1
Q
Proteins Function by Interacting
Dynamically with Other Molecules in Two Ways
A
– protein acting as a reaction catalyst, or enzyme, alters
the chemical configuration or composition of a bound
molecule
– neither the chemical configuration nor the composition
of the bound molecule is changed
2
Q
alters the chemical configuration or composition of a bound
molecule
A
protein acting as a reaction catalyst, or enzyme
3
Q
A molecule bound reversibly by a protein is called a
A
ligand
4
Q
A ligand binds a protein at a binding site that is complementary to the ligand in
A
size, shape, charge, and hydrophobic or hydrophilic character
5
Q
are proteins flexible
A
yes
6
Q
The binding of a protein and a ligand is often coupled to a
A
conformational change
7
Q
what does a conformational change do for a protein
A
makes the binding site more complementary to
the ligand, permitting tighter binding.
8
Q
The structural adaptation that occurs between protein and ligand is called
A
induced fit
9
Q
In a multisubunit protein, a conformational change in one subunit often affects
A
the conformation of other subunits
10
Q
are Interactions between ligands and proteins regulated?
A
yes
11
Q
A molecule bound reversibly by a protein is called a
A
ligand
12
Q
Oxygen Can Bind to a
A
Heme Prosthetic Group
13
Q
is oxygen diffusion through tissues is ineffective or effective over large distances
A
ineffective
14
Q
what has strong tendency to bind to oxygen
A
transition metals
15
Q
protein-bound prosthetic group
A
heme
16
Q
what is present in myoglobin and
hemoglobin
A
heme
17
Q
what structure does a heme have
A
ring structure,
protoporphyrin,
with a bound Fe2+ atom
18
Q
Coordination Bonds of Iron
A
– four to nitrogen atoms in the flat porphyrin ring
– two perpendicular to the porphyrin
19
Q
how many coordination bonds does iron have
A
six
20
Q
ligand binds a protein at a binding site that is complementary to the ligand in
A
size, shape, charge,
and hydrophobic or hydrophilic character.
21
Q
are ligand binding a protein interactions specific?
A
yes
22
Q
crucial in maintaining the
high degree of order in a living system.
A
These specific molecular interactions
23
Q
what are the two perpendicular coordination bonds
A
– one is occupied by a side-
chain nitrogen of a highly
conserved proximal His
residue
– one is the binding site for
molecular oxygen (O2)
* Fe2+ binds O2 reversibly
* Fe3+ does not bind O2
24
Q
Are a Family of Oxygen-Binding Proteins
A
Globins
25
widespread protein family
Globins
26
highly conserved
tertiary structure:
eight α-helical
segments
connected by
bends
Globins
27
most function in O2
transport or storage
Globins
28
bends in globins
globin fold
29
eight α-helical segments
connected by bends
highly conserved tertiary structure
30
how many binding sites does Myoglobin have for oxygen
one
31
what is Myoglobin made up of
153 residues + one molecule of heme
32
how are Myoglobin's bends named
bends named after the α-helical segments they
connect
33
equilibrium expression equatiom
34
describes the reversible binding of a protein (P) to a ligand (L):
equilibrium expression
35
provides a measure of
the affinity of the ligand L for the protein
association constant (Ka)
36
higher Ka =
higher affinity
37
equivalent to the ratio of the rates of the forward (association) and the reverse (dissociation)
reactions that form the PL complex
association constant (Ka)
38
association constant (Ka) formula
39
ligand binding formula
40
information we can gain from this graph
[L] at which ½ of the
available ligand-binding
sites are occupied (Y =
0.5) corresponds to 1/Ka
41
reciprocal of Ka
dissociation constant (Kd)
42
equilibrium constant for the release of ligand
dissociation constant (Kd)
43
lower Kd =
higher affinity
44
information we can gain from this graph
when [L] = Kd, ½ of the
ligand-binding sites are
occupied
45
partial pressure of O2 (pO2) is easier to measure than
[O2]
46
equals the [O2] at which ½ of the
available ligand-binding sites are occupied, or P50
Kd
47
formula you can get from this graph
48
binds free heme more than
20,000 times better than does O2
carbon monoxide (CO)
49
Affects How Ligands Bind
Protein Structure
50
differences in the what affect binding geometries
the orbital structures
51
Myoglobin’s what Increases
Heme’s Affinity for O2
Distal His
52
hydrogen bond between the imidazole side chain of His E7
and bound O2 does what to the Fe-O2 polar complex
electrostatically stabilizes
53
Transports Oxygen in
Blood
Hemoglobin
54
transport O2
erythrocytes (red blood cells)
55
what are erythrocytes (red blood cells) formed from
hemocytoblasts (precursor stem
cells)
56
main function is to carry hemoglobin
erythrocytes
57
In a multisubunit protein, a conformational change
in one subunit often affects the conformation of
other subunits
58
tetrameric protein
with 4 heme groups
hemoglobin
59
adult hemoglobin has two globin
types which are
two α chains (141 residues each)
and two β chains (146 residues each)
60
low or high structural similarity
Low sequence similarity
61
low or high structural similarity
High structural similarity
62
strong interactions between unlike subunits
– hydrophobic effect
– hydrogen bonds
– ion pairs (salt bridges)
63
α1β1 (and α2β2) interface involves how many residues
>30 residues
64
α1β2 (and α2β1) interface involves how many residues
19 residues
65
which state O2 has a
higher affinity for
hemoglobin
R state
66
which state is more stable when O2 is absent
T state
67
predominant conformation of
deoxyhemoglobin
T state
68
The binding of a protein and a ligand is often coupled to a conformational change in the protein that makes the binding site
more complementary to
the ligand, permitting tighter binding
69
The structural adaptation that occurs between protein and ligand is called
induced fit.
70
O2 binding to hemoglobin in the T state triggers
a conformational change to the R state
71
slide past each other and rotate
αβ subunit pairs
72
the pocket between the β subunits do what
get narrow
73
some ion pairs that stabilize the T state do what
break and some new ones form
74
t state or r state
t state
75
t state or r state
r state
76
t state or r state
t state
77
t state or r state
78
Tense state
T state
79
is T state or R state more stable
T state
80
does T state or R state have more interactions
T state
81
is T state or R state more flexible
R state
82
does T state or R state have a higher affinty for O2
R state
83
O2 binding triggers a what
T → R conformational change
84
Conformational change from the T state to the R state involves
breaking ion pairs between the α1- 2 interface
85
T state is stabilized by
a greater number of ion pairs,
many of which lie at the α1β2 (and α2β1) interface
86
hemoglobin has a what kind of
binding curve for oxygen
hybrid sigmoid
87
can Interactions between ligands and proteins be regulated
yes
88
binding of a ligand to one site affects the binding properties of another site on the same protein
allosteric protein
89
ligands that bind to an allosteric protein to induce a conformational change
modulators
90
normal ligand and modulator are
identical
homotropic
91
modulator is a molecule other than the normal ligand
heterotropic
92
How can the affinity to oxygen change
- multiple binding sites
- must be able to interact with each other
- cooperativity
93
Must be a protein with multiple binding sites
Binding sites must be able to interact with each other
cooperativity
94
first binding event increases affinity at remaining sites
positive cooperativity
95
what recognizes positive cooperativity
sigmoidal binding curves
96
first binding event reduces affinity at remaining sites
negative cooperativity
97
– all subunits in the same conformation
– ligand binds more tightly to the R state
MWC model = concerted model
98
– each subunit can be in either conformation
– equilibrium is altered as additional ligands are bound,
progressively favoring the R state
sequential model
99
what model is this
MWC model (concerted model)
100
what model is this
Sequential model
101
formula when for a protein with n binding sites, the equilibrium becomes
102
Equation is used to calculate cooperativity.
The Hill Equation
103
Hill coefficient
nH
104
slope of a Hill plot is = to what
nH
105
what happens If nH = 1,
ligand binding is not cooperative
106
what happens if nH > 1
indicates positive cooperativity
107
what happens if nH < 1
indicates negative cooperativity
108
Hill Plots for Myoglobin and
Hemoglobin
109
Blocks O2 binding
to Hemoglobin
Carbon Monoxide
110
why does Carbon Monoxide block O2 binding to Hemoglobin
CO has ~250-fold greater
affinity for hemoglobin than
does O2
111
Hemoglobin Also Transports what
H+ and CO2
112
two end products of cellular
respiration
H+ and CO2
113
catalyzes the hydration of CO2 to
bicarbonate
carbonic anhydrase
114
the structural effects of H+ and CO2 binding to
hemoglobin favor which state
T state
115
the binding of H+ and CO2 is related how to the binding of O2
inversely
116
describes the effect of pH and [CO2] on the binding and release of O2 by hemoglobin
Bohr effect
117
how does CO2 binding to hemoglobin contributes to the Bohr effect
by producing H+
118
when [O2] is high, hemoglobin does what
binds O2 and releases H+
119
when [O2] is low, hemoglobin does what
releases O2 and
binds H+
120
Oxygen Binding to Hemoglobin Is Regulated by
2,3-bisphosphoglycerate
(BPG)
121
greatly reduces the affinity of
hemoglobin for oxygen
2,3-bisphosphoglycerate
(BPG)
122
(BPG) binds to
a site distant from O2-binding site
123
BPG binds to
the cavity between the β subunits in the T state
124
cavity is lined with
positively charged residues
125
BPG stabilizes which state
T state
126
BPG concentration
increases at
high
altitudes
127
lowered oxygenation of
peripheral tissues
hypoxia
128
hypoxia does what affect to BPG
causes BPG increases
129
has lower affinity for BPG than
normal adult hemoglobin (Hb A)
Hb F
130
does Hb F (fetal) or (Hb A) adult have a higher affinity for O2
Hb F (fetal)
131
Hb F (fetal) stablizes which state
R state
132
Is a Molecular Disease of Hemoglobin
Sickle Cell Anemia
133
single amino acid substitution (Glu6 to Val6) β chains
produces a hydrophobic patch
sickle cell anemia
134
deoxygenated hemoglobin
becomes
insoluble
135
deoxygenated hemoglobin forms what
polymers that aggregate
136
normal hemoglobin remains
soluble upon deoxygenation
137
Vertebrates fight infections with soluble
antibodies
138
antibodies specifically bind to what
antigens
139
are substances that stimulate production of
antibodies
antigens
140
Recognized as foreign by the immune system
antigens
141
antigens Coat proteins of what
bacteria and viruses
142
are proteins that are produced by B cells and specifically bind to antigens
Antibodies
143
will mark the antigen for destruction or interfere with its
function
Binding
144
A given antibody will bind to a what of the antigen
small region (epitope)
145
major class of antibodies
immunoglobulin G (IgG)
146
one of the most abundant blood serum proteins
immunoglobulin G (IgG)
147
how many polypetide chains does immunoglobulin G (IgG) have
4 polypeptide chains: 2 heavy chains and 2 light
chains
148
cleavage with protease papain releases
the basal fragment Fc and two Fab branches (each with a single antigen-binding site)
149
variable domains
associate to
create the
antigen-binding
site
150
allows formation of an antigen-
antibody complex
heavy and light chains
151
conformational changes in the antibody and/or antigen allow the complementary groups to
interact fully
induced fit
Biochemistry 1
flashcards
Decks in class (16)
# Cards
-
Chapter 2: Water: the Solvent of Life67
-
Chapter 3: Amino Acids, Peptides, and Proteins100
-
Chapter 4: The Three- Dimensional Structure of Protein108
-
Iclicker Questions for Exam 114
-
Exam 1 Practice Questions49
-
Chapter 4 for Exam 213
-
Chapter 5: Protein Function151
-
Iclicker Questions for Exam 224
-
Si practice question for Exam 2133
-
Chapter 6: Enzymes179
-
Chapter 7: Carbohydrates and Glycobiology123
-
Exam 2 Practice Exam Questions33
-
Iclicker Questions for Exam 366
-
Chapter 10: Lipids17
-
Si practice questions for Exam 3173
-
Exam 3 Practice Exam Questions64
