delivery can increase.
Mention the function of Mb.
- Storage of oxygen in muscles
- Release of oxygen when rapidly contracting muscle need energy
Explain why myoglobin is not an effective transporter of O2.
The affinity of myoglobin to O2 is still considerably high in tissues, not much lower compared to the affinity in the lungs. Hence, not a lot of oxygen is released in the tissues by myoglobin under normal circumstances.
Explain, using examples, the relationship between the ligand binding affinity and Kd.
Ligand-binding affinity increases as Kd decreases.
