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Medical Physiology > Enzymology > Flashcards

Enzymology Flashcards

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USMLE® Step 1 flashcards
1
Q

From what are enzymes made?

A

Protein.

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2
Q

What are enzymes?

A

Biological catalysts.

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3
Q

What is the main function of enzymes?

A

They speed up reactions without being consumed in the process.

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4
Q

What do enzymes do?

A

They act on substrates to make products.

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5
Q

From what are enzymes consist of?

A

They have active sites in a specific shape which facilitate the shape of the substrate.

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6
Q

What does an active site of an enzyme contain?

A

Only a small number of amino acids.

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7
Q

What is a catalytic process?

A

The substrate binds to the active site before the enzyme can work.
Some of the active site amino acids are involved in substrate binding.
Other amino acids are involved in the catalytic process.
Then the substrate is converted into its products.
Then the products are released.

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8
Q

What are the enzyme-substrate interactions?

A

Very specific because, they have complementary shape, charge and hydrophobicity.

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9
Q

Why are the enzyme-substrate interactions very specific?

A

Because the enzymes can detect between very similar compounds.

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10
Q

Where are the the most selective enzymes found?

A

In the proofreading of gene transcription to make sure that mistakes are not made during DNA strand elongation.

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11
Q

Where are non-covalent interactions occur?

A

Between the enzyme and substrate.

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12
Q

What are the non-covalent interactions between the enzyme and substrate include?

A

Hydrogen bonds, ionic bonds and hydrophobic interactions.

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13
Q

What is the active site of an enzyme?

A

Flexible.

Its shape can be adjusted and moves the catalytic amino acids into place for the enzymes to work.

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14
Q

How do drugs work?

A

By binding to enzymes.

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15
Q

How does the drug “Novichock” work?

A

By binding acetyl choline esterase and preventing its action.
Acetylcholine does not break down in the synaptic cleft when is released.
It remains bound to the ‘ligand gated’ ion channels in a neurone.
The nerve is jammed on.
Paralysis and death are caused.

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16
Q

How do enzymes catalyse reactions?

A

They bring reactants together in the correct orientation.

They form reactions easier through transition-state stabilisation.

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17
Q

What is the original idea of how enzymes bring reactants together?

A

The enzyme is the clock.
The substrate fits in the rigid structure like a key.
They bind tightly.

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18
Q

But what does actually happen?

A

The active site and the substrates can change shape and distort.
‘Induced fit’ = The enzyme and substrate interact with each other and change shape, with the help of energy.

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19
Q

What can some enzymes have?

A

Co-factors.

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20
Q

What do co-factors include?

A 
Metal ions (Mg2+, Zn2+).
NAD+ (nicotinamide-adenine dinucleotide).
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21
Q

What are some co-factors?

A

Complex organic molecules.

Co-enzymes = haem group of haemoglobin.

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22
Q

What is a co-enzyme called when it is tightly bound?

A

A prosthetic group.

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23
Q

What do enzymes not do?

A

They do not change the endpoint or equilibrium of the reaction.

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24
Q

What are the biological reactions?

A

Thermodynamically spontaneous.
The energy state of the reactants is higher than the energy state of the products.
They do not occur ‘spontaneously’.
They require energy input to occur.

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25
Q

What is the activation energy?

A

The amount of energy that is provided to compounds for the reaction to proceed.
Reactants + Energy –> Products

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26
Q

What is needed for glucose and oxygen to turn into carbon dioxide and water?

A

An ‘energy barrier’ to overcome.

Sometimes it is the form of heat.

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27
Q

How do we overcome activation energy to drive a reaction?

A

We can use catalysts = enzymes.

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28
Q

What do enzymes do?

A

They bring the substrates close together.
Or they change their shape.
And then they reduce the activation energy required for a reaction to proceed.

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29
Q

What do enzymes do in a reaction?

A

They make reactions possible that otherwise would not be feasible.

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30
Q

What happens with nitrogen fixation?

A

The industry raises the temperature to 550 degrees, at 250 times atmospheric pressure and uses an iron catalyst.

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31
Q

When do bacteria can speed up their reactions?

A

At atmospheric pressure only 5-30 degrees.

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32
Q

How is the measurement of enzymes called?

A

Assaying.

33
Q

What should we be able to do when we study and exploit an enzyme?

A

Assay = measure its activity.
Measure the product formation.
Or measure the substrate consumption.
It can be done directly or indirectly.

34
Q

What does direct measurement mean?

A

Measuring the ‘normal’ reaction catalysed by the enzyme.

Example: Lactate dehydrogenase uses NAD+ and lactate to produce NADH and pyruvate.

35
Q

How can the reduction of NAD+ to NADH be measured?

A

In a spectrophotometer at 340 nm.
The wavelength of light the chemicals absorb changes during the reduction.
Or a coloured compound can be used as an alternative to the substrate.
Example: Alkaline phosphatases uses p-nitrophenyl phosphate as substrate analogue and the absorbance is changed to 405nm.

36
Q

How is the reaction measured in an indirect measurement?

A

By using a secondary reaction.
Example: The reaction catalysed by Alanine aminotransaminase catalyses Cahill cycle through which muscle gets rid of ammonium ions.
Alanine and α-ketoglutarate react to produce pyruvate and glutamate.
We measure the rate of pyruvate production by coupling it to the absorbance change during oxidation of NADH to NAD+.

37
Q

What can assays be?

A

Continuous.

Or stopped.

38
Q

What do we do in a continuous assay?

A

We take measurements as the assay progresses in a spectrophotometer.

39
Q

What do we do in a stopped assay?

A

The reaction is stopped.

A single measurement is made with an appropriate analytical technique.

40
Q

How do we calculate the rate of reaction?

A

We measure absorption over time.

41
Q

How does the reaction proceed?

A

It proceeds quickly.
When it is out of substrate.
Or when it is inhibited by the products it makes.
The reaction slows down.

42
Q

How can we calculate the reaction rate when it is linear in the early phase?

A

From the gradient.

With a single measurement.

43
Q

How can we calculate the reaction rate after 4mins?

A

By dividing y value by minutes on x.
We get the rate in absorbance unit per minute.
y/x.

44
Q

What happens to the rate of the reaction as the concentration of the enzyme increases?

A

It increases.
More enzyme substrate complex can form.
The product concentration increases rapidly.

45
Q

On what does the rate of the reaction depend?

A

The enzyme substrate complex = ES.

46
Q

How can imagine people and taxi in a reaction?

A

People = substrate.
Taxi = enzyme.
People in taxi = ES complex.
More taxis –> more people arrive faster.
More taxis than people = speed is not limited by people.
More people than taxis = speed slows down.

47
Q

What happens when substrate increases in a reaction?

A

More enzyme substrate complex is formed.
Reaction happen quicker.
Reaction rate increases and plateaus when all active sites are all occupied.

48
Q

What happens when all the active sites are available?

A

They all form ES.

49
Q

What happens when the active sites are full as substrate increases?

A

No more ES can form.

The reaction rate decreases.

50
Q

On what does the shape of the graph depend in a reaction?

A

On how well the enzyme and substrate bind together.

And how fast the ES complex is converted to product.

51
Q

What is the Maximum Velocity or Vmax?

A

The maximum rate that an enzyme can convert substrate to product.

52
Q

What is the Michaelis

constant Km?

A

The measure binding between enzyme and substrate.

53
Q

How does Km be measured?

A

By finding the substrate concentration that gives the half maximum initial velocity.

54
Q

What is the relationship between Km, Vmax, [S] and initial rate of reaction (Vi)?

A

Michaelis Menten equation = describes an enzyme catalysed reaction where there is only one substrate and no product inhibition.
Helps to predict how drugs and toxins affect enzymes and stop them from working.
Helps researchers decide if a molecule will work as a drug.

55
Q

Why sometimes it is not possible to reach Vmax in experiments?

A

Because of the solubility of the substrate.

56
Q

How can we work out the problem of measuring the Vmax accurately sometimes?

A

By using Linear plots and exploring the fit to the data.

57
Q

What can Linear plots show to us?

A

The estimation of Km and Vmax based on the Michaelis Menten equation.

58
Q

Which one is the most common Linear plot?

A

The Lineweaver Burk plot (double reciprocal).
We rearrange the equation and we find the reciprocal.
Vi becomes 1 over vi.
Equation: y=mx+c : for a straight line.

59
Q

What does the Lineweaver Burk Plot equation shows, y=mx+c?

A 
C = 1/Vmax
M = gradient = Km/Vmax
X = 1/substrate 
Y = 1/Vi
We can measure Vi and substrate concentration to derive the rest.
60
Q

What does the plot look like?

A

X axis = 1/substrate
Y axis = 1/Vi
1/Vmax = line crosses y axis
-1/Km = line crosses x axis.

61
Q

What can you workout by using the Lineweaver Burke plot?

A

Vmax and Km.

First convert 1/Km into Km and 1/Vmax into Vmax.

62
Q

How can we modify the rate of an enzyme reaction?

A

By using activators and inhibitors.

63
Q

How can the enzyme activity be modified?

A

By using reversible or irreversible inhibitors.

Through allosteric control and reversible covalent modification.

64
Q

How do irreversible inhibitors work?

A

They react with the active site.
Prevents substrate binding.
Then they destroy permanently the enzyme activity.
Inhibition is not comforted by adding excess substrate.
Examples: Fluorouracil –> inhibitor of thymidylate synthase and anticancer drug.
DFP (di-isopropyl phosphofluoridate) –> a nerve gas and an acetylcholine esterase inhibitor, like Novichock.
Sarin –> an inhibitor of acetylcholine esterase.
Malathion –> inhibits acetylcholine esterase, used as insecticide.

65
Q

How do reversible inhibitors work?

A

They bind reversibly to the active site, or another part of the enzyme.

66
Q

What can be a reversible inhibitor?

A

Competitive
Non-competitive
Uncompetitive

67
Q

What happens in competitive inhibition?

A

The substrate and inhibitor bind to the same site.
Increased substrate concentration can overcome inhibition.
Km is affected, increases = affinity of enzyme.
Vmax = max rate the enzyme can work, is not affected.
Example: When antifreeze is used by the Russian mafia to kill people. Ethylene glycol is catalysed by alcohol dehydrogenase and produces oxalic acid. Excess enzyme competes ethylene glycol.
Km app = apparent Km.
(I) = [inhibitor]
Km app = Km x ( 1 +[ (I) / Ki] ).
Ki = inhibitor constant –> how strong it is. Concentration required to produce half maximum inhibition.

68
Q

What happens in non- competitive inhibition?

A

Inhibitor binds the enzyme.
Prevents catalytic reaction.
Does not stop the substrate binding to the enzyme.
It cannot be overcome by extra substrate.
Vmax is affected, reduces= reaction rate is reduced.
Km is not affected.
Vmax app = Vmax x (1 + [ (I) / Ki ] ).

69
Q

What is an allosteric regulation?

A

A regulation by molecules when they bind somewhere other than the active site.

70
Q

What do allosteric compounds do?

A

They alter the affinity of the enzyme for the substrate.

Increase or decrease its activity.

71
Q

What are the Aspartate transcarbamoylasecatalyses ?

A

The first step in pyrimidine biosynthesis.

72
Q

What is the end point pf the pyrimidine biosynthesis pathway?

A

Cytosine triphosphate (CTP).

73
Q

What is CTP?

A

An allosteric inhibitor of enzyme.
A pyrimidine.
A negative feedback loop = product inhibits enzyme.

74
Q

What is ATP?

A

A purine.

An allosteric activator.

75
Q

What is a reversible covalent modification?

A

The addition of phosphate catalysed by a protein kinase.

Or removal of phosphate catalysed by a phosphatase.

76
Q

What do modifying enzymes do?

A

Control.

77
Q

How can enzyme activity be controlled?

A

By the binding of inhibitors or activators.

By the reversible covalent modification.

78
Q

What are the types of inhibitors?

A

Irreversible
Reversible
Allosteric

Medical Physiology (12 decks)

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