1.3 Protein function Flashcards
Label these proteins
What term would you use to describe the relationship between myoglobin and hemoglobin?
They are homologues or paralogues, as they exist in the same organism
What is a protomer?
The structural unit of a protein with quaternary structure - the smallest unit that can be replicated by symmetry
What is the structure of immunoglobin Gs (IgG)?
Consist of four subunits
2 heave chains
2 light chains
Both involved in binding to the antigen ligand
Why have antibodies evolved to be multivalent?
Multi valent binding is more efficient than binding through a single fold. More effective due to avidity
What are the two functions of Mb?
- Storage of oxygen in muscles
- Release of oxygen when rapidly contracting muscle needs energy
Where does oxygen bind?
Oxygen binds to the Fe2+ of the Heme group.
In what animals is Mb abundant in?
The muscle of diving animals - seals, otters and whales
What is the prostheic group of hemoglobin?
It is where O2 bind reversibly to the Fe2+ of the heme prothetic group.
It is a prosthetic group as it is separate to the protein itself
What is the equilibrium constant for association and dissociation?
What does thetha mean?
What happens when half the binding sites are occupied?
What is the relationship between Kd and affinity?
If there is a high Kd then there is low affinity and vice versa
What is biotin and what is it needed for?
- Biotin is a vitamin essential in the diet
- Needed for carboxylations
- It binds the protein avidin found in raw egg white
Explain the binding interaction of biotin and avidin with reference to the Kd
- Avidin in egg whites bind biotin
- The Kd of 10-15 is so small that the binding can be considered irreversible
- Biotin deficiency in humans is associated with long term consumption of raw eggs rich diets but when eggs are cooked the avidin unfolds and does not bind biotin
What can be deduced about Mb and oygen binding from the shape of this curve?
- Curve is very steep
- Demonstrates tight binding
- Half the ligand binding sites will be occupied at a very low partial pressure
With reference to kPa values of pO2, could myoglobin transport oxygen?
pO2 in the lungs is about 13 kPa so myoglobin will bind it.
pO2 in the tissues is about 4 kPa so it will not release it!
What is the T state of hemoglobin?
T = tense state
– more interactions, more stable
– lower affinity for O2
What is the R state for hemoglobin?
R = relaxed state
– fewer Interactions, more flexible
– higher affinity for O2
What is the conformational state change that hemoglobin undergoes?
O2 binding triggers a T ⇒ R conformational change
Involves breaking salt bridges between the residues at the a1B2 interface
What salt bridges are broken in going from T to R state?
Salt bridge between His and Asp
Name the salt bridges that are broken from T to S state?
What is the Hill equation?
What does the Hill plot’s slope indicate?
What does the slope of the HIll plot actually mean?
- It is a measure of the degree of interaction or the cooperativity of the binding sites
- Slope is called Hill coefficient nH
- The experimentally determined slope indicates the interaciton between binding sites rather than the actual number of binding sites
Name what state is which part of the Hill plot for Hb
Which model of cooperativity is which?
What is the key feature of the concerted model of cooperativity?
- Without a ligand the subunits are either all inactive T or all active R
- Active state is destabilised by ligand binding, but once it does then its more likely to transition to the active state
What are the key features of the sequential model of cooperativity?
- Each subunit can either be in T or R state, you can have a mix in the multimer
- Change in one subunit induces similar change in an adjacent subunit so binding of another ligand is more likely
What is the effect of pH on O2 binding to Hb?
There is a shift to the right
What happens to the affinity of Hb for O2 at lower pH?
Low pH is a high concentration of H+ which decreases affinity of Hb becuase H+ stabilises Hb in the T state
How is O2 able to be easily released at tissues due to H+?
- pH is lower in tissues due to metabolism that produces organic acids, lactic acid and Co2
- H+ lowers affinity of Hb for O2 to help release O2 from Hb to the tissues
- T state is stabilised becuase His HC3 is protonated which then forms a salt bridge with Asp FG1
How is the Hb O2 reaction written?
What is the Bohr effect?
The pH difference between the lungs and metabolic tissues increases the efficiency of O2 transport
How is Co2 produced by metabolism in the tissues exported?
How can Co2 contribute to the Bohr effect?
- Formation of carbamate yield a proton
- Forms additional salt bridges stabilising the T state
- Released when it reaches the lungs to favour R state
Where is 2,3-BPG found from?
How is 2,3-Bisphosphoglycerate a regulator of O2 binding?
- It is a negative allosteric regulator
- Small negatively charged molecule that binds to the positively charged central cavity of Hb
- Stabilises the T states
What is the binding mechanism for 2,3 BPG on Hb?
*
What does BPG essentially do at high altitudes?
At high altitudes you pick up less oxygen in the lungs but the right shift due to BPG means that you release more oxygen at the tissues because affinity for Hb to O2 decreases
How is the allosteric affect seen in binding of H+, BPG and Co2 to hemoglobin?
- Binding of the three ligands is allosteric as they bind at a site away from the O2 binding site
- Results in cooperativity of binding due to changes in teh conformation that are transmitted through subunits of Hb
How is CO a competitive inhibitor in terms of the shape of the molecule?
