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

Mb and Hb, & Proteins (Final) Flashcards

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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
What does a lower P50 value indicate?
higher affinity to O2 | - less oxygen pressure is required for 50% of Mb to be bound to O2
26
What is the equation for fractional saturation for Mb?
YO2 = (pO2) / (P50 + pO2)
27
How is YO2 affected in Mb when there are lower pO2 levels?
When pO2 levels are low, and they change there is a more dramatic change in Yo2
28
When is O2 released?
As pressure changes from arterial to venous blood
29
How much O2 is released when Mb travels from arterial to venous blood?
- 6% of bound oxygen is released | - not very efficient at releasing oxygen in our venous system
30
What is hemoglobin primarily responsible for?
- responsible for O2 transport in blood | - found in red blood cells
31
Describe the makeup of RBCs.
- 34% of their weight is hemoglobin | - they do not have a nucleus or organelles
32
What is the general structure of hemoglobin?
alpha2 beta2 tetramer
33
Describe the similarity of the alpha and beta subunits.
- between alpha and beta there is little 1 degree sequence homology, but high structural similarity (tertiary structures are similar)
34
How does O2 binding impact hemoglobin?
O2 binding causes a dramatic structural change
35
What occurs when crystallized deoxy Hb is exposed to O2?
The change in structure will cause it to shatter
36
What structural changes occur when deoxyhemoglobin turns into oxyhemoglobin (oxygen binds)?
- beta subunits move closer together - contacts between alpha1-beta2 and alpha2-beta1 change - there is 15 degree rotation of the alpha beta dimer
37
Describe the O2 - Mb binding (general).
- hyperbolic O2 binding curve | - non-cooperative (each binding event is independent of the other)
38
Describe the O2 - Hb binding (general).
- sigmoidal O2 binding curve | - cooperative binding (binding at one site affects other sites)
39
Describe the sigmoidal binding curve.
- high oxygen bound at high PO2 - low oxygen bound at low PO2 - releases O2 when at low arterial pressure
40
What is the hill equation?
- Equation that describes YO2 for hemoglobin
41
What type of binding curve does Hb follow?
Sigmoidal
42
What is the Hill coefficient and what does an increase Hill coefficient indicate?
- the value of n increases with the degree of cooperativity
43
What is n = 1, n > 1, and n < 1?
- 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
What is the linear hill equation?
45
For a linear hill equation, what is the slope and what are the x and y intercepts?
- slope = n - y-intercept = -nlogP50 - x-intercept = logP50
46
What is the y-axis and the x-axis in an hill graph?
``` y-axis = log(Yo2 / (1 - Yo2)) x-axis = logpO2 ```
47
What are the 3 zones of Hb linear hill graph?
``` 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
How is binding at one site affected by binding at another?
- binding information is transferred from one site to another through protein movement - conformational changes
49
What is T and R Hb?
T - no O2, deoxyHb | R - O2 bound, oxyHb
50
What structural changes occur in the T-R transition?
- 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
What structural changes occur in the T-R transition?
- 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
What 3 things affect T ->R transition?
- pH (Bohr effect) - CO2 levels - BPG
53
Explain the Bohr Effect.
- 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
What are the two ways that CO2 levels can affect T - R?
- the Bohr Effect (pH) | - covalent modification
55
What is the acid/base reaction that occurs in our blood and what is it catalyzed by?
[CO2] [HCO3-] + [H+] | This conversion is catalyzed by carbonic anhydrase
56
Describe CO2 levels in the muscle and how this impacts T - R.
- 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
Describe CO2 levels in the lungs and how this impacts T - R.
- 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
Explain covalent bonding of CO2 in Hb.
- 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
Which state of Hb is more likely to be modified by Hb binding of CO2?
T-state
60
Which state of Hb does BPG bind to and why?
- binds to T state | - T - R transition narrows binding pocket so BPG can no longer fit
61
How does BPG bind to Hb?
non-covalently
62
How do high levels of BPG impact T - R equilibrium?
- Increase in BPG increases the T-state | - BPG binds to the T state and causes the equilibrium to shift towards the T - state
63
What happens to our blood at high altitude?
- 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
Describe the structural differences in fetal hemoglobin.
- 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
Describe the different function of fetal hemoglobin.
- 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
What is the mutation in sickle cell anemia?
- 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
What is sickle cell Hb called?
Hbs
68
What must heterozygous sickle cell patients have? Homozygous?
Heterozygous - trait | Homozygous - disease
69
When does aggregation of Hb molecules occur in sickle cell disease?
When O2 levels are low
70
How are sickle cell patients treated and what does this do?
- treated with hydroxyurea which increase expression of fetal Hb - can replace deficient betaS form
71
What do sickle cell heterozygotes have?
protection from malaria
72
Explain how heterozygotes have protection from malaria.
- 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
What is the allosteric effect?
- binding of a ligand at one site affects binding of another ligand at a different site
74
What are the two models for the allosteric effect?
symmetry model and sequential model
75
What is the symmetry model?
- the 4 subunits can only exist as 4 in the T-state or 4 in the R-state
76
What is the sequential model?
- binding in one section causes small conformational changes in adjacent subunits
77

What value describes the conformation of a polypeptide backbone?

Torsion angles

78

What are the two torsion angles of a polypeptide backbone?

⍦ - C-C bond

∅ - C-N bond

-amide bond has little rotation because it is planar and has some double bond character

79

What is a Romachandran diagram?

  • indicates allowed conformations for a polypeptide (due to side chains only certain are allowed)
  • ⍦ vs ∅ plotted
80

What are the two exceptions to the romachandran diagram?

Proline and glycine

81

Describe proline's torsion angles.

  • ∅ values are restricted to -60
  • 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
  • more restrained motion
82

Describe glycine's torsion angles.

  • less steric hinderance, allowed angles are greater
  • no R group, just 2 Hs
83

Describe the structure of a typical alpha helix.

(handed, residues, pitch, bonds, side chains)

  • right handed helix
  • 3.6 amino acids/residues per turn
  • pitch (distance covered per turn) = 5.4Ă
  • carbonyl (C=O) of Nth residue is hydrogen bonded to the N-H of the N+4th residues
  • side chains point outward and downward
84

How are beta sheets stabilized?

-held together by H-bonds

-H-bonds are between neighboring polypeptide chains

85

What are the two types of beta sheets?

parallel and antiparallel

86

Describe parallel beta sheets.

  • polypeptides run in the same direction (N-C) and (N-C)
  • H-bonds between the strands are angled
  • the crossover connection between strands is longer and goes out of the plane
87

Describe antiparallel beta sheets.

  • polypeptides run in opposite directions (N-C) and (C-N)
  • H-bonds between the strands are parallel
  • the crossover connection between strands is shorter and on the same plane
88

What are the two classes of proteins?

  • fibrous and globular
89

Describe fibrous proteins.

  • have repeating second degree structures
  • are structural proteins: hair, nails, muscle tendons
  • keratin and collagen are examples
90

How are disulfide bonds formed?

cysteine residues have thiol groups that form disulfide bonds under oxidizing conditions

91

Describe globular proteins.

have non-repetitive second degree structures

92

What is the tertiary structure of a protein?

  • the folding of second degree structural elements
  • positions of each atom in a protein, including side chains
  • Where is every atom located in 3D space?
93

Describe the quaternary structure of proteins.

  • more than one polypeptide chain
  • eg. dimer, trimer
  • geometry of association of multiple polypeptides
  • non-covalent associations
94

What is the hydropathy scale?

  • (-4.5) - (4.5)
  • number rating how hydrophobic each amino acid is
  • larger = more hydrophobic
95

What are two examples of chaotropic agents?

urea, guanidinium

96

What are intrinsically disordered proteins?

  • unfolded
  • fold when in contact with their binding partner
97

When proteins fold, they go from _______ to _______

  • high energy, high entropy
  • low energy, low entropy
98

Describe the process of protein folding.

  1. Secondary structural elements and local segments of second degree structure form (Rapid process)
  2. Tertiary structure forms, second degree elements collapse to form tertiary structure (Slow process)
99

What chart illustrates protein folding?

  • folding funnel
  • energy x entropy
  • local energy minima are the dips
  • the lowest point is the most stable native structure
100

What do chaperone proteins do?

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

Biochemistry (12 decks)

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