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Biochm chpt 5 (test 2 review)


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What is a Ligand?
-a molecule reversibly bound
-can attach and release
-a small molecule that binds specifically to a larger one
What is a Binding Site?
a specific location on a protein where a ligand bonds
What is flexibility?
very important
-"induced fit"
What is regulation?
-important characteristic of binding site
What is an enzyme?
-a biomol., that catalyzes a specific chemical reaction.
-it does not affect the equilibrium of the catalyzed rxn
-it enhances the rate of a rxn path with a lower activation energy
What is a substrate?
the specific compounded acted upon by an enzyme
What is a catalytic (Active) site?
the region of an enzyme molecule that binds a substrate molecule and catalytically transforms it
Describe Oxygen binding?
1. it is important but poorly soluble because it is nonpolar
2. Transition metals (like Fe) can transport it but they can damage cells
3. so we need to sequester (hide) Fe but still have it the oxygen accessible.
4. this is accomplished by the heme group
Describe the heme binding Oxygen?
1. central Fe
2. bound to Oxygen
3. bount to two heme groups
4. prevents oxidation of Fe2 to Fe3+
5. also bound to N in histidine
6. oxygen can be bound and released
7. this heme group is hidden inside of either myoglobulin or hemoglobulin
Describe myoglobulin?
1. It is primarily a storage form for Oxygen.
2. It is alpha-helical.
3. It is relatively insensitive to [Oxygen] when binding, always the same affinity
Describe Hemoglobulin?
1. a free heme (not in Hb) binds CO 20,000X better than it binds Oxygen (so Kd for CO is 1/20,000 that of Kd for oxygen)
2. When heme is in hemoglobulin it binds CO only 200X better than oxygen
3. change is due to steric hindrance
4. Hb is very sensitive to [oxygen]
Hemoglobulin vs. Myoglobulin structure?
very similar 3-D structures but there is a lot of difference between AAs
-myoglobulin is mostly alpha-helical
What does theta represent?
fraction of sites occupied

theta = [L]/([L] + Kd)

theta = 50% when [L] = Kd = 1/Ka (this is when 1/2 the binding sites are occupied)
Association constant variable?
Dissociation constant variable?
Association constant eqn?
Ka = [P*L] / [P][L]
Dissociation constant eqn?
Kd = [P][L] / [PL]


Kd = 1 / Ka
Kd is the ? of Ka.
the reciprocal
In the AA acid sequence of Hb alpha and Hb beta what percentage is the same?
less than 50%
-but very similar structure
When comparing the AA sequence of Hb alpha, Hb beta, and myoglobulin structure what is observed?
only 27 of 140-150 AAs are the same but the 3-D structures are all very similar
If there is a high concentration of oxygen is hemoglobulin more likely or less likely to bind?
then it is very likely to bind
What is an allosteric protein?
a protein (generally with multiple subunits) with multiple ligand binding sites, such that ligand binding at one site affects the ligand binding at another
-has more than one conformation
What is a homotropic modulator?
An allosteric modulator that is identical to the normal ligand
What is a heterotropic modulator?
an allosteric modulator that is distinct from the normal ligand
Hb has how many oxygen binding sites?
What is cooperative binding as it relates to Hb?
As it binds oxygen at each site the binding subunits conformation changes and the affinity for oxygen increases
-the rich get richer
Example of an allosteric protein?
Example of a homotropic modulator?
Oxygen (b/c it is both modulator and ligand)
What does pO2 refer to?
how much oxygen is surrounding a molecule
Describe binding affinity of Hb as a function of pO2?
-displayed on sigmoid binding curve
-shows cooperative binding
-as pO2 increases Hb transitions from a low to a high affinity st.
-it has a hill coefficient greater than 1 which is indicative of the cooperative st.
-A high, ideal affinity st. is never seen and a low-affinity st. is rarel seen
Name the two possible conformations of Hb?
the T state and R state
T state vs. R state of Hb
1. T st. is primary in the absence of oxygen and has a low affinity for oxygen
2. R st. is primary in the presence of Oxygen and has a higher affinity for oxygen
Describe hill coefficient?
if >1 then cooperative binding
-if = 1 then not coop.
-if < 1 then negative coop
When [CO2] increase what happens to [H]?
it increases also
Describe Hb's affinity for Oxygen as it relates to [CO2] and [H]?
-inversely proportional
-if there is high [CO2] and [H] then there is low affinity for oxygen and vice versa
-so in the peripheral tissues Hb has a low affinity for Oxygen and releases it
-so in the lungs Hb has a high affinity for Oxygen
How do oxygen, CO2, and H bind to Hb?
at different sites. one site affects the conformation and affinity of the other sites
What is the Bohr effect?
The inversely proportional relationship between [CO2] and [H] with [O2] binding in Hb
BPG aka?
2,3 Bisphphoglycerate
-plays an important role in adaptation to high altitudes (low Oxygen partial pressure)
-binds to Hb at site far from oxygen site
Describe adaptation to high altitudes?
-at high altitudes, with less pO2 the body lowers the affinity for O2
-this is accomplished by BPG
-this allows the body to deliver about the same amount of oxygen to tissues
-however, at first there is a dip from 38% to 30%
-but then BPG conc. increases from 5mM to 8mM
-so affinity in lungs is reduced slightly, but peripheral tissues are more signigicantly, then about 37% of bound oxygen is delivered to peripheral tissue

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