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Biochemistry > Chapter 5- section 5.1 > Flashcards

Chapter 5- section 5.1 Flashcards

1
Q

two types of protein interactions

A

-interactions caused by enzymes
-interactions where neither the chemical configuration nor the composition of the interacting molecule is changed

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2
Q

what is the function of most proteins?

A

involves the reversible binding of other molecules called a ligand

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3
Q

what site does a ligand bind at?

A

binding site
-complementary to the ligand in size, shape, charge & hydrophobic/hydrophilic character

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4
Q

what is flexible? (where its said to “breathe”)

A

proteins

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5
Q

the binding of a protein and ligand is often coupled to a ?

A

conformational change

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6
Q

conformational change in the protein that makes the binding site more complementary to the ligand where this structural adaptation

A

induced fit

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7
Q

in a multisubunit protein, a conformation change in one subunit often affects the ?

A

conformation of other subunits

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8
Q

substrate

A

a molecule acting upon the enzyme instead of being called a ligand

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9
Q

active site (catalytic site)

A

where the ligand binding site is

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10
Q

oxygen can bind to a ? group

A

home prosthetic group (iron & copper have a strong tendency to bind to oxygen)

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11
Q

iron is usually in a proteinboound prosthetic group called ?

A

heme

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12
Q

what is a prosthetic group?

A

a compound permanently associated with a protein that contributes to the protein’s function

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13
Q

what does heme consist of?

A

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+)

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14
Q

iron in its Fe2+ state binds oxyxgen ? but in the Fe3 state it doesn’t bind oxygen

A

reversibly

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15
Q

globins are a family of ? binding protein

A

oxygen

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16
Q

stores oxygen and facilitates oxygen diffusion in muscle tissue

A

myoglobin

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17
Q

responsible for oxygen transport in the bloodstresm

A

hemoglobin

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18
Q

antibodies and cytokines defend against ?

A

pathogens

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19
Q

what two proteins are involved in muscle contraction?

A

myosin & actin

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20
Q

two proteins involved in biological catalysis

A

chymotrypsin & lysozome

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21
Q

Myoglobin has a ? binding site for oxygen

A

single; only has one molecule of heme

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22
Q

what are the helical segments in myoglobin named?

A

A through H
-His residue that is in the heme in myoglobin

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23
Q

What are the proximal His names?

A

His 93 aka His F8

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24
Q

What does myoglobin’s function depend on?

A

it depends on the protein’s ability to bind oxygen, release it, and where it is needed

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25
Q

-equilibrium expression of reversible binding of a protein to a ligand
-equilibrium constant

A

-P + L (<>) PL
-Ka = [PL] /[P]/[L]=Ka/Ka

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26
Q

at equilibrium, the association and dissociation rates are ?

A

equal when characterized by Ka

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27
Q

what are the rate constants

A

Ka and Kd (unit Ms-1)

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28
Q

What does Ka do?

A
  • 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
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29
Q

a higher value of Ka corresponds to ?

A

a higher affinity of the ligand for the protein

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30
Q

a molecule that binds to a specific protein binding site (usually a small molecule)

A

ligand

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31
Q

ligand protein interactions are stabilized by ?

A

noncovalent forces that dictate protein structure

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32
Q

what does Kd do?

A

-dissociation rate
-first-order PL > P +L
-release of a lligand

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33
Q

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

A

Fraction

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34
Q

At kd = [L] the position is ____ saturated

A

50% (when Y is 0.5 its equal to the Kd

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35
Q

A lower value Kd means a higher ________ of ligand for the protein

A

Affinity

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36
Q

The bonding of oxygen to myoglobin follows the same concepts expect its equation is what

A

Y = pO2/ pO2 + P50 (p50 partial pressure) or (Y= [O2]/ kd + [O2])

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37
Q

The binding of of oxygen to myoglobin makes a hyperbolic curve shape which means what?

A

All O2 binds with some affinity till saturated (P50 =2.8 torr for humans)

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38
Q

Delta G related to Kd how

A

Dleta G = -RTln Kd

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39
Q

Protein mstructure is affected how

A

By the way the ligand binds

40
Q

When heme is bound to myoglobin its affinity for O2 is selectively increased by the presence of the _________ his (or His E7 in myoglobin)

A

Distal His

41
Q

Heme prosthetic groups occupy a ___________ cleft within globin structure where the cleft is formed by 3 alpha helices & two loops in a 3D structure

A

Hydrophobic

42
Q

Heme Fe (2) protopohyrin IX provides 4 of 6 Fe ________

A

ligands (Fe binds to O2, NO2, H2S, & CO)

43
Q

__________ are the protein component of Mb & Hb

A

Globins

44
Q

_________ monomer binds one O2 for oxygen strage & dissfusion

A

Myoglobin

45
Q

________ tetramer binds four O2 for transport from lungs to tissues

A

Hemoglobin

46
Q

________ proteins creates a snug hydrophobic pocket for the heme

A

Globin ( myoglobin heme binds between the E & F helices)

47
Q

Oxygen binding properties of myoglobin & hemoglobin relate_______ & _______

A

Structure & functionm

48
Q

O2 binding measure the amount bound ( saturation) as a function of oxygen concentration) so graph axis are what?

A

Saturation vs O2 pressure

49
Q

Protein properties relates to their role in storage & _______ or transport

A

Disffusion

50
Q

Myoglobin _________ solubility & diffusion rate of O2 from capillaries to muscle tissues (Mb + O2 yields MbO2)

A

Increases

51
Q

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)

A

Lungs

52
Q

________ transport oxygen in blood

A

Hemoglobin

53
Q

Hemoglobin is a tetramer protein containing ______ heme prosthetic group

A

4

54
Q

________ has an alpha2beta2 tetramer which is a dimer of aphabeta protomers stabilized by a large number of interaction between subunits at one interface

A

Hemoglobins

55
Q

_______ structiure containm an alpha chain that has 7 alpha helices & beta chains

A

Globin

56
Q

________ structure allows for more complex O2 binding behavior

A

Multisubunit

57
Q

What are the two major conformations of hemoglobin?

A
  1. T state (oxy, high affinity)
  2. R state (deoxy, low affinity)
58
Q

O2 has a higher affinity to bind to hemoglobin in the ______ be O 2binding stabilizes the ____state

A

R

59
Q

When O2 is absent experimentally the ____ state is more stable & the predominant conformation of deoxy hemoglobin

A

T

60
Q

Hemoglobin binds oxygen ___________

A

Cooperatively

61
Q

Interaction between the ion pairs ___ & ______ of the beta subunit & between Lys C5 of the alpha subunit & His HC3 subunit stabilizes the T state

A

HC3 & Asp FG1

62
Q

What are the reasons why the T & R state occur in hemoglobin?

A
  1. Oxygen binding triggers proximal His movement & F8 helix & overall 15 degree twist of the protomer creation to each other
  2. Greatest changes occur hydrophobic & ion pair at the alpha 1 - beta 2 & alpha 2 - beta 1 interfaces & the central cavity IP to 6anstrogm
63
Q

What are the structural reasons for R & T state?

A
  1. Oxygen binding induces conformational change around the heme which transcribed through subunit interactions
  2. 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)
64
Q

A protein that bound O2 with high affinity would bind it efficiently in the lungs but would not _______ much of it in the tissues

A

Release

65
Q

If the protein-bound oxygen with _____ affinity to trelase it in the tissue, it would pick up much O2 in the lungs

A

Low

66
Q

_________ has a sigmoid (cooperative) binding curve for O2 showing the transition from low affinity (T state) to high affinity (R state)

A

Hemoglobin ( O2 binds to the lungs where pO2 is high & release O2 in the tissues where pO2 is low)

67
Q

Allosteric proteins

A

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)

68
Q

For protein with multiple binding sites (n) have to use what equation? (For proteins like Mb & Hb)

A

Hill’s equation

69
Q

Hill’s equation

A

YO2= (pO2)^n/ (p50)^n + (pO2)^n (n is the # of binding sites)

70
Q

The hill equation plot where the axis is what

A

log (Y/1-y) vs log [L] (y-intercept = log P50)

71
Q

The slope of the Hill plot is what

A

N(H) which is the hill coefficient that measures the degree of cooperativity

72
Q

If n(H) = 1 what does it means?

A

That the ligand is not cooperative ( can happen when the multisubunit don’t communicate)(hyperbolic curve)

73
Q

If n(H) is greater than 1 it indicates what?

A

Positive cooperativity in ligand binding

74
Q

What are the two models for cooperative binding of ligands to proteins with multiple binding sites?

A
  1. Concerted (MWC) model
  2. Seqential Model
75
Q

Concerted (MWC) model

A

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

76
Q

Sequential model

A

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)

77
Q

Hemoglobin also transport ____ & _______

A

H+ & CO2 (related to the bicarbonate bloof buffer system)

78
Q

Bohr Effect

A

pH affects O2 binding to hemoglobin

79
Q

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+

A

H+

80
Q

Hb affinity for oxygen depends on _____ since H+ binding stabilizes the T state

A

pH

81
Q

The ____ difference between lungs & metabolic tissues increases efficiency of the O2 transport

A

pH

82
Q

When O2 concentration is ____ (like in the lungs) hemoglobin binds O2 & release H+

A

High

83
Q

When O2 concentration is _____ (like in peripheral tissues) H+ is bound O2 is release

A

low

84
Q

Mb-O2 is a _____ curve which indicates a single equilibrium constant for O2 binding with saturation at high O2

A

Hyperbolic

85
Q

Hb-O2 is a _______ binding curve which reflects variable binding affinity for each binding event (one O2 per heme) which is a positive cooperativity

A

Sigmoid

86
Q

Oxygen binding is regulated by what?

A

Shifting the Hb T/R equilibrium

87
Q

_________ factors shift the conformation of the 4 structure R (oxy) & T (deoxy) forms have different binding affinities for O2

A

Allosteric

88
Q

What is the positive & negative stabilizers for T & R state?

A

Positive: O2 binding & negative pH, 2,3-BPG, & CO2

89
Q

Connection to the bicarbonate buffer system & dissolved Co2 also affects O2 ______

A

Affinity

90
Q

Disloved Co2 leads to blood pH______ & HCO3 increase

A

Decrease

91
Q

_______ favors ion pair formation (T state) & O2 release in tissues

A

High [H+]

92
Q

Muscle lactic acid decrease ______ & more efficient O2 releases with leaving respiration

A

pH

93
Q

Lungs high [O2] favors ____ binding & H+ release

A

O2

94
Q

Oxygen binding to hemoglobin is regulated by what?

A

2, 3 BPG (a negative allosteric effector)

95
Q

Regulation of Hb O2 binding by 2,3 BPG to & stabilize Hb _____ state which favors lower O2 affinity

A

T

96
Q

________ anemia is a molecular disease of hemoglobin

A

Sickel cell anemia

97
Q

Serine proteases

A

hydrolyze peptide and ester bonds with an active
site serine in the catalytic triad

Biochemistry (26 decks)

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