module 5 Flashcards
what is a ligand
-many protein undergo reversible interactions with other molecules
-these interaction can serve to regulate protein function
-a molecule reversibly bound by protein is called a ligand
-a ligand can be any kind of molecule, including other protein
what is the specificity of protein ligands?
-a ligand binds at a specific site on the protein called the binding site
-the binding sire is usually complimentary to the ligand in terms of shape. charge, hydrophobicity, hydrogen binding potential
-a given protein may have multiple binding sites for multiple ligands
-Ex: ligands of hemoglobin include oxygen and 2,3 biophosphosglycerate (2,3 BPG)
what is the induced fit of protein ligands?
-the binding of a ligand may cause a conformational change in the protein
-this induced fit can change the properties of the protein
-these changes in protein structure often relate to changes in function
what is the challenge of oxygen delivery and storage?
-every cell requires a constant supply of oxygen
what are the obstacles of oxygen delivery and storage?
-for multi-cellular organisms, the solubility of oxygen is too low to meet oxygen requirements through passive diffusion
-amino acid side chains not well suited for reversible binding of oxygen
-transition state metals have strong tendency to bind oxygen but produce damaging free radicals (like iron)
what is the solution for oxygen delivery and storage?
-specialized proteins for oxygen storage and delivery
-hemeglobin groups to safely harness iron’s oxygen binding properties
what is overview of myoglobin and hemoglobin?
-serve distinct but complimentary, physiological roles
-share many structural and functional features
what are the general definitions of myoglobin and hemoglobin?
-myo (Mb): monomeric protein that facilitates oxygen storage in peripheral tissue (binds to single O molecule)
-hemo (Hb): tetrameric protein found in red blood cells that transports oxygen from lungs to periphery (binds to 4 O molecules)
how is oxygen a limiting resource?
-O is poorly soluble in aqueous solutions
-emergence of larger, multi-cellular organisms depended on the evolution of proteins that could transport and store oxygen
-the amount of available oxygen which can be delivered within the organism can limits its size
-insects grown in the presence of elevated oxygen can achieve greater sizes
Fe2 seeks six coordinating interactions:
-four come from interactions with heme
-a fifth comes interactions with an imidazole group of a proximal histidine residue
-the sixth position is for O2 binding
-a distal histidine provides a stabilizing interaction for bound O2
what is heme?
-cellular iron is bound in forms that sequester it and or make it less reactive
-heme consists of a protoporphyrin ring system bound to a single Fe2 iron atom
-fe2 binds O2 reversibly, Fe3 does not bind O2
what does the ring system provide?
-four coordinating interactions with the iron atom
-the electron-donating characteristic of nitrogen prevent the conversion of Fe2 to Fe3
-myo and hemo both us heme
-heme is bound with discrete pockets of myo and hemo
what is carbon monoxide poisoning?
-CO has a similar molecular structure as O2
-CO binds heme with 200 times greater affinity than O2
-CO exerts its deadly effects by competing with oxygen for binding to heme
what is the structure of myoglobin?
-153 amino acids
-single subunit, and example of tertiary structure
-with single heme group, can bind to one oxygen molecule
what is the structure of hemoglobin?
-four sub-units, quaternary structure
-with four heme groups, hemoglobin can bind four oxygen molecules
-each sub-unit of hemo closely resembles myoglobin
what is the difference in curves of hemo and myo?
-myo has a hyperbolic curve of oxygen binding
-binding of oxygen by hemo displays sigmoidal behavior (indicates coopertivity of oxygen binding)
what is the detailed structure of myoglobin?
a small globular protein consisting of:
-a single polypeptide of 153 residues arranged in eight alpha-helices
-a heme (iron porphyrin) prosthetic group
how did we initially find the protein structure of myoglobin?
-sperm whale myoglobin was first protein structure determined by x-ray crystallography
-because loaded with myoglobin ( need oxygen for underwater for hours)
what is the oxygen saturation curve of myoglobin?
-is hyperbolic, indicating a single O2 binding constant
-the amount of O2 required to half saturate the protein is quantified by P50 (P50 of myo is 3 torr)
-the pO2 in the lungs (where O2 concs are highest) is typically 100 torr and 20 torr in the periphery (where O2 are lowest)
what is the fraction saturation of myoglobin?
-fraction of myoglobin saturated with oxygen at a given partial pressure of oxygen is calculated by: PICTURE
-myo has a very high affinity for O and is normally nearly saturated with O everywhere in the body
what is hemoglobin?
-contained within erythrocytes (red blood cells)
-is an allosteric protein whose oxygen affinity is regulated through various physiological signals
what is the general description of allosteric proteins?
-the word allosteric is derived from the Greek words allos (meaning other) and stereos (meaning structure). allosteric=other structure
-have T (inactive) and R (active) forms
-these T and R forms are in rapid equilibrium
how does hemoglobin solve the problem? whats the problem?
-a protein that binds O2 with high and constan affinity would saturate effectively with O2 in the lungs but not release it to tissues
-a protein with a lower O2 affinity would be able to release O2 to tissues would not have sufficient affinity to saturate in the lungs
-solves by undergoing transition from high and low affinity states
-myoglobin cannot achieve this affect (single ligand binding site proteins cant)
what are allosteric effectors?
-allosteric effectors (modulators) bind allosteric proteins at specific sites
-effectors can either be activators or inhibitors
what are allosteric activators and inhibitors?
-activators: stabilize the R state
-inhibitors: stabilize the T state
what are the allosteric properties of hemoglobin? example?
-the binding and release of O2 from Hb are allosterically regulated
example
-O2 is homotropic allosteric activator of Hb
-binding of the first O2 by Hb causes a conformational change making easier to bind subsequent O2 (positive cooperativity)
-O2 binding promotes and stabilizes the R state of hemoglobin which has higher O2 affinity than the T state
what is the transition from the T to R state?
-with T state Hm, the iron atom is just outside the plane of the heme ring
-with transition to the R state (O2 bound) the iron moves into plane of the ring
-this minor movement within one subunit causes structural changes that are translated to the quaternary structure of the protein
what is the oxygen saturation curve of hemoglobin?
-at partial pressure of O found in lungs, Hb completely saturates with O2
-at partial pressure of O2 found in periphery, Hb releases over half of its O2 load
-P50 og Hb closely matches the partial pressures of O2 found in periphery
-Hb is most sensitive for O2 release at the partial pressures of O2 found in the periphery
-this allows Hb to sense and respond to changes in O2 levels in regions at greatest risk for hypoxia
what did intial investigations of hemoglobin reveal about affinity for oxygen?
-initial investigations with highly purified hemoglobin indicated an extremely high affinity for oxygen
-this would limit the ability of the protein to release oxygen to the periphery
what was revealed about what 2,3 bisphosphoglycerate do to Hb?
-replacing various components of blood revealed that 2,3 biophophoglycerate decreased hemoglobins’ affinity for oxygen
what is 2,3 bisphosphoglycerate?
-a heterotropic allosteric inhibitor of hemoglobin
-regulate Hb affinity for O (decrease)
what is the structure of 2,3 biphospho-D-glycerate?
-carries five units of negative charge
-the pocket formed at the interface between the subunits of deoxyhemoglobin contains six positively charged residues
-this pocket is unique to deoxyhemoglobin
what is fetal hemoglobin?
-a fetus “breathes: in the womb by stripping O2 away from the maternal blood
-Fetal Hb has a higher affinity than adult Hb
-Adult Hb has six (+) residues at the 2,3 BPG binding sire, fetal Hb has four (his 143 replaced by Ser)
-decreased affinity for 2,3 BPG translates into higher O2 affinity for fetal Hb
-lower affinity for the allosteric inhibitor bestows higher affinity for O2
what is the high altitude adaptation?
-there is less O2 at high altitude
-adaptation to high altitude can rapidly occur through increased production of 2,3 BPG
-increased 2,3 BPG decreases Hb’s O2 affinity to ensure sufficient O2 delivery to the periphery
-activity at extreme altitudes usually requires artificial means to provide O2
Active tissues have lower pH due to:
-increased muscle activity increases production of CO2 (this CO2 eventually decreases pH)
-in extreme exercise, muscles produce lactic acid to further decrease pH
what is the Bohr Effect?
describes the pH dependence of hemoglobin’s affinity of O2
-at decreased pH Hb has a lower affinity for O2 (in active cells)
-serves to coordinate increased release of oxygen to active tissues
what are the two primary challenges to cellular respiration and metabolism?
-delivering sufficient O2 to the tissues
-removing CO2 (the “exhaust” of metabolism) from the periphery
what increases with muscle activity?
-both the oxygen requirements and carbon dioxide production increase with increased muscle activity
-the body has adapted effective strategies to coordinate these needs
what is mechanism #1 for coordination of O2 delivery and CO2 removal?
-CO2 is taken up into red blood cells and converted to bicarbonate and a proton by the enzyme carbonic anhydrase
the more active the tissues ____________________________________?
the greater the production of CO2, the greater the production of CO2, the greater the release of O2
what happens through the reaction of mechanism 1?
1) CO2 is converted into a soluble form for transport to the lungs
2) the decreased pH decreases hemoglobin’s O2 affinity to promote O2 release to active tissues
what is mechanism 2 of coordination of O2 delivery and CO2 removal?
-CO2 can form a covalent carbamate linkage to the N terminus of each chain of hemoglobin chain to form carbaminohemoglobin
what are the three important outcomes of mechanism 2?
-converts CO2 into a more soluble form to assist in its transport to the lungs
-carbamino hemoglobin has a lower O2 affinity than hemoglobin to promote O2 release
-the released proton promotes O2 release through the Bohr effect
what is sickle cell anemia?
a molecular disease of hemoglobin
how is sickle cell anemia formed?
-results from a single amino acid change (Glu6Val)
-formation of fibers from the deoxy forms of HbS
-fibers tend to form in the capillaries (where O2 concentration is the lowest) which blocks blood flow to the extremities of the body
where is sickle cell anemia the most common? what does it have to do with malaria supposedly?
-SCA primarily affects african americans and africans; selected for in regions where malaria imposes a selection pressure
-one theory of why individuals heterozygous for SCA have resistance to malaria
what are the reasons they thing people heterozygous for sickle cell anemia have resistance to malaria?
-malaria infects red blood cells
-infection decreases pH in red blood cells
-decreased pH causes release of oxygen from Hb
-for individuals with SCA, deoxy HbS form fibers deforming the red blood cell
-these deformed red blood cells (which contain malaria) are selectively destroyed by the spleen
what is an other oxygen transport protein?
hemocyanin
-some invertebrates, like horseshoe crabs
how is hemocyanin distinct from hemoglobin?
-hemocyanin uses copper rather than iron (blue blood rather than red)
-two copper atoms bind a single oxygen molecules
-there is no heme ring groups, the copper atom is coordinated through histidine residues
-hemocyanin is not localized within specialized oxygen-transport cells
what is heterotropic and homotropic
-when the normal ligand and modulator are the same, the interaction is homotropic
-when the modulator is different from the normal ligand the interaction is heterotropic
