Lecture 3: Structure/Function Relationships of Proteins: Myoglobin & Hemoglobin Flashcards
What is a molecule that binds?
ligand
What is the small region where the ligand binds?
binding site
What forces are used during non-covalent binding?
non-covalent forces
What is K?
Equilibrium Constant
What is k?
Rate constant
What is another name for the ligand-binding site?
Catalytic (Active) site
Are the Kd and Ka inverse?
Yes
True or False; Better drugs have a larger kd
False; Better drugs have a smaller kd (disassociation constant) which means they have a higher association constant and high affinity.
Which will have the highest affinity?
ka= 10^5 ka= 10^-5
ka= 10^5
What are (3) notes to remember about binding? (Exam review)
1) Binding occurred at Eq
2) Binding is reversible
3) Total [L]= Pre[L] because protein is saturated with ligand
What is kd in reference to [L]?
[L] at which 1/2 protein bound to ligand
What can we assume at y-max as it relates to protein availability?
All of protein is bound to ligand
What is the Langmuir Isotherm Equation
[PL]= [P]total [L] total/ Kd + [L] Total
*Shows difference bt amounts of protein/ligand
What are suicide inhibitors?
They induce a lot of side effects and are very reactive
Which model only allow certain ligands to bind?
Lock & Key Model
What are (3) ways Lock & Key Model complement?
size shape charge hydrophobic/hydrophilic character
Which model occurs upon ligand binding and causes a conformational change
Induced Fit Model
True or False: Induced Fit allows for loose binding of the ligand
False; Induced Fit allows for tight binding of the ligand.
True or False: Induced fit can increase the affinity of the protein for a second ligand
True
True or False; only the ligand can change their conformations in Induced Fit
False; Both the ligand and protein can change their conformations
What is a goal of Myoglobin?
need to store O2 for metabolism but protein side chains lack an affinity for O2
How does Myoglobin store O2?
Capture molecule with Heme moiety,
True or False; Myoglobin is the main O2 storage in bacteria
False; Main O2 storage in Mammals.
True or False; Increase in Delta G means an unfavorable and increase in kd
True; increase in kd means decrease in affinity and unfavorable reaction
True or False; Transition metals that bind to Myoglobin cause free radicals
True
True or False; O2 binds to myoglobin irreversibly
False; binds to myoglobin reversibly
How many subunits does Heme contain?
2
What are the subunits that Heme contain
Alpha2-Beta2
True or False; Heme is a weak chromophore
False; it is a strong chromophore
What is the prosthetic Group of Hemoglobin
Heme
What are the 2 interchangable structural states of Hemoglobin
T/R
What do we know about T structural states?
Most stable when NOT bound to O2
What do we know about R structural states?
O2 binding promotes transitioning
True or False; O2 binding is allosteric and cooperative
True
True or False; Hemoglobin has a few binding sites
False; Hb has multiple binding sites
What is it called when binding sites are able to interact with each other?
Cooperatively
What is bound to iron in Heme?
4- Pyrole Rings
Proximal His
O2
What does R in R-state stand for?
Relaxed State
What does T in T-State stand for?
Tense state
T transforms to R when what happens
O2 binds to T causing a conformational change
Which state has a high affinity for O2>
R-state
True or false: Blood in lungs has a higher pH than blood in tissues
True; The blood is most acids in the tissues
True or false; O2 has a higher affinity for a lower pH
False; O2 has a higher affinity for a higher pH
When is O2 released? at higher or lower pH?
Lower pH
What is the Bohr Effect
the pH difference between the lungs and metabolic tissues increasing the O2 transfer efficiency
Explain how Hb picks up and distributes O2?
Hb pick up O2 from Lungs (high affinity/high pH) and distributes it to the tissues of the body (low affinity/low pH)
True or False; When protonated, His favors the T-state
True (lower pH)
pronated (acidic)
True or False; When deprotonated, His favors the T-state
False; depronation= His favors R-state
depronated (higher pH)
What AA contributes to the Bohr Effect
Histidine
How is CO2 exported via Hemoglobin?
1) Dissolved bicarbonate in the blood
2) In the form of a carbamate on the Amino Terminal Residue of each Hb polypeptide subunit
True or False; When Hb binds to O2 in the lungs, CO2 is released
True
BPG is found where?
RBC;
Where does BPG bind to O2?
Between the Beta subunits
True or False; BPG stabilizes the R-State
False; it stabilizes the T-state
True or False; purified HB has a lot of BPG in the blood>
True
How can you force a drug to bind to a protein if it has a very high Kd?
Increase amount of ligand present; downside will give you lots of side effects
What does Kd depend on?
pH
specificity between the protein and ligand
What are (3) assumptions about Langmur Equation?
1) Binding is at eq
2) Binding is reversible
3) Total [L] > Total [P] meaning protein is saturated with ligand. So most of the ligand is NOT bound to the protein.
True or False; Fractional occupancy of the protein receptor increases as the binding affinity increases
True
True or False; Heme group has a porphyrin ring with a Fe atom
True
Is Hb tetrameric or monomeric?
tetrameric
Is Mb tetrameric or monomeric?
Monomeric
How many O2 can Hb bind to?
4-O2
How may O2 can Mb bind to?
1-O2
How many peptide chains does Mb consist of?
single
Where is Mb found
tissues
What is bound to iron in Heme?
4-Pyrole rings, Distal histidine, O2
Wha type of binding does Hb bind?
Cooperative Binding
What type of bonds does 2,3-BPG form with the R-state?
None. It only binds to the T-state/stabilizes it. (via ion interactions)
