Chapter 5- section 5.1 Flashcards
two types of protein interactions
-interactions caused by enzymes
-interactions where neither the chemical configuration nor the composition of the interacting molecule is changed
what is the function of most proteins?
involves the reversible binding of other molecules called a ligand
what site does a ligand bind at?
binding site
-complementary to the ligand in size, shape, charge & hydrophobic/hydrophilic character
what is flexible? (where its said to “breathe”)
proteins
the binding of a protein and ligand is often coupled to a ?
conformational change
conformational change in the protein that makes the binding site more complementary to the ligand where this structural adaptation
induced fit
in a multisubunit protein, a conformation change in one subunit often affects the ?
conformation of other subunits
substrate
a molecule acting upon the enzyme instead of being called a ligand
active site (catalytic site)
where the ligand binding site is
oxygen can bind to a ? group
home prosthetic group (iron & copper have a strong tendency to bind to oxygen)
iron is usually in a proteinboound prosthetic group called ?
heme
what is a prosthetic group?
a compound permanently associated with a protein that contributes to the protein’s function
what does heme consist of?
complex ring structure called protoporphyrin where its bound by a simple iron in its ferrous state Fe 2+ (prevents iron to turning to its ferric state (Fe 3+)
iron in its Fe2+ state binds oxyxgen ? but in the Fe3 state it doesn’t bind oxygen
reversibly
globins are a family of ? binding protein
oxygen
stores oxygen and facilitates oxygen diffusion in muscle tissue
myoglobin
responsible for oxygen transport in the bloodstresm
hemoglobin
antibodies and cytokines defend against ?
pathogens
what two proteins are involved in muscle contraction?
myosin & actin
two proteins involved in biological catalysis
chymotrypsin & lysozome
Myoglobin has a ? binding site for oxygen
single; only has one molecule of heme
what are the helical segments in myoglobin named?
A through H
-His residue that is in the heme in myoglobin
What are the proximal His names?
His 93 aka His F8
What does myoglobin’s function depend on?
it depends on the protein’s ability to bind oxygen, release it, and where it is needed
-equilibrium expression of reversible binding of a protein to a ligand
-equilibrium constant
-P + L (<>) PL
-Ka = [PL] /[P]/[L]=Ka/Ka
at equilibrium, the association and dissociation rates are ?
equal when characterized by Ka
what are the rate constants
Ka and Kd (unit Ms-1)
What does Ka do?
- association constant that describes the equilibrium between the complex and the unbound components of the complex
-provides a measure of the affinity of the ligand L for the protein
a higher value of Ka corresponds to ?
a higher affinity of the ligand for the protein
a molecule that binds to a specific protein binding site (usually a small molecule)
ligand
ligand protein interactions are stabilized by ?
noncovalent forces that dictate protein structure
what does Kd do?
-dissociation rate
-first-order PL > P +L
-release of a lligand
To measure the binding behavior of a ligand to a protein have to determine the ______ of occupied binding sites (Y or delta) for the reaction equation is delta = [L]/ [L] + kd
Fraction
At kd = [L] the position is ____ saturated
50% (when Y is 0.5 its equal to the Kd
A lower value Kd means a higher ________ of ligand for the protein
Affinity
The bonding of oxygen to myoglobin follows the same concepts expect its equation is what
Y = pO2/ pO2 + P50 (p50 partial pressure) or (Y= [O2]/ kd + [O2])
The binding of of oxygen to myoglobin makes a hyperbolic curve shape which means what?
All O2 binds with some affinity till saturated (P50 =2.8 torr for humans)
Delta G related to Kd how
Dleta G = -RTln Kd
Protein mstructure is affected how
By the way the ligand binds
When heme is bound to myoglobin its affinity for O2 is selectively increased by the presence of the _________ his (or His E7 in myoglobin)
Distal His
Heme prosthetic groups occupy a ___________ cleft within globin structure where the cleft is formed by 3 alpha helices & two loops in a 3D structure
Hydrophobic
Heme Fe (2) protopohyrin IX provides 4 of 6 Fe ________
ligands (Fe binds to O2, NO2, H2S, & CO)
__________ are the protein component of Mb & Hb
Globins
_________ monomer binds one O2 for oxygen strage & dissfusion
Myoglobin
________ tetramer binds four O2 for transport from lungs to tissues
Hemoglobin
________ proteins creates a snug hydrophobic pocket for the heme
Globin ( myoglobin heme binds between the E & F helices)
Oxygen binding properties of myoglobin & hemoglobin relate_______ & _______
Structure & functionm
O2 binding measure the amount bound ( saturation) as a function of oxygen concentration) so graph axis are what?
Saturation vs O2 pressure
Protein properties relates to their role in storage & _______ or transport
Disffusion
Myoglobin _________ solubility & diffusion rate of O2 from capillaries to muscle tissues (Mb + O2 yields MbO2)
Increases
Hemoglobin transport O2 from ______ & efficient release in capillaries due to cooperative O2 binding (depends on O2 concentration & regulation by tetramer conformational changes induced by allosteric regulators)
Lungs
________ transport oxygen in blood
Hemoglobin
Hemoglobin is a tetramer protein containing ______ heme prosthetic group
4
________ has an alpha2beta2 tetramer which is a dimer of aphabeta protomers stabilized by a large number of interaction between subunits at one interface
Hemoglobins
_______ structiure containm an alpha chain that has 7 alpha helices & beta chains
Globin
________ structure allows for more complex O2 binding behavior
Multisubunit
What are the two major conformations of hemoglobin?
- T state (oxy, high affinity)
- R state (deoxy, low affinity)
O2 has a higher affinity to bind to hemoglobin in the ______ be O 2binding stabilizes the ____state
R
When O2 is absent experimentally the ____ state is more stable & the predominant conformation of deoxy hemoglobin
T
Hemoglobin binds oxygen ___________
Cooperatively
Interaction between the ion pairs ___ & ______ of the beta subunit & between Lys C5 of the alpha subunit & His HC3 subunit stabilizes the T state
HC3 & Asp FG1
What are the reasons why the T & R state occur in hemoglobin?
- Oxygen binding triggers proximal His movement & F8 helix & overall 15 degree twist of the protomer creation to each other
- Greatest changes occur hydrophobic & ion pair at the alpha 1 - beta 2 & alpha 2 - beta 1 interfaces & the central cavity IP to 6anstrogm
What are the structural reasons for R & T state?
- Oxygen binding induces conformational change around the heme which transcribed through subunit interactions
- O2 binding to Fe2+ reduces its electron density (size) so that it slips into the porphyrin ring cavity (stabilized Hb conformation actually resist O2 binding)
A protein that bound O2 with high affinity would bind it efficiently in the lungs but would not _______ much of it in the tissues
Release
If the protein-bound oxygen with _____ affinity to trelase it in the tissue, it would pick up much O2 in the lungs
Low
_________ has a sigmoid (cooperative) binding curve for O2 showing the transition from low affinity (T state) to high affinity (R state)
Hemoglobin ( O2 binds to the lungs where pO2 is high & release O2 in the tissues where pO2 is low)
Allosteric proteins
Proteins where the binding of a ligand to one site affects the binding properties of another site on the same protein ( have conformation induced by binding of modulator)
For protein with multiple binding sites (n) have to use what equation? (For proteins like Mb & Hb)
Hill’s equation
Hill’s equation
YO2= (pO2)^n/ (p50)^n + (pO2)^n (n is the # of binding sites)
The hill equation plot where the axis is what
log (Y/1-y) vs log [L] (y-intercept = log P50)
The slope of the Hill plot is what
N(H) which is the hill coefficient that measures the degree of cooperativity
If n(H) = 1 what does it means?
That the ligand is not cooperative ( can happen when the multisubunit don’t communicate)(hyperbolic curve)
If n(H) is greater than 1 it indicates what?
Positive cooperativity in ligand binding
What are the two models for cooperative binding of ligands to proteins with multiple binding sites?
- Concerted (MWC) model
- Seqential Model
Concerted (MWC) model
Is an all or nothing model where it assumes that the subunits of a cooperatively binding protein are fundionally identical & that each subunit can exist in (at least) two conformation to the other simultaneously
Sequential model
Ligand binding can induces a change of conformation in an individual subunit & a conformational change in one subunit makes a similar change in an adjacent subunit (so a change in one subunit make a change in the other & so on)
Hemoglobin also transport ____ & _______
H+ & CO2 (related to the bicarbonate bloof buffer system)
Bohr Effect
pH affects O2 binding to hemoglobin
Actively metabolizing tissues generate ____ to lower blood pH compared to the lungs where relates to CO2 hydrated in blood results to an increase in H+
H+
Hb affinity for oxygen depends on _____ since H+ binding stabilizes the T state
pH
The ____ difference between lungs & metabolic tissues increases efficiency of the O2 transport
pH
When O2 concentration is ____ (like in the lungs) hemoglobin binds O2 & release H+
High
When O2 concentration is _____ (like in peripheral tissues) H+ is bound O2 is release
low
Mb-O2 is a _____ curve which indicates a single equilibrium constant for O2 binding with saturation at high O2
Hyperbolic
Hb-O2 is a _______ binding curve which reflects variable binding affinity for each binding event (one O2 per heme) which is a positive cooperativity
Sigmoid
Oxygen binding is regulated by what?
Shifting the Hb T/R equilibrium
_________ factors shift the conformation of the 4 structure R (oxy) & T (deoxy) forms have different binding affinities for O2
Allosteric
What is the positive & negative stabilizers for T & R state?
Positive: O2 binding & negative pH, 2,3-BPG, & CO2
Connection to the bicarbonate buffer system & dissolved Co2 also affects O2 ______
Affinity
Disloved Co2 leads to blood pH______ & HCO3 increase
Decrease
_______ favors ion pair formation (T state) & O2 release in tissues
High [H+]
Muscle lactic acid decrease ______ & more efficient O2 releases with leaving respiration
pH
Lungs high [O2] favors ____ binding & H+ release
O2
Oxygen binding to hemoglobin is regulated by what?
2, 3 BPG (a negative allosteric effector)
Regulation of Hb O2 binding by 2,3 BPG to & stabilize Hb _____ state which favors lower O2 affinity
T
________ anemia is a molecular disease of hemoglobin
Sickel cell anemia
Serine proteases
hydrolyze peptide and ester bonds with an active
site serine in the catalytic triad
