Midterm 1 Flashcards
(89 cards)
1
Q
stable interactions/prosthetic group
A
molecule permanently associated with a protein and required for its function
2
Q
transient interactions/ligand
A
molecule that is bound reversibly by a protein
3
Q
binding site
A
region of protein surface that interacts with a ligand
4
Q
binding site is complementary to ligand in
A
size, shape, charge, hydrophobic properties
5
Q
substrates vs ligands
A
ligands don’t change structure, substrates produce product and change shape
6
Q
induced fit
A
protein undergoes conformational change to make binding site more complementary
7
Q
free iron
A
can promote formation of reactive oxygen species, tendency is reduced when iron is bonded to heme
7
Q
myoglobin
A
monomer, binds and stores O2 in muscle
8
Q
hemoglobin
A
tetramer, 2 alpha-globins, 2 beta-globins, 4 polypeptide chains with 1 heme each, O2 transporter in vertebrates
9
Q
leghemoglobin
A
found in leguminous plants, sequesters O2 protecting O2 sensitive enzymes in N2 fixing bacteria
10
Q
mass of molecule
A
kDa/average molecular weight (110)
11
Q
globin structure
A
8 alpha-helices labeled A-H, connecting loops identified by helices they join
12
Q
c-terminus
A
HCX (where X is number)
13
Q
myoglobin heme binding pocket
A
between E and F helices, surrounded by mostly non polar residues and 2 histidines
14
Q
proximal histidine
A
F8 directly bonded to Fe2+, 5th coordination bond
15
Q
[P]
A
concentration of free protein (no ligand)
15
Q
breathing
A
small <1A molecular motions of AA side chains
16
Q
[L]
A
ligand concentration
17
Q
[PL]
A
concentration of ligand bound protein
18
Q
Kd
A
dissociation constant, measures strength of interaction, [L] where half ligand binding sites are occupied
19
Q
Ka
A
association constant, 1/Kd
20
Q
Kd formula
A
[P][L]/[PL]
21
Q
Y/occupancy/theta=
A
[L]/[L]+Kd, binding site occupied/total binding sites
22
Q
pO2
A
partial pressure O2
23
P50
partial pressure O2 at which half ligand binding sites are occupied
24
strongest hemoglobin subunit interactions
a1-b1 and a2-b2
25
porphyrins
heme is an example, 4 pyrrole rings connected by methine bridges, 4 N in middle, substitutions at x
26
heme
6 spots, 4 coordination bonds, fifth for residue, sixth for O2
27
distal histidine
E7 close but not bonded to heme, interacts with O2, O2 binds to FE2+ on this side
28
measuring O2 binding by globins
double bond system of heme causes strong light absorption, bonding of O2 alters this, oxy: blue light, deoxy: red light
29
eqn for O2 binding proteins
theta= pO2/pO2+P50
30
steric hinderance
slowing of chemical reactions due to steric bulk
31
hemoglobin and myoglobin structures
tertiary similar, only ~40 of AA are identical
32
interactions holding hemoglobin together
hydrophobic, H bonds, ion pairs/ salt bridges
33
hemoglobin ion pairs at a2b1 and a1b2
b1 His HC3 with b1 Asp FG1 and a2 Lys C5
34
hemoglobin affinity for O2
higher that myoglobin in lung, lower than myoglobin in blood, binds O2 in lungs and releases in peripheral tissues
35
hemoglobin conformational change
low affinity T state to high affinity R state
36
cooperative binding
allosteric effect, one O2 binds making it easier for other sites to bind
37
allosteric protein
binding of a ligand to one site affects binding properties at another site
38
homotropic allosteric modulators
ligand and modulator are identical
39
heterotropic allosteric modulator
ligand and modulator are different
40
allosteric modulators
bind to receptors outside of active site to change activity, can be activators/+ or inhibitors/-
41
O2 allosteric modulator
+/activating homotropic modulator
42
binding of O2 changes (initiates T-R)
Fe2+ in heme moves reducing pucker of porphyrin ring, proximal histidine pulled causing shift in helix F, breaking ion pairs of His HC3 and moving to middle
43
hill equation
see phone
44
nH
hill coefficient, nH<1: negative cooperativity, nH=1: ligand binding not cooperative, nH>1: positive cooperativity
45
NB n
number of sites
46
concerted (MWC) conformational change model
subunits change conformation simultaneously, subunits can exist in >1 conformation
47
sequential conformational change model
ligand binding can induce conformational change in subunits independently
48
anemia vs co poisoning
co more severe, O2 can bind but cannot be released
49
relationship between O2 binding vs H+/CO2
inverse, both not binding at same time, negative heterotropic allostery
50
bohr effect
effect of pH and CO2 on O2 binding
51
bohr effect in peripheral tissues
pH is lower, H+ and CO2 is high, Hb binds H+/CO2 decreasing affinity for O2
52
bohr effect in capillaries of lung
CO2 excreted, pH rises, Hb releases H+/CO2 increasing affinity for O2
53
hemoglobin binding of H+
binds several side chains including His HC3, stabilizes Hb in T state
54
hemoglobin binding of CO2
reacts with a-amino groups at amino terminus of each globin (4), produces carbaminohemoglobin, stabilizes T state
55
2,3-bisphosphoglycerate (BPG)
binds in center of HB, forms salt bridges with B subunits, stabilizes T state, reduces affinity for O2
56
enzyme
proteins that catalyze chemical transformation of substrate to product
57
michaelis-menton equation
Vo= Vmax*[S] / Km+[S]
58
regulatory enzymes
multi step metabolic pathways with rate limiting step, catalysis of rate limiting step is mediated by regulatory enzymes
59
feedback inhibition
enzymes activity is inhibited by an enzymes end product, inhibition is reversible
60
allosteric enzyme
regulatory enzyme with catalytic activity modulated by noncovalent binding of a specific compound at not the active site
61
non-competitive inhibition vs negative allosteric modulator
non competitive are non physiological and cannot be overcome by adding more substrate
62
allosteric enzyme specifics vs non regulatory enzymes
structurally more complex, have regulatory sites, conformational changes, do not obey michaelis-menten kinetics
63
homotropic vs heterotropic modulators
homotropic both modulators and substrates, heterotropic only modulators
64
aspartate transcarbamoylase (ATCase)
highly regulated enzyme, catalyzes biosynthesis of pyrimidine nucleotides, transfers carbamoyl group onto aspartate
65
ATCase structure
subunits: 2 catalytic with 3 chains each, 3 regulatory with 2 chains each, 12 polypeptide chains, subunits interact via zinc domains
66
CTP modulator for ATCase
(-) heterotropic modulator, feedback inhibition, binds not to active site
67
ATP modulator for ATCase
+ heterotropic modulator, binds not to active site
68
ATCase substrate and modulator binding
substrates bind to c chains at center, modulators bind to r chains at outside
69
PALA
nonreactive bisubstrate analog that mimics reaction intermediate of ATCase, cannot be consumed, binds 2 places and changes quaternary structure
70
structural changes during activation of ATCase
flexing at c chain interfaces, change in r chain bends, trimers and dimers rotate
71
enzyme regulation by reversible phosphorylation
attachment of phosphoryl group catalyzed by protein kinase, can be removed by phosphatase
72
protein kinase A (PKA)
phosphorylates proteins at sites with sequence X-R-[RK]-X-[ST]-B, B=hydrophobic amino acid
73
activation of PKA by cAMP
cAMP production triggered, regulatory subunit binds 2 cAMP molecules, regulatory subunit releases catalytic subunit allowing it to phosphorylate substrates
74
phosphoryl groups introduce
bulky group for steric exclusion, charge for electrostatic interactions, O2 for H bonds, site for protein-protein interactions
75
glycogen phosphorylase
catalyzes the phosphorolysis of glycogen, 2 forms: a (active) and b (inactive), changed into active form by phosphorylase kinase, targets Ser14
76
glycogen synthase kinase 3 (GSK3)
phosphorylates GS at different sites, more potent inhibition of glycogen synthase
77
SH2 function
can bind to sites with phosphorylated tyrosine
78
inactive precursors
zymogen activated by protease, proenzyme activated by non-protease, irreversible proteolytic cleavage activates enzyme
79
chymotrypsin
serine protease, activated by proteolysis, highly sensitive to pH
80
activation of chymotrypsin
His57 deprotonated, acts as proton acceptor inducing nucleophilic character in Ser195, a-amino group of Ile16 protonated and forms ion pair with Asp194
81
clotting cascade
intrinsic and extrinsic pathways, activated serine proteases cleave different target serine proteases activating them, final protease is thrombin
82
thrombin
cleaves N-terminal of fibrinogen allowing it to assemble into fibers
83
promoters of clotting
vitamin K, CA2+, thrombin, factor XIIIa
84
vitamin K
carboxylation of prothrombin into strong chelator, electron source for rxn
85
substances that reduce clotting
dicoumarol and warfarin, blood thinners, look like vitamin K but don't provide activity
86
fibrinogen clotting
thrombin cleaves into fibrin, cleaved ends bind the globular domains of other fibrin, results in clot
87
factor XIIIa
transglutaminase, activated by thrombin, forms amide bond covalently linking fibrine monomers, converts soft clots to hard clots
