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Biochemistry > Quiz Four > Flashcards

Quiz Four Flashcards

1
Q

What is denaturation?

A

Loss of structural integrity and activity

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2
Q

What are the different ways that proteins can be denatured?

A

Heat or cold
PH
Organic solvents
Chaotropic agents

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3
Q

What can be used to denature disulfide bonds?

A

2-mercaptoethanol

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4
Q

What is the ribonuclease refolding experiment?

A

2-mercaptoethanol and urea were added to ribonuclease
Ribonuclease was then denatured fully
When 2-mercaptoethanol and urea were removed from the solution, ribonuclease refolded with the correct disulfide bonds

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5
Q

Who conducted the ribonuclease refolding experiment?

A

Chris Anfinsen

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6
Q

What is levinthal’s paradox?

A

Proteins fold to the lowest energy state within seconds, however if proteins were to try every possible conformation it would take longer than the earth has been around

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7
Q

How can proteins fold to the correct conformation so quickly?

A 
Hydrophobic collapse (huge factor)
Hydrogen bonds
Electrostatic interactions
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8
Q

What catalyses disulfide bond interchange so the correct disulfide bonds can be formed?

A

Protein disulfide isomerase

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9
Q

What is used to refold misfolded proteins?

A

GroEL/ES chaperonin

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10
Q

How does the GroEL/ES chaperonin work?

A

Misfolded proteins will have their hydrophobic areas exposed, these areas will bind to GroEL
GroES binds to GroEL with a protein inside the pocket
Protein folds inside the structure and is then released because the hydrophobic areas will no longer be exposed

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11
Q

What are the functions of globular proteins?

A 
Storage of ions and molecules
Transport of ions and molecules
Muscle contraction
Defense against pathogens
Biological catalysis
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12
Q

What forces do ligands bind with?

A

Non-covalent forces
Hydrogen bonds
Electrostatic interactions
London dispersion forces

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13
Q

What is ka?

A

Association rate constant

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14
Q

What is kd?

A

Disassociation rate constant

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15
Q

What is Ka?

A

Equillibrium constant

ka/kd

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16
Q

What does the fraction of bound sites depend on?

A

Free ligand concentration and Kd

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17
Q

How can Kd be determined graphically?

A

Go to where Theta is equal to 0.5, from there go over until you intersect the graph and then go down to find the Kd value

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18
Q

What is Theta equal to?

A

[L] / ( [L] + Kd )

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19
Q

What is Kd equal to?

A

kd/ka

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20
Q

How is Kd and amount of ligands bound relate?

A

Higher the Kd, lower the binding

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21
Q

How are ligands and binding sites complentary?

A

Size
Shape
Charge
Hydrophobic/hydrophilic character

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22
Q

What is the lock and key model?

A

Assumes that complementary surfaces are preformed and fit together without any change

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23
Q

What is induced fit specificity?

A

Conformational changes may occur upon ligand binding so that they will fit together
Both the ligand and the protein can change conformation

24
Q

What are the benefits to induced fit specificity?

A

Allows for tighter binding

Can increase the affinity of the protein for a second ligand

25
Q

What is the main oxygen storage protein in mammals?

A

Myoglobin

26
Q

Why does Carbon Monoxide have such a higher binding affinity than Oxygen?

A

CO has a filled lone electron pair that can be donated to vacant d-orbitals on the Fe2+

27
Q

Why is Myoglobin not a strong O2 transporter?

A

Pressure of oxygen in the lungs is about 13 kPa
Pressure of oxygen in the tissue is about 4 kPa
The YO2 difference between these two values is not great enough to cause a high release of oxygen once myoglobin reaches the tissue

28
Q

Why is hemoglobin a better O2 transporter than myoglobin?

A

High affinity for O2 at higher pressure
Low affinity for O2 at lower pressures
Cooperativity

29
Q

What is cooperativity?

A

Multiple binding sites interact with each other

30
Q

What is positive cooperativity?

A

First binding event increases affinity at remaining sites

31
Q

What is negative cooperativity?

A

First binding event reduces affinity at remaining sites

32
Q

How can cooperativity be recognized on a graph?

A

Sigmoidal binding curves

33
Q

How does the structure of hemoglobin change when oxygen binds?

A

Oxygen binds to Fe2+ which causes it to transition to Fe3+
Ionic radius shrinks, electrons are pulled closer because of the additional positive charge
The Iron ion now fits in the protoporphyrin ring, pulling the His and F helix with it

34
Q

What state of hemoglobin favors oxygen binding?

A

Relaxed state

35
Q

Which subunits are more stable in the T state?

A

deoxyhemoglobin

36
Q

How is the transistion from the T state to the R state done?

A

Ion pairs between A1 and B2 interfaces are broken

37
Q

What effect does pH have on Hemoglobin binding to oxygen?

A

Oxygen binds well at a higher pH (lungs)

Oxygen releases well at a lower pH (tissues)

38
Q

What is the Bohr effect?

A

Increasing pH (removing protons) stimulates hemoglobin to bind to more O2

39
Q

What converts CO2 into HCO3+?

A

Carbonic anhydrase

40
Q

What does CO2 form when it binds with hemoglobin, where does it bind?

A

Forms carbamate

Binds on the amino terminal residue

41
Q

What type of graph does stripped blood resemble?

A

Hyperbolic curve

42
Q

What type of graph does whole blood resemble?

A

Sigmoidal curve

43
Q

What happens when CO2 is added to stripped blood?

A

Shifts it to the right

44
Q

What happens when BPG is added to stripped blood?

A

Shifts it to the right, more than CO2 does

45
Q

How does BPG decrease the binding affinity of oxygen to hemoglobin?

A

BPG binds to deoxyhemoglobin and stabilizes the T-state

46
Q

Why does high elevation affect oxygen delivery ability?

A

When at higher altitudes there is more BPG that is produced, this shifts the curve to the right, which decreases oxygen delivery
More BPG = more stable T-state
Long stays at high altitudes causes a decrease in oxygen binding in lungs but an increase in oxygen release

47
Q

What adaptation does fetal hemoglobin?

A

Fetal hemoglobin has a higher affinity for oxygen at lower pressures (shift graph to the left)
This allows the fetus to rip oxygen away from the parent

48
Q

Why does fetal hemoglobin have a higher affinity for hemoglobin than adult hemoglobin?

A

Fetal hemoglobin has a serine rather than a histidine
This removes a positive amino acid and replaces it with a neutral one
Less of a positive charge means the T-state is not as favored

49
Q

What are the two theories describing cooperative binding?

A

Symmetry or concerted model

Sequential model

50
Q

What is the symmetry or concerted model of cooperative binding?

A

An oligomer contains either R or T state conformational states
Never has both R and T state

51
Q

What is the sequential model of cooperative binding?

A

Conformational changes occur sequentially as more binding sites are occupied
Supported by the binding curve of hemoglobin, change in affinity throughout

52
Q

What happens in sickle cell anemia?

A

Deoxy hemoglobin forms are insoluble

53
Q

What is the only effective treatment for sickle cell?

A

Hydroxyurea

54
Q

What is the major physiological role of myoglobin?

A

Facilitate oxygen diffusion in muscle

55
Q

What is Yo2 equal to?

A

Fraction of O2 binding sites occupied by O2

YO2 = pO2 / (K + pO2)

56
Q

How is the bohr effect applicable in the human body?

A

pH difference between lungs and metabolic tissues increases the O2 transfer efficiency

57
Q

What is the amino acid change that produces sickle-cell?

A

Glu changes to Val

Biochemistry (4 decks)

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