BIOMG 3300 - Exam Prep Questions
Solved 100% Correct
Explain the sigmoidal (cooperative) binding curve - Answer This can be viewed a hybrid curve
reflecting the transition from low-affinity state to a high affinity state. It is more sensitive to
small differences in O2 concentration and binds allosterically.
ligand - Answer a small molecule that binds specifically to a larger one (i.e., protein). For
example, a hormone is the ligand for its specific protein receptor [a molecule bound reversibly
by a protein.
binding site - Answer the location (crevice or pocket) on a receptor protein to which a
ligand binds
induced fit - Answer The change in shape of the active site of an enzyme so that it binds
more snugly to the substrate, induced by entry of the substrate. Renders the substrate
catalytically active.
Substrate - Answer The reactant on which an enzyme works.
catalytic (active) site - Answer the ligand-binding site
Why do mulitcellular organisms transport oxygen on Fe+2 incorporated into a heme group? -
Answer Multicellular organisms transport oxygen on Fe+2 incorporated into a heme group
,because the oxygen is poorly soluble in aqueous solutions; also oxygen can only diffuse in very
short distances (and no amino acids can transport it, so Fe+2 it is...). However, Fe+2 promotes
the formation of highly reactive oxygen species that can damage DNA, etc., so it must be bound
in forms that sequester it and make it less reactive.
Heme - Answer A prosthetic group with a protoporphyrin ring and a central iron (Fe) atom.
Pyrrole ring - Answer 4 membered ring containing nitrogen as a part of heme group
6 coordination points in porphyrin Ring - Answer 4 Nitrogen
1 Nitrogen on Proximal histidine
1 Oxygen. Distal histidine is behind oxygen.
Discuss the oxidation state of iron in myoglobin. - Answer We have to keep Fe+2 and no Fe+3!
Nitrogens have an electron-donating character to help keep conversion of the heme iron to
the ferric (Fe+3) state. Iron in Fe+2 state binds O2 reversibly whereas Fe+3 cannot. Also to
keep Fe+2 from converting, heme is located deep in the structure. Heme sequesters Fe+2
along with histidine. Fe+3 also damages DNA and other macromolecules.
Draw the porphyrin ring. - Answer
What is a "globin"? - Answer The globins are a superfamily of heme-containing globular
proteins involved in binding and/or transporting oxygen. These proteins all incorporate
the globin fold, a series of 8 alpha helices. Two prominent memebers include myoglobin
and hemoglobin. Myoglobin is a single polypeptide chain and hemoglobin is a tetramer.
Describe the location of heme group in the protein. - Answer Heme is located deep in
the globular protein to prevent oxidation.
How does the myoglobin fold? What does its structure look like? - Answer The interior consists
of almost entirely of NONpolar resides. In fact, the two histidines are the ONLY polar residues
, inside which play an integral role in the binding of oxygen. The outside of the protein has
both polar and nonpolar resides.
Hydrophobic forces still drive protein folding.
Water bonds strongly to itself, so will reorient to form the maximum amount of H-bonds
when in the presences of nonpolar residues (increasing entropy).
It is surprising that His can be found inside bc it is charged! However, His keeps Fe+2 from
oxidizing and helps bind oxygen.
What is the physiological role of myoglobin? - Answer Myoglobin facilitates oxygen diffusion in
muscle tissue; its' Fe+2 group is suited for reversible binding of oxygen molecules. Myoglobin
is also relatively insensitive to small changes in the concentrations of dissolved oxygen (unlike
hemoglobin) and so it functions well as an oxygen-storage protein.
What is meant by the statement that the binding of O2 is cooperative? - Answer Binding
oxygen as one subunit causes a change in the other subunits to allow more oxygen to bind- this
REQUIRES multiple subunits.
Basically, the binding of oxygen just gets easier and easier as more oxygen binds.
Do isolated hemoglobin subunits exhibit cooperativity in O2 binding? Why or why not? -
Answer No, because there is only one of them therefore cannot bind cooperatively.
Estimate the P50 of oxygen binding for hemoglobin. Compare the P50 for myoglobin. Which
protein has a higher affinity for oxygen? - Answer P50 of hemoglobin: 3.75 pKa (26 Torr)
This is higher than myoglobin's, which is about 2 Torr, meaning that Hemoglobin has a
lower oxygen affinity.
Which protein is more sensitive to small changes in oxygen concentration at physiologically
relevant O2 concentrations? - Answer Hemoglobin is more sensitive to moderate changes in
O2 concentrations (can bind and unbind oxygen); myoglobin has a higher affinity for oxygen so
will bind all of them (though at very low levels of PO2 will unbind ALL of them)
Solved 100% Correct
Explain the sigmoidal (cooperative) binding curve - Answer This can be viewed a hybrid curve
reflecting the transition from low-affinity state to a high affinity state. It is more sensitive to
small differences in O2 concentration and binds allosterically.
ligand - Answer a small molecule that binds specifically to a larger one (i.e., protein). For
example, a hormone is the ligand for its specific protein receptor [a molecule bound reversibly
by a protein.
binding site - Answer the location (crevice or pocket) on a receptor protein to which a
ligand binds
induced fit - Answer The change in shape of the active site of an enzyme so that it binds
more snugly to the substrate, induced by entry of the substrate. Renders the substrate
catalytically active.
Substrate - Answer The reactant on which an enzyme works.
catalytic (active) site - Answer the ligand-binding site
Why do mulitcellular organisms transport oxygen on Fe+2 incorporated into a heme group? -
Answer Multicellular organisms transport oxygen on Fe+2 incorporated into a heme group
,because the oxygen is poorly soluble in aqueous solutions; also oxygen can only diffuse in very
short distances (and no amino acids can transport it, so Fe+2 it is...). However, Fe+2 promotes
the formation of highly reactive oxygen species that can damage DNA, etc., so it must be bound
in forms that sequester it and make it less reactive.
Heme - Answer A prosthetic group with a protoporphyrin ring and a central iron (Fe) atom.
Pyrrole ring - Answer 4 membered ring containing nitrogen as a part of heme group
6 coordination points in porphyrin Ring - Answer 4 Nitrogen
1 Nitrogen on Proximal histidine
1 Oxygen. Distal histidine is behind oxygen.
Discuss the oxidation state of iron in myoglobin. - Answer We have to keep Fe+2 and no Fe+3!
Nitrogens have an electron-donating character to help keep conversion of the heme iron to
the ferric (Fe+3) state. Iron in Fe+2 state binds O2 reversibly whereas Fe+3 cannot. Also to
keep Fe+2 from converting, heme is located deep in the structure. Heme sequesters Fe+2
along with histidine. Fe+3 also damages DNA and other macromolecules.
Draw the porphyrin ring. - Answer
What is a "globin"? - Answer The globins are a superfamily of heme-containing globular
proteins involved in binding and/or transporting oxygen. These proteins all incorporate
the globin fold, a series of 8 alpha helices. Two prominent memebers include myoglobin
and hemoglobin. Myoglobin is a single polypeptide chain and hemoglobin is a tetramer.
Describe the location of heme group in the protein. - Answer Heme is located deep in
the globular protein to prevent oxidation.
How does the myoglobin fold? What does its structure look like? - Answer The interior consists
of almost entirely of NONpolar resides. In fact, the two histidines are the ONLY polar residues
, inside which play an integral role in the binding of oxygen. The outside of the protein has
both polar and nonpolar resides.
Hydrophobic forces still drive protein folding.
Water bonds strongly to itself, so will reorient to form the maximum amount of H-bonds
when in the presences of nonpolar residues (increasing entropy).
It is surprising that His can be found inside bc it is charged! However, His keeps Fe+2 from
oxidizing and helps bind oxygen.
What is the physiological role of myoglobin? - Answer Myoglobin facilitates oxygen diffusion in
muscle tissue; its' Fe+2 group is suited for reversible binding of oxygen molecules. Myoglobin
is also relatively insensitive to small changes in the concentrations of dissolved oxygen (unlike
hemoglobin) and so it functions well as an oxygen-storage protein.
What is meant by the statement that the binding of O2 is cooperative? - Answer Binding
oxygen as one subunit causes a change in the other subunits to allow more oxygen to bind- this
REQUIRES multiple subunits.
Basically, the binding of oxygen just gets easier and easier as more oxygen binds.
Do isolated hemoglobin subunits exhibit cooperativity in O2 binding? Why or why not? -
Answer No, because there is only one of them therefore cannot bind cooperatively.
Estimate the P50 of oxygen binding for hemoglobin. Compare the P50 for myoglobin. Which
protein has a higher affinity for oxygen? - Answer P50 of hemoglobin: 3.75 pKa (26 Torr)
This is higher than myoglobin's, which is about 2 Torr, meaning that Hemoglobin has a
lower oxygen affinity.
Which protein is more sensitive to small changes in oxygen concentration at physiologically
relevant O2 concentrations? - Answer Hemoglobin is more sensitive to moderate changes in
O2 concentrations (can bind and unbind oxygen); myoglobin has a higher affinity for oxygen so
will bind all of them (though at very low levels of PO2 will unbind ALL of them)
