Unit 3 Flashcards
(114 cards)
Ligand
Small molecule that binds to a larger one. Ligands are bound reversibly to a protein
Binding site
A ligand binds a protein at a binding site that is complementary to the ligand in size, shape, charge, and hydrophobic or hydrophilic character
Induced Fit
The binding of a protein and ligand is also paired with a conformational change in the protein that makes the binding more complementary to the ligand, permitting tighter binding
Why do multicellular organisms transport oxygen on FE2+ incorporated into a heme group?
- Oxygen is poorly soluble in aqueous solution and cannot be carried to tissues in sufficient quantity if put in the bloodstream because oxygen diffusion is ineffective over greater distances.
- Multicellular organisms cannot use protein alone to transport oxygen because no amino acid side chains are suited for the reversible binding of oxygen molecules
- Metals like Fe2+ can bind to oxygen but having free FE2+ promotes the formation of highly reactive oxygen species. (like hydroxy radical)
- Fe2+ must be sequestered to be less reactive. It is incorporated into a protein bound prosthetic group called a heme to do this
Pyrrole Ring (draw structure)
There are four pyrrole rings
What are the 6 coordination points to iron? (draw)
Iron has 6 places where it can bond. 4 of them are in the plane. One is going up and the other is going down.
What is the oxidation state of Fe2+ in myoglobin and hemoglobin?
The oxidation state is Fe2+.
*Fe3+ doesn’t bind oxygen and it is formed when there is a O2 molecule on each side of the Fe.
Protoporphyrin
Refers to the the porphyrins lacking metal ions in the structure
Porphyrins
Pyrrole rings with metal inside the structure. A heme group is a specific type of poryphyrin with Fe2+
What is a globin?
Globins are a family of proteins that have heme groups
Describe the secondary and tertiary structure of myoglobin
- Myoglobin secondary structure is composed entirely of alpha helices and non helical residues. There are around 8 alpha helices in myoglobin
Where is the location of the heme group in myoglobin?
The heme group is in the core of the protein
How does myoglobin folding occur? Describe the polar or nonpolar character of the inside and outside of the native protein. The oxygen binding site in myoglobin involves the heme group and two histidine residues. Is it surprising to find histidine residues in the interior of a protein?
Myoglobin folding occurs through the hydrophobic effect. It makes it favorable to fold the protein into a tertiary structure. The inside of a protein is typically non=polar and the outside is polar. It is surprising to find histidine residues in the interior of a protein because it is hydrophobic/polar which means that it should be on the outside of the protein.
What is the physiological role of myoglobin?
Facilitates oxygen diffusion in muscle tissue. Oxygen storage protein
What is the meaning of P50
The pressure at which half of the possible binding spots are bound to the myoglobin. The myoglobin is 50% saturated.
To put it simply, if we have a population of myoglobin molecules, at the P50 value, half of these myoglobin molecules will have oxygen bound to their binding sites, while the other half will not have oxygen bound.
What is the P50 of oxygen binding to myoglobin
0.26 kPa
What does the hyperbolic shape of the binding curve tell you about the sensitivity of myoglobin to changes in ligand concentration?
- It is relatively insensitive to small changes in concentration of dissolved oxygen, so it functions well as an oxygen-storage protein
Discuss the role of the distal histidine in the myoglobin ligand binding site
The role of the distal histidine is to create a bond with the oxygen and to prevent the bonding of carbon monoxide.
- Due to the linear conformation of carbon monoxide, there would be too much steric rubbing with the histidine. This is effective at preventing the bonding of carbon monoxide. The oxygen is bent which prevents steric hindrance.
- There is an H on Histidine N at certain pH’s, permitting it ot create hydrogen bonds with oxygen which stabilize the structure
Discuss the role of the globin protein in preventing heme iron oxidation
Free heme molecules leave the Fe2+ with two “open” coordination points. having simultaneous reaction of O2 molecules on both coordinate points can irreversibly convert Fe2+ to Fe3+. This reaction is sequestered if there is a protein taking up one coordinated bond
What is “molecular breathing” and why is it important in terms of myoglobin function
- If the protein were rigid, O2 could not readily enter or leave the heme pocket. however, rapid molecular flexing of the amino acid side chains produces transient cavities in the protein structure of O2 so it can make its way in and out
Is there a myoglobin T and R state?
Not in the way it is for hemoglobin. Myoglobin does undergo conformational changes upon oxygen binding, but these changes are limited to the tertiary structure of the protein, rather than the quaternary structure. When oxygen binds to the heme group within myoglobin, it induces a slight rotation in the heme group and associated helices, leading to a more compact and stable conformation. This conformational change enhances myoglobin’s affinity for oxygen and promotes oxygen binding and release within muscle tissues.
*salt bridges aren’t involved in this
ASK ABOUT THIS ITS CONFUSING
Hemoglobin’s role
In red blood cells, transports oxygen from teh lungs to the tissues
Discuss the quaternary structure of hemoglobin
- Contains 4 heme prosthetic groups, one associated with each polypeptide chain
- Has 2 alpha and Beta chains. Their interactions are mostly salt bridges between each other.
Compare the tertiary structure of the single subunit of hemoglobin to myoglobin
They are very similar to each other reflecting their evolution. essentially 4 myoglobins make up a hemoglobin