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Biochemistry > Mb and Hb, & Proteins (Final) > Flashcards

Mb and Hb, & Proteins (Final) Flashcards

1
Q

Describe Myoglobin.

A
  • monomer
  • muscle cells
  • takes O2 from the bloodstream and distributes it to muscles
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2
Q

Describe Hemoglobin.

A
  • tetramer
  • red blood cells
  • takes O2 from our lungs and delivers it to the periphery and back
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3
Q

What is the primary function of Mb and Hb?

A

Oxygen binding

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4
Q

What was the first protein to be crystallized?

A

Sperm whale myoglobin

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5
Q

What is the secondary structure of myoglobin?

A
  • it is made up of 8 alpha helices labelled helix A->H
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6
Q

What is the key functional group of myoglobin?

A

the heme group

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7
Q

What is heme?

A
  • a porphyrin derivative
  • made of 4 pyrrole rings
  • heme is a planar molecule
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8
Q

Describe the structure of a pyrrole ring?

A
  • 5 membered ring with 1 nitrogen molecule
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9
Q

What is the purpose of pyrrole nitrogen?

A

Pyrrole N is critical to the function of heme because that is where iron binds

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10
Q

What are the 6 things Fe binds to in a heme in myoglobin?

A
  • 4 pyrrole Ns
  • 1 histidine
  • O2
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11
Q

Describe the heme complex in myoglobin?

A

Valine and phenylalanine are two hydrophobic groups that pack against porphyrin and keep your heme groups in place in the protein

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12
Q

Show the reaction that Fe participates in in an isolated heme.

A

Fe(II) + O2 —> Fe(III) - O - O(-)

  • Fe is reduced in the beginning, it donates electrons and gets oxidized in this reaction
  • Oxygen accepts electrons and gets reduced in this reaction
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13
Q

What does an isolated heme mean?

A

A heme not found in myoglobin

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14
Q

What does the protein portion of myoglobin cause?

A

The protein portion of myoglobin makes O2 binding reversible

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15
Q

In myoglobin what is oxygen binding dependent on?

A

Binding is dependent on [O2]

- O2 concentration

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16
Q

What else can a heme bind to?

A
  • heme can bind to CO, NO, H2S
  • heme binds to these molecules with greater affinity than O2, and this binding is not/not as reversible
  • CO poisoning
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17
Q

What does Mb primarily facilitate?

A
  • O2 diffusion into muscle
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18
Q

Describe seal/whale Mb.

A
  • In seals and whales Mb stores O2

- these animals (marine mammals) have 50x higher Mb than humans

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19
Q

What is fractional saturation?

A
  • YO2
  • amount of oxygen bound myoglobin over total myoglobin
  • (Percent of total Mb bound to oxygen)
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20
Q

What do you graph in an oxygen binding curve?

A
  • YO2 (fractional saturation/percent oxygen bound) on Y axis

- pO2 - partial pressure of oxygen on X axis

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21
Q

What is the dissociation constant for myoglobin?

A

k = [Mb][O2] / [MbO2]

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22
Q

What is pO2?

A

partial pressure of O2 / oxygen tension

- measured in torr

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23
Q

What do low and high pO2 indicate in general about YO2?

A

Low pO2 = low Yo2

High pO2 = high Yo2

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24
Q

What is P50?

A
  • the value of pO2 where 50% of the total Mb is bound to oxygen
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25
Q

What does a lower P50 value indicate?

A

higher affinity to O2

- less oxygen pressure is required for 50% of Mb to be bound to O2

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26
Q

What is the equation for fractional saturation for Mb?

A

YO2 = (pO2) / (P50 + pO2)

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27
Q

How is YO2 affected in Mb when there are lower pO2 levels?

A

When pO2 levels are low, and they change there is a more dramatic change in Yo2

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28
Q

When is O2 released?

A

As pressure changes from arterial to venous blood

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29
Q

How much O2 is released when Mb travels from arterial to venous blood?

A
  • 6% of bound oxygen is released

- not very efficient at releasing oxygen in our venous system

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30
Q

What is hemoglobin primarily responsible for?

A
  • responsible for O2 transport in blood

- found in red blood cells

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31
Q

Describe the makeup of RBCs.

A
  • 34% of their weight is hemoglobin

- they do not have a nucleus or organelles

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32
Q

What is the general structure of hemoglobin?

A

alpha2 beta2 tetramer

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33
Q

Describe the similarity of the alpha and beta subunits.

A
  • between alpha and beta there is little 1 degree sequence homology, but high structural similarity (tertiary structures are similar)
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34
Q

How does O2 binding impact hemoglobin?

A

O2 binding causes a dramatic structural change

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35
Q

What occurs when crystallized deoxy Hb is exposed to O2?

A

The change in structure will cause it to shatter

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36
Q

What structural changes occur when deoxyhemoglobin turns into oxyhemoglobin (oxygen binds)?

A
  • beta subunits move closer together
  • contacts between alpha1-beta2 and alpha2-beta1 change
  • there is 15 degree rotation of the alpha beta dimer
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37
Q

Describe the O2 - Mb binding (general).

A
  • hyperbolic O2 binding curve

- non-cooperative (each binding event is independent of the other)

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38
Q

Describe the O2 - Hb binding (general).

A
  • sigmoidal O2 binding curve

- cooperative binding (binding at one site affects other sites)

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39
Q

Describe the sigmoidal binding curve.

A
  • high oxygen bound at high PO2
  • low oxygen bound at low PO2
  • releases O2 when at low arterial pressure
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40
Q

What is the hill equation?

A
  • Equation that describes YO2 for hemoglobin
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41
Q

What type of binding curve does Hb follow?

A

Sigmoidal

42
Q

What is the Hill coefficient and what does an increase Hill coefficient indicate?

A
  • the value of n increases with the degree of cooperativity
43
Q

What is n = 1, n > 1, and n < 1?

A
  • N = 1 indicates non-cooperative binding and a hyperbolic binding curve
  • N > 1 indicates a positively cooperative binding pattern and O2 affinity increases as O2 sites are occupie
  • N < 1 indicates a negatively cooperative binding pattern in which binding to one site reduces affinity for other sites
44
Q

What is the linear hill equation?

A
45
Q

For a linear hill equation, what is the slope and what are the x and y intercepts?

A
  • slope = n
  • y-intercept = -nlogP50
  • x-intercept = logP50
46
Q

What is the y-axis and the x-axis in an hill graph?

A 
y-axis = log(Yo2 / (1 - Yo2))
x-axis = logpO2
47
Q

What are the 3 zones of Hb linear hill graph?

A 
1. YO2 < .1
 y-axis < -.095 
non-cooperative
slope = 1
p50 = 30 torr
2. .1 < YO2 < .9, 
 -.095 < y-axis < .095 
cooperative
slope = 2.8
p50 = 26 torr
3. .9 < YO2
.095 < y-axis
slope = 1
p50 = 0.3 torr
non-cooperative
48
Q

How is binding at one site affected by binding at another?

A
  • binding information is transferred from one site to another through protein movement
  • conformational changes
49
Q

What is T and R Hb?

A

T - no O2, deoxyHb

R - O2 bound, oxyHb

50
Q

What structural changes occur in the T-R transition?

A
  • Fe(II) moves into the plane
  • Iron drags Histidine F8 (bound to iron) -> causing the F-helix to tilt
  • Shifts alpha 1, beta 2 and alpha 2, beta 1 interfaces
  • c-termini ion-pair interactions: the electrostatic interactions holding the molecule together are disrupted
51
Q

What structural changes occur in the T-R transition?

A
  • Fe(II) moves into the plane
  • Iron drags Histidine F8 (bound to iron) -> causing the F-helix to tilt
  • Shifts alpha 1, beta 2 and alpha 2, beta 1 interfaces
  • c-termini ion-pair interactions: the electrostatic interactions holding the molecule together are disrupted
52
Q

What 3 things affect T ->R transition?

A
  • pH (Bohr effect)
  • CO2 levels
  • BPG
53
Q

Explain the Bohr Effect.

A
  • O2 affinity increases as pH increases
  • electrostatic interactions involved the N-term amino group and the Histidine residue in C-term (too high of a pH de-protonates these molecules)
  • as pH increases salt bridges are broken, which favors the R-state (higher O2 affinity)
54
Q

What are the two ways that CO2 levels can affect T - R?

A
  • the Bohr Effect (pH)

- covalent modification

55
Q

What is the acid/base reaction that occurs in our blood and what is it catalyzed by?

A

[CO2] [HCO3-] + [H+]

This conversion is catalyzed by carbonic anhydrase

56
Q

Describe CO2 levels in the muscle and how this impacts T - R.

A
  • In the muscle there are HIGH CO2 levels, this increases bicarbonate and H+
  • Increase in H+ lowers pH
  • Lower pH lowers O2 affinity, more T state Hb
57
Q

Describe CO2 levels in the lungs and how this impacts T - R.

A
  • In the muscle there are LOW CO2 levels, this decreases bicarbonate and H+
  • Decrease in H+ increases pH
  • Higher pH increases O2 affinity, more R state Hb
58
Q

Explain covalent bonding of CO2 in Hb.

A
  • covalent modification of N-term (of T-state Hb) by CO2
  • this occurs when CO2 is high
  • shifts towards more T-state, lower O2 affinity
59
Q

Which state of Hb is more likely to be modified by Hb binding of CO2?

A

T-state

60
Q

Which state of Hb does BPG bind to and why?

A
  • binds to T state

- T - R transition narrows binding pocket so BPG can no longer fit

61
Q

How does BPG bind to Hb?

A

non-covalently

62
Q

How do high levels of BPG impact T - R equilibrium?

A
  • Increase in BPG increases the T-state

- BPG binds to the T state and causes the equilibrium to shift towards the T - state

63
Q

What happens to our blood at high altitude?

A
  • BPG concentration in our bloodstream increases when we go from low to high altitude
  • This is because arterial pressure drops at high altitude, so BPG concentration must increase to increase the P50 value
  • An increase in p50 value causes a lower percent of Hb to be bound to O2 at the same venous pressure, therefore allowing more to be released during this transition from arterial to venous
64
Q

Describe the structural differences in fetal hemoglobin.

A
  • has alpha2, gamma 2 subunit instead of alpha 2 beta 2
  • Has a serine instead of a histidine
  • Histidine is important for BPG binding so fetal hemoglobin doesnt bind BPG
65
Q

Describe the different function of fetal hemoglobin.

A
  • Fetal hemoglobin doesn’t bind BPG
  • During pregnancy the mothers BPG is increased so mothers blood has a lower affinity for O2, but fetal Hb is not affected by this increase bc it doesn’t bind BPG
  • ensures transfer of O2 from mother to fetus
66
Q

What is the mutation in sickle cell anemia?

A
  • A glutamate to valine
  • causes 2 mutant beta globin chains
  • the chains interact and cause the cells to sickle
  • valine binds a hydrophobic pocket in another Hb unit which leads to aggregation of Hb molecules and linear polymer structures
67
Q

What is sickle cell Hb called?

A

Hbs

68
Q

What must heterozygous sickle cell patients have? Homozygous?

A

Heterozygous - trait

Homozygous - disease

69
Q

When does aggregation of Hb molecules occur in sickle cell disease?

A

When O2 levels are low

70
Q

How are sickle cell patients treated and what does this do?

A
  • treated with hydroxyurea which increase expression of fetal Hb
  • can replace deficient betaS form
71
Q

What do sickle cell heterozygotes have?

A

protection from malaria

72
Q

Explain how heterozygotes have protection from malaria.

A
  • malaria is caused by plasmodium which infects RBCs and lowers their pH
  • lower pH causes hemoglobin to shift to T-state
  • carriers express some Hbs, as T state increases Hbs aggregates and parasite infected RBCs sickle (lower oxygen affinity state)
  • spleen can selectively remove sickled cells that are infected
73
Q

What is the allosteric effect?

A
  • binding of a ligand at one site affects binding of another ligand at a different site
74
Q

What are the two models for the allosteric effect?

A

symmetry model and sequential model

75
Q

What is the symmetry model?

A
  • the 4 subunits can only exist as 4 in the T-state or 4 in the R-state
76
Q

What is the sequential model?

A
  • binding in one section causes small conformational changes in adjacent subunits
77
Q

<p>What value describes the conformation of a polypeptide backbone?</p>

A

<p>Torsion angles</p>

78
Q

<p>What are the two torsion angles of a polypeptide backbone?</p>

A

<p>⍦ - C-C bond</p>

<p>∅ - C-N bond</p>

<p>-amide bond has little rotation because it is planar and has some double bond character</p>

79
Q

<p>What is a Romachandran diagram?</p>

A

<ul><li>indicates allowed conformations for a polypeptide (due to side chains only certain are allowed)</li><li>⍦ vs ∅ plotted</li></ul>

80
Q

<p>What are the two exceptions to the romachandran diagram?</p>

A

<p>Proline and glycine</p>

81
Q

<p>Describe proline's torsion angles.</p>

A

<ul><li>∅ values are restricted to -60</li><li>restricted to one side of the plot, can only rotate on the side that has the H, not on the side with the R-group</li><li>more restrained motion</li></ul>

82
Q

<p>Describe glycine's torsion angles.</p>

A

<ul><li>less steric hinderance, allowed angles are greater</li><li>no R group, just 2 Hs</li></ul>

83
Q

<p>Describe the structure of a typical alpha helix.</p>

<p>(handed, residues, pitch, bonds, side chains)</p>

A

<ul><li>right handed helix</li><li>3.6 amino acids/residues per turn</li><li>pitch (distance covered per turn) = 5.4Ă</li><li>carbonyl (C=O) of Nth residue is hydrogen bonded to the N-H of the N+4th residues</li><li>side chains point outward and downward</li></ul>

84
Q

<p>How are beta sheets stabilized?</p>

A

<p>-held together by H-bonds</p>

<p>-H-bonds are between neighboring polypeptide chains</p>

85
Q

<p>What are the two types of beta sheets?</p>

A

<p>parallel and antiparallel</p>

86
Q

<p>Describe parallel beta sheets.</p>

A

<ul><li>polypeptides run in the same direction (N-C) and (N-C)</li><li>H-bonds between the strands are angled</li><li>the crossover connection between strands is longer and goes out of the plane</li></ul>

87
Q

<p>Describe antiparallel beta sheets.</p>

A

<ul><li>polypeptides run in opposite directions (N-C) and (C-N)</li><li>H-bonds between the strands are parallel</li><li>the crossover connection between strands is shorter and on the same plane</li></ul>

88
Q

<p>What are the two classes of proteins?</p>

A

<ul><li>fibrous and globular</li></ul>

89
Q

<p>Describe fibrous proteins.</p>

A

<ul><li>have repeating second degree structures</li><li>are structural proteins: hair, nails, muscle tendons</li><li>keratin and collagen are examples</li></ul>

90
Q

<p>How are disulfide bonds formed?</p>

A

<p>cysteine residues have thiol groups that form disulfide bonds under oxidizing conditions</p>

91
Q

<p>Describe globular proteins.</p>

A

<p>have non-repetitive second degree structures</p>

92
Q

<p>What is the tertiary structure of a protein?</p>

A

<ul><li>the folding of second degree structural elements</li><li>positions of each atom in a protein, including side chains</li><li>Where is every atom located in 3D space?</li></ul>

93
Q

<p>Describe the quaternary structure of proteins.</p>

A

<ul><li>more than one polypeptide chain</li><li>eg. dimer, trimer</li><li>geometry of association of multiple polypeptides</li><li>non-covalent associations</li></ul>

94
Q

<p>What is the hydropathy scale?</p>

A

<ul><li>(-4.5) - (4.5)</li><li>number rating how hydrophobic each amino acid is</li><li>larger = more hydrophobic</li></ul>

95
Q

<p>What are two examples of chaotropic agents?</p>

A

<p>urea, guanidinium</p>

96
Q

<p>What are intrinsically disordered proteins?</p>

A

<ul><li>unfolded</li><li>fold when in contact with their binding partner</li></ul>

97
Q

<p>When proteins fold, they go from \_\_\_\_\_\_\_ to \_\_\_\_\_\_\_</p>

A

<ul><li>high energy, high entropy</li><li>low energy, low entropy</li></ul>

98
Q

<p>Describe the process of protein folding.</p>

A

<ol><li>Secondary structural elements and local segments of second degree structure form (Rapid process)</li><li>Tertiary structure forms, second degree elements collapse to form tertiary structure (Slow process)</li></ol>

99
Q

<p>What chart illustrates protein folding?</p>

A

<ul><li>folding funnel</li><li>energy x entropy</li><li>local energy minima are the dips</li><li>the lowest point is the most stable native structure</li></ul>

100
Q

<p>What do chaperone proteins do?</p>

A

<ul><li>assist with protein folding when stuck in minima</li><li>eg. heat shock proteins (Hsp70/90)</li><li>many of these are ATPases that catalyze the hydrolysis of a phosphate to allow a reaction that would not otherwise occur happen</li></ul>

Biochemistry (12 decks)

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