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Biocheem > Lecture 15 > Flashcards

Lecture 15 Flashcards

1
Q

How are Quaternary Structures named?

A

By the number and type of subunits ex. 2 subunits is a dimer

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2
Q

What is a Homodimer?

A

A quaternary structure with two identical subunits

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3
Q

What is a Heterodimer?

A

A quaternary structure with two non-identical subunits

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4
Q

What stabilizes 4º strucutre?

A

The same forces as Tertiary structure
•Hydrophobic interactions
•H-bonds, ion pairs fine tune them

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5
Q

Where are Hydrophobic interactions predominant in quaternary structure?

A

Where the different subunits are in contact with each other in the overall tertiary structure

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6
Q

What kind of bonds are not necessary in Quaternary Strucutre?

A

Covalent bonds

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7
Q

What are the two subunits that hemoglobin contains?

A

Two alpha and two beta

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8
Q

What kind of Quaternary Structure can hemoglobin be described as?

A

A heterotetramer

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9
Q

What is the function of a protein determined by?

A

Its strucutre

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10
Q

What is the three-dimensional structure of a protein determined by?

A

Its 1º structure (the sequence of the amino acids in the polypeptide chain)

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11
Q

What kind of 4º is Myoglobin?

A

A monomer

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12
Q

What kind of 4º is Hemoglobin?

A

An Oligomer

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13
Q

What kind of Amino acids would we expect to be on the inside if a polypeptide structure?

A

Non-polar hydrophobic amino acids

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14
Q

What are both Hemoglobin and Myoglobin involved in?

A

Reversible oxygen binding

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15
Q

What does Hemoglobin in RBCs do?

A

Binds to O2 in the lungs and releases it in the tissues

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16
Q

Where does Myoglobin bind to O2?

A

Im muscles cells

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17
Q

What is the difference between oxygen binding of Hemoglobin and Myoglobin?

A

They bind to O2 with different affinities and under different conditions

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18
Q

What kind of cells is Myoglobin found in?

A

Myocytes

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19
Q

What is Myoglobin involved in in myocytes?

A

Transporting oxygen from the cell membrane to the mitochondria

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20
Q

What takes oxygen from the lungs to the peripheral tissue?

A

Hemoglobin

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21
Q

What acts as a local reserve of O2 during intense exercise?

A

Myoglobin

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22
Q

What stores O2 in aquatic animals?

A

Myoglobin

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23
Q

What kind of interaction is it when Myoglobin binds to oxygen?

A

Simple ligand binding

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24
Q

What is the equilibrium in free ligang binding?

A

There is an equilibrium of the ligand binding to the protein and the ligand-protein complex

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25
Q

What occurs in the dissociation process of the protein-ligand complex?

A

The protein-ligand complex dissociates into free protein and free ligand

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26
Q

What is Kd?

A

The dissociation constant

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27
Q

What is the equation of the dissociation constant?

A

The concentration of the the free ligand and the concentration of the free protein multiplied. This is all divided by the concentration of the ligand protein complex

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28
Q

What does it mean if the ligand has a strong affinity for the protein?

A

Dissociation is less favored because the complex is stable

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29
Q

How is Kd affected by affinity?

A

Kd gets smaller as affinity increases

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30
Q

How does Kd affect the stability of a protein ligand complex?

A

The smaller the Kd the more stable the protein ligand complex is

31
Q

What is on the X and Y axis of ligand binding curves?

A

The X axis is the concentration of the Ligand and the Y axis is the percent saturation of the Protein

32
Q

Why is there a Plateau on Ligand Binding curves?

A

Because there isn’t anymore protein to bind to that ligand and so the proteins are reaching 100% saturated

33
Q

What kind of approach is the plateau of a ligand binding curve?

A

An asymptotic approach

34
Q

Why does a Hyperbolic binding curve occur?

A

Because there is an unchanging affinity between the ligand and protein

35
Q

What is the Affinity like in Asymptotic Binding curves?

A

Affinity is constant

36
Q

Where is the Ligand Protein affinity not constant?

A

In Allosteric binding curves

37
Q

What is equal to the value of Kd?

A

50% bound to a particular ligand

38
Q

How is the %saturation affected by Kd?

A

The smaller the value of Kd the more you would expect to be bound to the protein at a particular concentration

39
Q

What would have a higher affinity in terms of ligand binding to a protein and Kd?

A

A lower Kd would have a higher affinity

40
Q

With what kind of affinity does myoglobin bind to oxygen?

A

With constant affinity

41
Q

What does Myoglobin bind to?

A

Oxygen

42
Q

What is the Tertiary structure of Myoglobin?

A

A single polypeptide chain (with alpha helices and irregular structure) that is associated with a heme prosthetic group

43
Q

How many helices are in the structure of myoglobin?

A

Eight helices (A through H)

44
Q

What is the prosthetic group in Myoglobin?

A

The heme group

45
Q

What is responsible for binding of the oxygen in Myoglobin?

A

The heme group

46
Q

What kind of molecule is heme?

A

It is an organic molecule that contains an organic molecule

47
Q

What is the shape of Heme?

A

It is circular and planar

48
Q

What is the polarity of heme?

A

For the most part it is quite hydrophobic with two polar/charged carboxyl groups so it is amphipathic

49
Q

What happens to the hydrophobic portion of heme?

A

It is tucked into a hydrophobic binding pocket

50
Q

What is exposed to solvent in Heme?

A

The two Propionyl groups (the groups containing carboxylic acids)

51
Q

Which myoglobin helices is the hydrophobic pocket found between?

A

Helices E and F

52
Q

Why is Heme a delocalized structure?

A

Because of its conjugated double bonds

53
Q

What level structure are prosthetic groups a part of?

A

Tertiary structure

54
Q

Where do the four nitrogens around the iron in heme come from?

A

The overall heme structure

55
Q

How many structures does the iron in heme have a preferred interaction with?

A

Six different coordinating structures

56
Q

Where do four of the places that the iron in heme bind with come from?

A

The Heme

57
Q

What is the 5th coordination position on heme occupied by?

A

A nitrogen in the side chain of histidine

58
Q

What is the Proximal histidine?

A

The histidine in the 5th coordination position of heme

59
Q

What is the 6th coordination position of heme occupied by?

A

Oxygen

60
Q

What is the Porphyrin ring held in place by?

A

Hydrophobic interaction by coordination bond between iron and a histidine

61
Q

What are the other names for the Proximal Histidine?

A

His 93

His F8

62
Q

What are the functions of the proximal histidine?

A
  • It is an additional binding interaction of heme into the binding pocket to make sure heme stays tightly associated with the polypeptide and doesn’t end up dissociating from the structure
  • Ensures the iron remains in the correct oxidation state for the binding of oxygen
63
Q

What is found in the 6th coordination position?

A

Oxygen

64
Q

What does is meant by histidine and oxygen coordinate the heme group?

A

The bind to the overall structure to prevent it from dissociating

65
Q

How does oxygen bound to heme coordinate the iron atom?

A

It uses one of its lone pairs and H bonds to an H bound to N on the distal histidine

66
Q

What are the other names for the Distal Histidine?

A
  • Histidine 64

* Histidine E7

67
Q

What does the distal histidine do?

A

Forms a H-bonding interaction with the oxygen atom at the 6th coordination position

68
Q

What happens every time we create a favorable interaction between the protein and ligand what is the result?

A

An increase in the affinity

69
Q

What is the function of the distal histidine binding?

A
  • Increases oxygen binding affinity
  • Lowers affinity for other molecules
  • Increases specificity for oxygen
70
Q

What is the affinity of carbon monoxide for the heme in relation to oxygen?

A

Carbon monoxide has a way higher affinity for heme than oxygen

71
Q

What is specificity?

A

Preference for binding one thing relative to another thing

72
Q

What other amino acids create specificity for the oxygen molecule besides the distal histidine?

A

Phe and Val

73
Q

What are the binding sites in myoglobin designed to do?

A

Optimize binding specificity and affinity

74
Q

What is the difference in binding between oxygen and carbon monoxide binding to the 6th coordination position?

A

O2 binds at an angle and carbon monoxide binds in a straight line and occupies the same place of E7 increasing specificity for oxygen

Biocheem (38 decks)

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