protien metabolism

Protein Function

Structure will determine the function of the protein

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Key ideas and terms

• protein can bind a ligand in the binding site

• For an enzyme, the ligand is a substrate and they bind in what is called the active site

• ligand has to be the correct shape

• ligand has to have the complementary charges and hydrophobicity or hydrophilicity


Lock and Key Hypothesis

• Protein and ligand have complementary shapes.

• Interactions must also be complementary– If enzyme charge is

negative, substrate must be positive

– If pocket is nonpolar, ligand must be nonpolar

• Antibodies


Induced Fit

• Induced Fit: when the protein and ligand bind, the protein may change conformation to allow for tighter binding

• Frequently, both the ligand and the protein change conformation


Examples: O2 binding proteins: myoglobin and hemoglobin

• oxygen is not water soluble yet needs to be transported

• diffusion is not effective

• myoglobin is found primarily in muscle tissue

• Hemoglobin is in the blood

• Both proteins contain heme


Heme Group

consists of a Fe2+ and a protoporphyrin ring to help stabilize the iron(II) ion


Heme Group

the iron must be a 2+ to bind oxygen. The heme group is buried deep within the protein so that the iron is not oxidized to 3+

• there must be flexibility in the protein to allow for oxygen to attach and then let go

• Iron has 6 coordination sites. – Four of them used by porphyrin. Unshared pairs on nitrogen

complex to iron

– Fifth and 6th for oxygen and protein

• Heme is planar


Myoglobin

• has heme group

• eight alpha helical segments

• dense hydrophobic core

– all but two polar groups on outside

– room for only 4 water molecules

• flat heme in pocket

• iron coordinated to poryphorin and H

• As well as the heme


Myoglobin Binding Curve

• Hyperbolic binding curve

• Relatively insensitive to small changes in oxygen concentration


Myoglobin

• The P50 (oxygen partial pressure required for half saturation) for myoglobin is very low

• Myoglobin has a high affinity for oxygen-an important characteristic for a protein that must extract oxygen from the small amounts present in blood.

• At the oxygen concentration existing in the capillaries, the myoglobin in adjacent tissues is nearly saturated.

• When cells are metabolically active, their internal PO2 falls

to levels where myoglobin will lose (deliver) its oxygen.


Hemoglobin

Quaternary structure : 4 subunits

• Each subunits is like myoglobin

• Each subunit has heme group

• 2 alpha chains; 2 beta chains

• Few contacts between alpha and betas, more between alphas and betas


Hemoglobin

• Exists in two states

– R state (high affinity for O2)

– Where would this state be favored? • In the lungs

– T state (low affinity for O2) (deoxyhemoglobin)

– Where would this state be favored? • In the tissue

– Sensitive to pressure changes

– On oxygenation, one pair of subunits shifts with respect to the other by a rotation of 15 degrees.


Hemoglobin

• deoxy hemoglobin (T) oxy hemoglobin (R)


Oxygen Binding to Heme in Hemoglobin

• Fe is coordinated to a histidine in helix 8 of the Hb molecule

• In deoxy form, porphyrin is puckered and Fe is out of the plane of the heme

• When oxygen binds the Fe (at other coordination site) the Fe is pulled into the plane of the heme

• This pulls on the histidine, which pulls on the helix, changing the shape of the molecule.

Fe2+

His F8

0.6 A

O2


Hemoglobin

• Conformational changes in hemoglobin alter its binding ability

• Binding of oxygen in one subunit causes conformational changes in the next subunit

• This is called cooperative binding• This can happen because it is composed of 4 independent

subunits• produces a different binding curve that is sigmoidal• The modulation of the affinity of a site for a ligand by

ligand binding at another site is called Allostery.


Hemoglobin Binding Curve


Bohr Effect

• Hemoglobin's affinity for oxygen is decreased in the presence of carbon dioxide and at lower pH.

• Carbon dioxide reacts with water to give bicarbonate, carbonic acid free protons via the reaction:

CO2 + H2O ---> H2CO3 ---> H+ + HCO3-

• Protons bind at various places along the protein and carbon dioxide binds at the alpha-amino group forming carbamate.

• This causes a conformational change in the protein and facilitates the release of oxygen.


Bohr Effect

• Blood with high carbon dioxide levels is also lower in pH (more acidic). (recall the equilibrium)

• Conversely, when the carbon dioxide levels in the blood decrease (i.e. around the lungs), carbon dioxide is released, increasing the oxygen affinity of the protein.


Bohr Effect Summary

• High CO2 in tissues

• Higher H+• Lower pH

• Affinity for O2 decreases

• O2 released to tissues

• T state favored

• Low CO2 in lungs

• Lower H+• Higher pH

• Affinity for O2 increases

• O2 binds hemoglobin

• R state favored


Hemoglobin and CO poisoning• Other ligands can compete with oxygen for binding to

hemoglobin

• The binding of oxygen is affected by molecules such as carbon monoxide (CO) (For example from tobacco smoking, cars and furnaces). CO competes with oxygen at the heme binding site.

• Hemoglobin binding affinity for CO is 200 times greater than its affinity for oxygen, meaning that small amount of CO can dramatically reduces hemoglobin’s ability to transport oxygen.

• Hemoglobin also has competitive binding affinity for Nitrogen Dioxide and Hydrogen sulfide .


Oxygen and Carbon Monoxide

• Oxygen and carbon monoxide same size and shape.

• Carbon monoxide, however has formal charge

• Sticks to Fe better• Blocks oxygen

binding

O OFe2+

Fe2+

C O+


Hemoglobin and 2,3 DPG

• In people acclimated to high altitudes, the concentration of 2,3-diphosphoglycerate (2,3-DPG) in the blood is increased, which allows these individuals to deliver a larger amount of oxygen to tissues under conditions of lower oxygen tension.

• This phenomenon, where molecule Y affects the binding of molecule X to a transport molecule Z, is called a

heterotropic allosteric effect.

O P O

O

O

C

C

CH2OH

H

OOP O

O

O


Sickle Cell Anemia

• Sickle cell disease is caused by an abnormal adult hemoglobin, called hemoglobin S. People with sickle cell disease make hemoglobin S instead of hemoglobin A.

• Single amino acid substitution – glutamate changed to valine

• To show condition, have to have mutation in both genes (Homozygous)


Sickle vs normal hemoglobin

• first 9 amino acids of normal hemoglobin beta chain v h l t p e e k s

• first 9 amino acids of sickle hemoglobin beta chain v h l t p v e k s

Notice the single amino acid change?


Sickle Cell Anemia

• Position 6 is on outside of molecule• Glutamate is polar• Valine substitution causes “sticky spot” on

outside of hemoglobin• Causes hemoglobin molecules to stick

together• Forms long chains which cause red blood

cell to sickle


protien metabolism

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