Term
|
Definition
| a ligand is a molecule that is bound reversibly, that is, it is bound non-covalently and can be disattached |
|
|
Term
| what kind of molecule can a ligand be |
|
Definition
| a ligand can be any kind of molecule, including another protein |
|
|
Term
what does a ligand bind onto
and how is it complementary to the ligands size |
|
Definition
a ligand binds at the binding site on a protein
which is complementary to the ligand's size, hydrophobicity (hydrophobic and hydrophillic), charge and shape |
|
|
Term
|
Definition
| the actual structural adaptation that occurs between protein and ligand |
|
|
Term
proteins act upon other enzymes, which represent a special case of proteins
what is a substrate
and
where does it bind to |
|
Definition
these are the molecules that enzymes influence
and
they bind to the catalytic sites also called the active site |
|
|
Term
| what does heme consist of |
|
Definition
a complex organic ring structure, protoporphyrin IX, with a
bound iron atom in its ferrous (Fe2+) state. |
|
|
Term
| what does a pyrrole look like |
|
Definition
|
|
Term
| iron is often incorporated into a protein-bound prosthetic group called |
|
Definition
|
|
Term
| the iron atom in a protein-bound prosthetic group called heme has six coordination bonds, four to nitrogen atoms that are part of the flat____________. |
|
Definition
| porphyrin ring system and two others that are perpendicular to the to the porphyrin |
|
|
Term
| what does a heme group look like |
|
Definition
|
|
Term
| This view shows the two coordination bonds to Iron (2+) that are perpendicular to the porphyrin ring |
|
Definition
[image]
One is occupied by a His residue, sometime called the proximal His; the other is the binding site for oxygen |
|
|
Term
give an example of a family of proteins that has similar primary and tertiary structures
then give an example of it |
|
Definition
globins do
a myoglobin is a 153 amino acid residue polypeptide with
one molecule of heme associated with it |
|
|
Term
what does myoglobin consist of
and why is this globin considered "abrupt" in some fashion |
|
Definition
the 8 alpha helical segments are labeled A through H
Some of the interconnecting segments are "abrupt" meaning sudden or unexpected and do not contain any residues |
|
|
Term
| in general, the reversible bind of protein (P) to a ligand (L) can be described by a simple equation: |
|
Definition
[image]
C being the protein-ligand "complex" |
|
|
Term
| The reversible bind of protein (P) to a ligand (L) is a reaction characterized by two equilibrium constants |
|
Definition
|
|
Term
|
Definition
Ka is the association constant that describes the equilibrium between complex and the unbound components
[PL]/[P][L] |
|
|
Term
|
Definition
| this is the reciprocal of Ka (Kd=1/Ka) and is the dissociation constant |
|
|
Term
| what do these terms: rates of association & rates of disassociation tell us about an organism in its environment |
|
Definition
| this equilibrium is going to allow th organism to react to its environment |
|
|
Term
| what is the number one cause of illness |
|
Definition
| protein malfunction; a single macromolecule in the cell is not doing its job |
|
|
Term
|
Definition
|
|
Term
| how is the interaction of ligand to protein more favorable than with water |
|
Definition
the size, shape, CHARGE, concentration, polarity and HYDROPHOBICITY
|
|
|
Term
| there must be a driving force to get the ligand to bind to the protein, what is it |
|
Definition
water will clump a ligand and protein together to reduce the overall "order" imposed onto it
also, the presence of ligand will force the protein to change shape to fit the ligand better |
|
|
Term
| when discussing the induced fit of a ligand to a protein, what can be said that is in agreeance with the thermodynamic theory |
|
Definition
| there are two stable thermodynamic states when discussing protein ligand binding; the first is when the protein and ligand are separate-this is the thermodynamic state with respect the the environment, the second is the protein ligand complex-this is the new thermodynamic state that is Produced |
|
|
Term
| what can be said about the secondary and tertiary structures of a protein if the thermodynamic theory is applicable-that is, there are two variant thermodynamic states |
|
Definition
| yes, secondary and tiertiary structures would be altered |
|
|
Term
Myoglobin, porphrin, iron & oxygen
put these in a sequence that describes which is the other's ligand |
|
Definition
| porphrin is myoglobin's ligand, iron is porphrin's ligand & oxygen is iron's ligand |
|
|
Term
| a porphrin ring has 8 variable areas, what are the two distinct areas |
|
Definition
| 6 are non-polar and 2 are polar regions |
|
|
Term
| how does ferrous iron (2+) fix itself into a prophrin ring |
|
Definition
| it uses four coordination to lock itself in and two coordination bonds to interact with oxygen |
|
|
Term
| what is the measure of affinity of P to L |
|
Definition
|
|
Term
| what does a higher Ka mean |
|
Definition
| if Ka is high, it means that it has a high affinity to associated protein and ligand |
|
|
Term
| by a simple rearrangement of the equation Ka=[PL]/[P][L], we show the the ratio of bound to free protein is directly proportional-describe how |
|
Definition
| when the concentration of ligand is much greater than the concentration of ligand-binding sites, the binding of ligand by the protein does appreciably change the conccetration of free (unbound) ligand, that is, [L] remains constant |
|
|
Term
| give the equation of hyperbola |
|
Definition
|
|
Term
| what does a higher Kd mean |
|
Definition
| low affinity for protein ligand complex, but more affinity for protein and ligand separate |
|
|
Term
| how does a heme group get into the globin to form hemoglobin |
|
Definition
polypeptides are dynamic, breaking and forming helicies, that is, molecules are not static
this is how heme groups slip into the polypeptide |
|
|
Term
| how are heme groups held in the polypeptide |
|
Definition
| not by covalent bonds but by weak forces holding them together |
|
|
Term
| what does the term cooperativity mean when discussing the four distinct binding sites of oxygen in hemoglobin |
|
Definition
| when one ligand is bound, it influences the second ligand to bind oxygen (this is influencing the affinity) |
|
|
Term
| what is negative cooperativity |
|
Definition
when describing negative cooperativity, illustrate the picture of the dorm hall Dr. Richardson drew, if the person you hate moves in first, you will move into the room furthest from that person
that is the subsiquent ligand is negatively favorable |
|
|
Term
| how does nature react thermodynamically in positive cooperativity |
|
Definition
| nature will choose which ever room is more thermodynamically favorable when positive cooperativity is present |
|
|
Term
| how does the term allosteric fit in the discussion of cooperativity |
|
Definition
| when a substrate allosterically binds to a protein, it increases the stability of the polypeptide by altering secondary strucutures of the polypeptide chain |
|
|
Term
| what is the difference between T-state and R-state |
|
Definition
t-state is more rigid and has no oxygen bound
r-state is more relaxed and all four sites have bound oxygen, also, the cavitity within the hemoglobin is turked and smaller than when in t-state- how does it get turked, the electronegativity is balanced out |
|
|
Term
| give an example of a polypeptide that is cooperative and allosteric |
|
Definition
|
|
Term
| give an exmaple of a protein ligand complex that is purely cooperative |
|
Definition
the binding of ligand 1 influences the binding of ligand 2
[image] |
|
|
Term
| how does this allosteric affinity occur in hemoglobin |
|
Definition
there are multiple electrostatic interactions between all four domains of hemoglobin
HYDROGEN BONDS |
|
|
Term
| how do we know that hydrogen bonds are used for communication |
|
Definition
| all amino acids are linked together with hydrogen bonds, that way it makes them vital for interactions with the amino acids beside each other |
|
|
Term
| what does the Hill's equation give the user the ability to determine |
|
Definition
| the Hill's equation gives the user the ability to associate binding of ligand 1 to its influence on binding of second ligand by concentration of ligand |
|
|
Term
| the hill coefficient is a ratio that describes |
|
Definition
| the degree of the cooperativity between binding sites when multiple binding sites are present |
|
|
Term
the hill coefficient can have three outcomes, Nh>1, Nh<1, & Nh=1
what do each of these outcomes mean in terms of cooperativity between binding sites |
|
Definition
Nh>1 shows that there is positive cooperativity between binding sites on enzyme (ligand 1 influences affinity of ligand 2)
Nh<1 shows that there is negativie cooperativity between binding sites on enzyme
Nh=1 shows that there is no difference between ligand 1 and ligand 2, so there is no cooperativity |
|
|
Term
the hill plot, and its coefficients, can describe the affinity between binding sites and also the cooperativity that is present on that enzyme
but what can't it do |
|
Definition
| it can not tell which domain (binding site) gets bound first, and it also cannot tell how many binding sites there are on the enzyme |
|
|
Term
| what is essential to the Hill's equation and hill plot science |
|
Definition
| how one binding site influences another binding site |
|
|
Term
| there are moments when an enzyme is considered concerted, what does this mean |
|
Definition
| a concerted enzyme is one in which each binding site is fulfilled, and each domain is in the same conformation as all |
|
|
Term
| when discussing hemoglobin, when does this polypeptide have a lower affinity for oxygen |
|
Definition
| when it is in the tense state |
|
|
Term
| by this point, it is known that the T-state and the R-state are both thermodynamically stable conformations, and we also know that when oxygen is present, it_____ |
|
Definition
| acts as a tipping model and the R-state becomes more favorable |
|
|
Term
once these thought experiments on ligand and binding site affinities was clarified with experimental data, several models where formed
what are they |
|
Definition
the KNF model which is when one unit (binding site) induces a conformational change when ligand is bound- and this is called a local model
the other one is the global model-all or nothing so to speak |
|
|
