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BMS 102 > Enzymes > Flashcards

Enzymes Flashcards

1
Q

What is an enzyme

A

A highly specific protein that functions as a biological catalyst in order to speed up biochemical reactions

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2
Q

One of the fastest enzymes known is

A

Carbonic anhydrase

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3
Q

What is enzyme specificity due to?

A

Precise interactions of substrate with enzyme (precision due to 3D structure of enzyme)

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4
Q

What are the six classes of enzymes

A
  1. oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases
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5
Q

Oxidoreductases

A

Catalyze oxidation-reduction reactions

  • transfer electrons between molecules
    ex. lactate dehydrogenase

*these reactions require the coenzyme NAD

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6
Q

Transferases

A

Catalyze the transfer of functional groups between molecules

-ex. alanine transaminase

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7
Q

Hydrolyases

A

Catalyze hydrolysis by cleaving molecules by the addition of water
ex. trypsin and pyrophosphatase

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8
Q

Lyases

A

Catalyze the addition of atoms or functional groups to a double bond OR removes them to form a double bond

ex. fumarase

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9
Q

Isomerases

A

Catalyze the movement of functional groups within a molecule
~generally the simplest enzymatic reactions as only 1 substrate and 1 product
“iso” = same, so within the SAME molecule

ex. alanine racemase

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10
Q

Ligases

A

Catalyze bond formation or joining two molecules at the expense of ATP

ex. DNA ligase or glutamine synthetase

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11
Q

What is an enzyme without its co-factor?

A

An apoenzyme

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12
Q

What is the name of a complete catalytically active enzyme?

A

A holoenzyme

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13
Q

Co-factors can be:

A
  1. small organic molecules derived from vitamins called coenzymes or
  2. metals
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14
Q

What are tightly bound coenzymes called?

A

Prosthetic (helper) groups

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15
Q

Enzymes may speed up a chemical reaction but properties of the reaction (for example if it occurs at all) depends on _____

A

Free energy differences

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16
Q

What is free energy (G)

A

Measure of useful energy

-the ability to do work

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17
Q

What is the free energy change of a reaction? delta G

A

Informs us as to whether a reaction can take place spontaneously

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18
Q

A reaction can take place spontaneously is delta G is…

A

Negative (exergonic)

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19
Q

A reaction cannot take place spontaneously if delta G is…

A

Positive (endergonic)

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20
Q

When is delta G zero?

A

At equilibrium there is no net change in concentration of products and reactants, so delta G is 0

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21
Q

T/F delta G provides information about the rate of a chemical reaction

A

False

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22
Q

Can enzymes alter the equilibrium of a chemical reaction

A

No

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23
Q

X‡ is?

A
  • an unstable arrangement of atoms – chemical bonds are in the process of being broken or formed
  • called a Transition State – it has higher ∆G than does S or P
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24
Q

What is the function of an enzyme?

A

lower the ∆G‡ OR facilitate the formation of the transition state

25
Q

What is at the heart of enzyme catalysis

A

Stabilization of the transition state

26
Q

Enzyme do’s

A
  • lower the ∆G‡ for the reaction
  • Stabilise the Transition State
  • Make the forward reaction much more favourable
27
Q

Active site

A
  • Is a 3D cleft or crevice
  • Small part part of the total volume of an enzyme
  • The substrates bind to the active site on an enzyme by multiple weak attractions
  • Binding specificity depends on precisely defined arrangements of atoms in the active site
28
Q

Lock and Key Theory

A

Enzyme is a rigid template (lock) and the substrate is a matching key

  • Active site of the enzyme is complementary in shape to the substrate
  • This theory says that the active site resides are completely immobile
29
Q

Induced fit theory

A

This theory takes the flexible nature of protein structure into account
-The active sites some enzymes assume a shape that is complementary to that of the substrate only AFTER the substrate has been bound

*INDUCED FIT b/c the enzyme and substrate slightly change shape to suit each other after they bind

30
Q

Binding energy…when is maximal binding energy released

A
  • The weak interactions between complementary enzyme and substrate
  • Only when the enzyme facilitates formation of the transition state
31
Q

Transition state analogues

A
  • Potent inhibitors of enzymes

- Very unstable

32
Q

Kinetics

A

Study of the rates of chemical reactions

33
Q

Velocity (V)

A

The quantity of reactant, A, that disappears in a specified unit of time, t.

Velocity is directly related to concentration of A by a constant, k, called the rate constant

V=k[A]

34
Q

First-order reactions

A

Reactions in which V is directly proportional to reactant concentration

  • have the unit s^-1
  • the initial rate of reaction doubles when the reactant is doubled
35
Q

Second-order reactions

A

Involve two reactants and have the units M^-1s^-1

-the initial rate of the reaction quadruples when the reactant is doubled

36
Q

Michaelis-Menten Model

A

Initial velocity rises linearly as [S] increases and then begins to level off (plateau)

v0 (initial velocity)= the rate of increase in product with time when [P] is low
–measured for each substrate concentration by measuring the rate of product formation before P accumulates

37
Q

Km

A

Michaelis constant… is unique to each enzyme and independent of enzyme concentration

Is equal to substrate concentration at which the reaction velocity is half is maximum value (half of the active sites are filled)

values depend on environmental conditions

38
Q

Vmax

A

Directly dependent on enzyme concentration and can only be attained when all the enzyme is bound to substrate
-tells us about the turnover number of an enzyme

39
Q

Low Km value

A

Tight substrate binding

40
Q

Turnover number of an enzyme

A

Number of substrate molecules that an enzyme can convert into product per unit time when the enzyme is fully saturated with substrate

Kcat

41
Q

Kcat/Km =

A

Measure of catalytic efficiency

42
Q

Lineweaver-Burk plot

A

Graph of the reciprocal of both sides of the michaelis-menten equation

43
Q

Sequential reactions

A

All substrates must bind to enzyme before any product released
*can either be ordered or random

44
Q

Double displacement reactions

A

One or more products are released before all substrates bind enzymes
-substrates/products bounce on and off an enzyme (like a ping-pong ball)

45
Q

Allosteric enzymes

A

Enzymes that regulate the flux of biochemical compounds in metabolic pathways

  • Have a second regulatory site (allosteric site), which is distinct from the active site
  • catalyze the committed step of metabolic pathways
  • DO NOT CONFORM TO MICHAELIS-MENTEN KINETICS
  • activators can lower Km, inhibitors can raise Km
46
Q

How do feedback inhibitors work?

A

They bind to a distinct regulatory site on the allosteric enzyme

47
Q

Phosphofructokinase

A

Catalyzes the committed step in glycolysis

-ATP acts as an allosteric inhibitor while fructose 1,6-biphosphate acts as an allosteric activator

48
Q

What are the four mechanisms that enzymes use to form the transition state

A
  1. covalent catalysis
  2. acid-base catalysis
  3. metal ion catalysis
  4. stabilization of the transition state
49
Q

Covalent catalysis

A

Active site contains a reactive group (usually powerful nucleophile) that becomes temporarily covalently modified during catalysis.

50
Q

Acid-base catalysis

A

A molecule other than water plays the role of a proton donor or acceptor (e.g. chymotrypsin uses a histidine residue as a base catalyst to enhance nucleophilic power of serine

51
Q

Metal ion catalysis

A
  1. can bind substrates to increase binding energy
  2. may generate a nucleophile by increasing acidity of a nearby molecule
  3. stabilize or shield negative charges by acting as an electrophilic catalyst
52
Q

Metalloenzymes

A

Contain tightly bound metal ions (usually Fe 2+, Fe3+, Zn 2+)

53
Q

Metal activated enzymes

A

Contain loosely bound metal ions (usually Na+, K+, Mg 2+, or Ca2+)

54
Q

What is the optimal pH for most enzymes?

A

Between 5 and 9

55
Q

3 main types of reversible inhibition

A
  1. competitive
  2. uncompetitive
  3. noncompetitive
56
Q

Competitive inhibition

A
  • the inhibitor usually resembles the substrate and binds only to free enzyme (not the ES complex)
  • competitive inhibitor reduces the proportion of enzyme molecules bound to the substrate thus decreasing catalysis
  • Has no effect on Vmax but increase Km
57
Q

Uncompetitive inhibition

A
  • inhibitor binds only to the ES complex NOT the free enzyme
  • decreases Vmax and decreases Km
58
Q

Noncompetitive inhibition

A
  • inhibitor can bind simultaneously with the substrate to the enzyme at different binding sites
  • can bind to both free enzyme and the enzyme-substrate complex
  • decreases Vmax and Km does not change
59
Q

Irreversible inhibition

A

-inhibitors form stable covalent bonds with the enzyme

BMS 102 (5 decks)

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