Biochem Protein Lecture 11 Flashcards by michael perna

Changes in the positions of key ________ chains surrounding heme may cause the change from T to R

Amino Acid Side Chains

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When in the T state, the ______ ring of heme is slightly puckered.

The heme iron protrudes to some extent on the DISTAL/PROXIMAL His side

Porphyrin

Proximal His side

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When O2 binds to heme initially in the T state, it pulls the ____ a short distance down into the heme resulting in a more planar heme

Fe2+ (Ferrous Iron)

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What occurs to relieve the strain caused by oxygen binding to heme in the T state caused by the more planar state

Rearrangment

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What shifts its position to perpendicular to relieve strain caused by O2 binding heme in the T-state?

What else does it shift?

What does it result in?

Proximal His

The F helix and FG corner

R state

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After the proximal His moves, _______ is pushed to the right and its H bond with ______ is broken.

H bonds and salt bonds that connect FG corners of one unit with C helices of another subunit are STRENGHTENED/WEAKEND?

Val FG5, Tyr HC2

Weakened

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In sum, binding of O2 pulls the ferrous iron a fraction of a nanometer into the heme, causing a larger shift in the surrounding structure, particularly at the ______.

The result is increased

α-β interfaces

Oxygen binding

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As stated in the previous lecture, Mb with its hyperbolic binding curve, it would bind with HIGH/LOW affinity in the lungs, but it WOULD/WOULD NOT release much of it in the tissues

High affinity, would not release

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Could a protein with a hyperbolic curve bind O2 at a low enough affinity to release it in the tissue, but it wouldn’t pick up enough O2 in the lungs?

Yes, the opposite of Mb

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How does Hb deal with the pressure difference posed in the lung and the hyperbolic curve?

Going from a transition state from the low affinity (T state) to the high affinity (R state)

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The binding curve for Hb is _____ because O2 binding is coopoerative.

Sigmoidal (S-curve) look at graph

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This term means that the binding of O2 to the heme Fe in one subunit increases the Ka (binding affinity) of oxygen in the other subunits

Cooperative

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The first O2 molecule interacting with deoxy Hb binds strongly or weakly?

By the time the last (4th) O2 molecule binds, it binds to a heme subunit already in the

Weakly (T-state)

R-state

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Because of cooperative binding, Hb will be almost fully ____ at the pO2 of the lungs but only partially ____ (same word) at the pO2 in the tissues

Saturated.

Most of the O2 bound by Hb is released into the tissues

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A protein where the binding of a small molecule (ligand) to one site on a protein affects the binding at another site on the same protein

Allosteric Protein

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These are ligands which induce different conformation of allosteric proteins when the bind to the protein

Modulators

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This type of interaction occurs when the normal ligand and modulator are identical

This type of interaction occurs when the modulator is a molecule other than the normal ligand

Homotropic Interaction

Heterotropic Interaction

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An example of allosteric bind is the cooperative binding of O2 to ____

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O2 is both a ___ and an activating _______ modulator

Ligand; homotropic modulator

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The binding sites of an allosteric protein contain stable segments in close proximity to

Unstable segments (allows small shifts in conformation)

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Note: just [P] means the concentration of the free protein in the Ka equation

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What is the Hill equation to the binding of oxygen in Hb?

log [θ/(1-θ)] = n log pO2–n log P(50)

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What does Kd = in the Hill equation?

K= [L]n (0.5)

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A plot of Log (θ/ (1-θ)) vs log [L] is a

Hill plot

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What is P(50)

The pressure at which half the subunit sites are occupied.

What is theta?

The fraction of oxygen that is bound

For Mb, what is the Hill plot like? What is it for Hb?

A straight line with a slope of 1 Not linear, the maximum slop is a measure of the cooperativity of binding

For the Hill plot of Hb, the greater the slope, the LESS/MORE cooperative the binding?

More cooperative

The slope of the hill plot variable is ____, a degree of the measure of cooperativity

n(H), the Hill coeffictient

If n(H) =1, ligand binding is If n(H)> 1, there is ____ cooperativty If n(H)<1 there is ___ cooperativity

Not cooperative Positive cooperativity Negative cooperativity

Hb is an example of ___ cooperativity In this type of cooperativity, the binding of one ligand impedes the binding of others. It's pretty rare

Positive cooperative n(H)>1 Negative cooperativity

What are the two models that attempt to explain the cooperative binding of ligands to multisubunit proteins?

MWC model (or concerted model) and Sequential Model

This model assumes the subunits of a cooperatively binding protein are functionally ______, that each subunit can exist in greater than or equal to ___ conformations, and that all subunits undergo simultaneous transition from one ___ to the other

MWC model Functionally identical greater than or equal to 2 conformations Simultaneous transition from one conformation to the other

In the MWC model, are the subunits in different conformations?

No. No protein has subunits in different conformations

In the MWC model, the two conformations are in ________

Equilibrium

In this model of cooperative binding, ligand binding can induce a change of conformation in an individual subunit. A conformational change in one subunit makes a similar change in an adjacent subunit, and the binding of a second ligand is more likely

Sequential Model

The sequential model has more potential ___ states than the MWC model

Intermediate states

Hb carries ___ and _____, two end products from cellular respiration, from the tissues to the lungs and kidneys

H+ and CO2

When Hb carries H+ and CO2 from tissues to the lungs and kidneys, CO2 is hydrated to form

Bicarbonate CO2 + H2O --> H+ + HCO3-

If CO2 (insoluble) were no converted to bicarbonate, what would happen?

Bubbles of CO2 would form in the tissues and blood

Hydration of CO2 results in a/n INCREASE/DECREASE in the H+ concentration

Increase in H+ concentration (decrease in pH)

Hb transports about what percent of the total H+ and about what percent of the CO2 formed in tissues to the lungs and kidneys?

40% of total H+ 15-20% of total CO2

How is the binding of H+ and CO2 related to the binding of O2?

Inversely

In _______ (where there is low pH and high CO2), the affinity of Hb for oxygen decreases as H+ and CO2 are bound, causing O2 to be released

Peripheral tissues

In the _____, CO2 is excreted, blood pH rises, and affinity of Hb for oxygen increases. Hb binds more O2 for transport to tissues

The Lungs

The effect of pH and CO2 on oxygen binding and release by Hb is called the

Bohr Effect

What is the Bohr Effect Equation

HHb(+) + O2 --> HbO2 + H(+)

From the Bohr effect equation, we know the binding of oxygen to Hb is influenced by

H+

Hb binds to any of several ______ in the protein

Amino Acid Residues

A major contribution to the Bohr effect is made by ____ of the β subunits. When protonated, ____ residue forms one of the ion pairs to _____ that stabilizes deoxyHb in the T-state; oxyHb releases O2

His 146 (HC3) His146 forms one of the ion pairs to Asp 94 (FG1)

Carbon dioxide binds as a ____ group to the α-amino group at the amino-terminal end of each globin chain to form carbaminoHb This reaction produces ___ which contributes to the Bohr effect

Carbamate group H+

Bound carbamates also form additional _____ that stabilitze the T state (deoxy T state) and promote O2 release

Salt Bridges

H+ and CO2 are ___ effector molecules for Hb

Allosteric effector molecules

____ is another allosteric effecteor molecule for Hb (regulates oxgen binding to Hb)

BPG (2,3 bisphosphoglycerate)

BPG is present in relatively high concentrations in

Erythrocytes

BPG greatly reduces the affinity of Hb for oxygen by binding to groups that stabilize the _____ state

deoxy (T) state

HbBPG + O2 --> HbO2 + BPG

The site of the BPG binding to Hb is the cavity between the ___ subunits in the T state (positively charged residues interact with negatively charged groups of BPG)

At high altitudes, BPG concentration in the blood rises, leading to an INCREASE/DECREASE in the affinity of Hb for oxygen At sea level, the situation is reversed

Decrease, O2 is released into the tissues

Since a fetus must get oxygen from its mother's blood, fetal hemoglobin must have a greater oxygen affinity than maternal hemoglobin. Fetal Hb synthesizes __ subunits rather than β, forming ___

`γ α2γ2Hb

The α2γ2Hb tetramer in fetuses has a HIGHER/LOWER affinity for BPG corresponding to a HIGHER/LOWER affinity for O2

Lower affinity for BPG, higher affinity for O2

This is a genetic disease in which an individual inherits the allele for sickle cell Hb from both parents

Sickle Cell Anemia

Sickle Cell anemia is characterized by a large number of immature cells with many long, thin, crescent shaped _____ that look like a sickle cell blade

Erythrocytes

When sickle Hb is deoxygenated, it becomes ___ and forms polymers which aggregate into tubular fibers

Insoluble Normal Hb remains soluble on deoxygenation

Altered properties of HbS result from a single aa substitution, ___ instead of ____ at position 6 in the two β chains

Valine instead of Glutamate

HbS has two fewer __ charges. A sticky ____ contact at position 6 is created causing aggregation into bundles of fibers, resulting in serious medical complications

Negative Charges Hydrophobic Contact

___ binds to Hb 250 times better than oxygen to form COHb

Carbon monoxide (CO)

The tight bonding of CO to Hb means that COHb can accumulate over time as people are exposed to a constant low level source of CO

Smokers have increased levels of ___

COHb