Topic 1 - Module 3 Flashcards
Describe the structural differences between myoglobin and haemoglobin.
Mb has one polypeptide chain with a single globin fold that makes up the protein domain, along with one heme unit. This is why it is known as a monomer.
Hb has 4 subunits, each with one globin fold and one heme unit involved. Hb is a tetromer, also a dimer made up of two alpha-beta protomers.
What does multivalent mean?
Explain multivalent binding and provide an example of when it does occur.
Multivalent describes a versatile nature of an action, in multivalent binding, it means that the protein can have multiple binding sites which is much more effective due to the avidity of the bond.
This is prevalent in antigen/antibody binding (avidity) when variable regions on the antibody undergo conformational change when interacting with an antigen.
Explain how haemoglobin has evolved to be multimeric.
It is advantageous for Hb to have multiple binding sites as they can then exhibit allosteric cooperativity.
This concept underpins an improved efficiency in the uptake and subsequent release of oxygen, particularly in dynamic oxygen conditions.
What is a key difference between myoglobin and haemoglobin? What are their functions in the body system?
Mb has an isolated, singular binding site (due to one heme group) whereas haemoglobin has 4 oxygen-binding sites. Hence, their oxygen-binding properties are what sets them apart from one another.
This is why Mb is readily involved in storing oxygen, whereas Hb is highly involved in the delivery of oxygen.
Explain how myoglobin has been optimised to efficiently store oxygen.
Mb exists primarily in muscle cells.
They have positive charges spread out along the surface of each Mb molecule, enabling each molecule to repel with one another, reducing the possibility of clumping.
This, therefore, allows Mb to be found in high concentrations that then results in steady reserves of oxygen that can be rapidly released to respiring myocytes.
What does the equilibrium dissociation constant (Kd) tell us?
For a particular interaction (protein - ligand) the Kd will show us when exactly half of the binding sites have been occupied.
Otherwise defined as the concentration of free ligand at which the protein has been 50% saturated.
A diet overly rich in raw eggs can lead to biotin deficiency. Cooked eggs do not cause this problem. Why?
Cooked eggs means that there has been a significant increase in temperature, possibly below ideal protein folding conditions.
As such, the protein avidin is likely to denature, and unfold from its original shape, losing its biological function as the result.
This means that avidin will no longer be able to bind to biotin and extract it from cells/bacteria, resulting in a lack of biotin deficiency.
For oxygen binding to hemoglobin the affinity for oxygen should be (…) at lower oxygen partial pressures.
lower.
Because, lower partial oxygen pressures means that more oxygen will be released, to be used in respiring tissues.
Should acidic conditions make hemoglobin bind oxygen more tightly or more weakly? Does that make sense in terms of what you know about exercise physiology?
Low pH conditions will result in increased acidity, which corresponds to the lowering of oxygen affinity, relating to a release of oxygen molecules from the haemoglobin.
This is corresponding to the exercise ideas, where more oxygen is needed as muscles are respiring at a greater rate when exercising.
Could myoglobin be used to transport oxygen? Why or why not?
myoglobin binds oxygen very tightly, even at very low partial pressures.
Hence, won’t be effective in delivering oxygen to other areas of the body, where partial pressures are significantly higher than 4kPa, given its inability to efficiently release those molecules.
Moreover, reducing the binding affinity of Mb would not be helpful, as more Mb units will be needed to deliver sustainable levels of oxygen (one molecule per unit).
Describe the two states of hemoglobin units. Then, explain how Hb transitions between these two units.
Tense state refers to the loosely bound oxygen molecules, showing lower binding affinity and more interactions with oxygen molecules - resulting in greater stability. The Relaxed state is the opposite of this, showing its ability to bind strongly to oxygen molecules in the lungs.
Hb undergoes a conformational change, when the salt-bridges between residues at each alpha-beta interface is disrupted, a cascade initiated by the binding of oxygen molecules (T to R).
The transition becomes favourable, as the Hb unit is temporarily destabilised.
A change in alpha-helix positions, and domains sliding over one another, will create the R-state conformation, that results in oxygen tightly bound to the heme group (planar in the R-state)
How is the T-state of Hb stabilised?
It is through the interactions between residues of each domain, particularly the symmetry of Hb unit itself, that stabilises the T-state in its low affinity conformation.
Explain the meaning of cooperative binding
Cooperative proteins have multiple ligand-binding sites, which means that proteins can exhibit positive/negative cooperativity - whereby the binding of a ligand initiates a cascade of reactions.
Summarise the hill plot of cooperativity.
the plot shows that at optimal points of partial pressure, oxygen can rapidly start to occupy the binding sites, showing a transition from T state to R state.
the gradient of the plot, the Hill constant, (Kh) outlines the degree of interaction/cooperativity between binding sites (ie positive, negative or independent of one another) and highlights the average occupancy of the binding site at that particular partial pressure.
Highlight the similarities and differences between the concerted model and the sequential model.
The concerted model emphasises that successive binding of ligands to the inactive state (T) will make the transition to an active state (R) more likely, as it is under this condition that more favourable transitions will occur.
The sequential model emphasises that a change in conformation in one subunit will induce similar changes to those around it spatially. This means that both states are equally populated, and eventually results in all subunits transformed into R-state.
Ultimately, both models show that the transformation into the R-state is inevitable.
