Lecture 3 Flashcards
5 Functions of globular proteins
storage of ions and molecules, transport of ions and molecules, defense against pathogens, muscle contraction, and biological catalysis
Ligand
molecule that binds to the protein
Binding site
region in the protein where the ligand binds
How do ligands typically bind?
Via non-covalent forces, which enables the interactions to be transient
Suicide inhibitors
inhibitors that bind in a covalent manner.
k(a)
association rate constant
k(d)
dissociation rate constant
K(a)
association constant at equilibrium
K(d)
dissociation constant at equilibrium. 1/2 Vmax
Large K(d)
Lots of free protein and ligand. Low affinity
Low K(d)
Protein-ligand complex in high concentration. High affinity of protein
Langmuir Isotherm Equation
[PL] = ( [P]t [L]t )/( K(d) + [L]t ).
describes association between a protein and its ligand
3 assumptions for Langmuir Isotherm Equation
Binding is at equilibrium, binding is reversible, free ligand concentration = total ligand concentration if ligand concentration is much larger than protein concentration
Fractional occupancy
ratio of the signal to the max signal.
= [L]t / (K(d) + [L]t)
K(d) in relation to K(a)
K(d) = 1 / K(a)
pH and K(d)
pH can change the protonation state and thus change the structure and affinity.
Induced fit
conformational changes occur upon ligand binding. Allows for tights fit of binding. Increases affinity of the protein for a second ligand.
Function of myoglobin
Store oxygen for metabolism in the tissues.
Prosthetic group in myoglobin
Iron on a porphyrin ring (with Iron it is a Heme)
Important residue in myoglobin
Proximal histidine
Chromophore
the heme group absorbs light in UV and visible range
Myoglobin light visibility appearance
deoxymyoglobin appears purplish (429 nm). oxymyoglobin appears red (414 nm).
Hemoglobin structure
tetramer of two subunits (alpha and beta)
partial pressure of oxygen in lungs and in tissues
lungs - 13kPa
tissues - 4 kPa
type of graph for hemoglobin
sigmoidal. Hemoglobin has a much lower affinity in the tissues
Positive cooperativity
first binding event increases affinity at remaining sites
Negative cooperativity
first binding event reduces affinity at remaining sites
3 important residues in deoxyhemoglobin
Lysine, Histidine, and aspartic acid
T state
Tense state, has low affinity for oxygen
R State
Relaxed state, has high affinity for oxygen
Important residue for transition of T state to R state
Proximal histidine
pH in lungs, blood, and tissues
lungs: 7.6
blood: 7.4
tissues: 7.2
Bohr effect
the pH difference between lungs and metabolic tissues increases the oxygen transfer efficiency. When lower pH, the His (protonated) favors the T state
CO2 export
some dissolved as bicarbonate. some exported as carbamate on the amino terminal residues of each hemoglobin subunit
Carbamate formation
condensation that produces a hydrogen which will protonate the histidine and promote oxygen dissociation
Allosteric effector for hemoglobin
BPG (2,3-biphosphoglycerate). Negatively charged and stabilizes it in the T state
