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Intro to Biochemistry > 12 and 13 Enzymes and their mechanisms > Flashcards

12 and 13 Enzymes and their mechanisms Flashcards

1
Q

What does a catalyst do?

A

A catalyst reduces the activation energy (Ea), also called the free energy of activation (ΔGdagger). The catalyst provides an alternate route of reaction and can put reactants in the correct orientation, the catalyst is not changed in the reaction.

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2
Q

What are two ways for improving the likelihood that a reaction will proceed?

A

Increasing the temperature, pressure and using a metal catalyst. These things either add energy or put material in the correct orientation.

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3
Q

Why do living systems use catalysts? Why do they then use enzymes for catalysts?

A

Living systems use catalysts because raising the temperature may damage structures. They use enzymes because many free metals are harmful to the organism. Also enzymes are very specific for their substrate.

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4
Q

How much can a enzyme increase a reaction rate?

A

Up to 10^7 to 10^19

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5
Q

What is free energy of activation?

A

The amount of energy to convert 1 mol of substrate (reactant) from the ground state to the transition state

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6
Q

What is the active site of an enzyme?

A

A site on an enzyme that binds the substrate. it has amino acid side chains that actively catalyze and it can optimally orient the substrate to achieve the transition state at a lower energy.

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7
Q

What are the two models of enzyme binding to substrate?

A

Lock and key

Induced fit

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8
Q

What are two non-protein components that often allow enzymes to function?

A

Cofactors (ions)
Coenzymes (complex organic molecules)

Coenzymes facilitate the binding of substrate to enzyme

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9
Q

What are holoenzymes?

A

Intact functional enzymes with cofactors (prosthetic groups)

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10
Q

What is a enzyme called which has only its protein component (no cofactor/prosthetic groups)?

A

Apoenzyme

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11
Q

What is the lock and key model of enzyme-substrate binding?

A

Proposed by Emil Fischer, each enzyme binds toa single type of substrate because the active site and the substrate have complementary structures. Shape and charge distribution allows interaction.

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12
Q

What is the induced fit model of enzyme-substrate binding?

A

Flexible structure of protein taken into account, substrate does not fit precisely at first. Non-covalent interactions between the enzyme and substrate causes a conformation change in the enzyme that llows the active site to change its shape to that of substrate.

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13
Q

Do enzymes bind to many substrates?

A

No, there are only a few known samples where an enzyme moonlights for another substrate.

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14
Q

What are the six major categories of enzymes?

A
  1. Oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. ligases
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15
Q

What is the rate/velocity of a reaction

A

The change of a concentration of reactant or product per unit time

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16
Q

What is initial velocity (Vo)?

A

The velocity at the beginning of a reaction when the concentration of substrate greatly exceeds enzyme concentration

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17
Q

What are enzyme kinetics?

A

Information about rates, the quatitative study of enzyme catalysis as well as the enzyme affinity for substrates and inhibitors

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18
Q

What are first order reactions? What is the rate equation?

A

Determined experimentally. A unimolecular reaction (no collision is required). The rate equation is rate=k[A]

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19
Q

What is half life

A

The time for one-half of the reactant molecules to be consumed

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20
Q

What are second order reactions and their rate equation?

A

Bimolecular reactions with two substrates (eg. A+B = P).

Rate=k[A][B]

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21
Q

What is a zero order reaction?

A

The rate is not affected by adding more substrate, enzyme active sites are saturated. It is the point on a reaction coordinate graph where the line flattens out horizontally

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22
Q

What is the concept of enzyme-substrate complexes and who developed it? What is the equation and the three contants?

A

Michaelis-Menten kinetics explains the formation and dissociation of the Enzyme-Substrate Complex (ES). It goes like this:

E + S ⇌ ES -> E + P

E - Enzyme
S - Substrate
ES - Enzyme-substrate complex
P - Product

There are three rate constants for this formation and dissociation.

k1 - Rate constant for ES formation (E + S -> ES)

k-1 - Rate constant for ES dissociation (ES ⇌ ES E + S)

k2 - Rate constant for product formation and release from the active site (ES -> E + P)

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23
Q

What is the equation for the rate of formation of ES

A

Rate of formation of ES = k1[E][S]

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24
Q

What is the equation for the rate of ES dissociation?

A

Rate of ES dissociation = (k-1 + k2)[ES]

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25
Q

What is the steady state assumption?

A

The steady state assumption states that the rate of formation of ES is the same as its dissociation

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26
Q

What is the Michaelis constant (Km)

A

The lower Michaelis constant, the greater the affinity of the enzyme for its substrate

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27
Q

Vmax is?

A

Vmax is the maximum velocity that a reaction can attain

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28
Q

What is kcat k(cat) (catalyst constant) and what is the equation for it?

A

The catalytic constant is the number of substrate molecules converted to product per unit time. Kcat=(Vmax)/[Et]

[Et] = total enzyme concentration

It can also be thought of as the maximum capacity for a particular enzyme or the turnover number

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29
Q

What is the specificity constant and its equation? What is it used for?

A

The specificity constant is a measure of efficiency for an enzyme. It is the relationship between Kcat and Km (reaction speed and binding affinity).

Specificity constant = Kcat/Km

Specific activity is a measure used to identify enzyme purification

30
Q

What is the Michaelis-Menten equation?

A

v = (Vmax x [S]) / ([S] + Km)

31
Q

What is a Lineweaver-Burk plot?

A

A Lineweaver-Burk plot is a graph made using the reciprocal (eg. 1/x) of the Michaelis Menten equation. This gives a more accurate determination of the values.

32
Q

What is the slop of a Lineweaver-Burk plot line?

A

Km/Vmax

33
Q

What is the Y intercept of a Lineweaver-Burk plot

A

1/ Vmax

34
Q

What is the X intercept of a Lineweaver-Burk plot?

A

-1/Km

35
Q

What are two types of multisubstrate reactions with enzymes?

A

Sequential
The reactions cannot proceed until all the substrates are bound to the enzyme active site. It is ordered (first and then second) or random (third then second than fourth etc.).

Double-displacement reactions
The first product is released before second substrate binds. The enzyme is altered by first phase of the reaction.

36
Q

What are the steps of a double-displacement multisubstrate enzyme reaction?

A

The side chains of enzyme involved make a covalent bond with substrate (covalent catalysis). It reacts with the enzyme so that the product is bound to the enzyme. The second substrate comes along and a transient modification of the enzyme occurs. This leaves the two substrates as product and the enzyme is returned to its old normal whole.

37
Q

Is enzyme inhibition reversible?

A

It can be. There are reversible inhibitions that can be counteracted by increasing substrate levels or by removing the inhibitor. There are also irreversible inhibitions that occur when the inhibitor permanently impairs the enzyme (usually by a covalent interaction).

38
Q

What are three types of reversible inhibitions on enzymes?

A

Competitive
Noncompetitive
Uncompetitive

39
Q

What is reversible competitive inhibition in enzymes?

A

It is the most common type of reversible inhibition. The inhibitor competes with the substrate for the active site, the inhibitor has a similar structure to the substrate to complete this by binding reversibly to the active site. This slows down the reaction, but by putting enough substrate it can still reach the same Vmax as if it were uninhibited but with different Km and therefore lower specificity constant (less efficient)

Competitive inhibitors and the enzyme for the enzyme-inhibitor complex (EI)

40
Q

What is reversible noncompetitive inhibition for enzymes?

A

A non competitive inhibitor binds reversibly to a non-active site place on the enzyme and makes the active site less efficient. This site is usually distal and on the surface of the enzyme, causes a change in conformation. With noncompetitive inhibition the enzyme can never get to the same Vmax, but it can get the same Km because no competition for binding site. Forms a EI +S and EIS complex

41
Q

What is uncompetitive inhibition?

A

A type of noncompetitive inhibition where there is binding only after the substrate is bound (eg. it is ineffective at low substrate concentrations)

42
Q

How can you distinguish competitive, noncompetitive and uncompetitive inhibition from one another?

A

By using a kinetic analysis of enzyme inhibition using double-reciprocal plots

43
Q

What type of enzymes do Michaelis-Menten kinetics not apply to?

A

Allosteric enzymes, they have a signoidal curve rather than a hyperbolic one.

44
Q

What is macromolecular crowding and its implications?

A

Heterogenous filling in cells that impede molecular movement. This has a non-predictable effect on equilibriums, reaction rates, increased protein folding etc.

45
Q

What are three methods to understand catalytic mechanisms of enzymes?

A

X-ray crystallography, chemical inactivation and computer modeling

46
Q

What is a reaction mechanisms?

A

It is a step-by-step description of a reaction showing the electron flow from nucleophile to electrophile

47
Q

What are some common reactive intermediates during the course of a reaction?

A

Free radicals
Carbocations
Carbanions

48
Q

What is the effect of stabilizing the transition state?

A

Stabilizing the transition state will decrease the energy of that state and therefore decrease energy of activation and increase reaction rate

49
Q

What are the three most important factors (effects) of enzyme catalysis?

A

Proximity effects
Strain effects
- Proximity of functional groups to the active site creates an non-covalent interaction (strain) which might change the conformation of the substrate
- Straining might effect electrostatic bonds, it can remove the hydration shell around interacting species

Electrostatic effects
- Charge distribution in the anhydrous active site may help position the substrate

50
Q

Is the active state hydrous or anhydrous

A

It is anhydrous

51
Q

Acid-Base catalysis is what?

A

Proton transfer that factors into chemical reactions. An example is hydrolysis of an ester. There is also hydroxide ion catalysis. Acid catalysis (eg. take proton to make acid) works better in low pH. Basic hydrolysis (such as protonating to form a hydroxide ion with hydroxylase) works better at high pH

Side chains of amino acids can be used as general acids or bases, but this depends on the state of protonation, which is based on the pKa of functional groups

About 80% of enzyme catalysis involves acid/base catalysis, the other 20% involves covalent catalysis. Many are both.

52
Q

What is covalent catalysis? Where is the nucleophilic group on? Where is the electrophilic group on?

A

The formation of an unstable covalent bond with a nucleophilic group on the enzyme and an eletrophilic group on the substrate.

53
Q

What role does the active site on enzymes play?

A

Some residues on the active site bing to substrate, provide structural space, do electrostatic interactions, hydrophobic interactions. The residues on the active site can be catalytic OR noncatalytic

54
Q

What two requirements need to be met for an enzyme to participate in catalysis? (properties)

A

Polar and charged

55
Q

What type of residues does acid/base catalysis need?

A

ionizable residues

56
Q

What two things do noncatalytic residues in enzyme active sites do?

A

Orient substrate
or

Stabilize transition state

57
Q

What two types of metals are most likely to be used as prosthetic group cofactors in enzyme catalysis?

Metals are good Lewis ______s and effective _____philes

A 
alkali metals (Na, K, Mg, Ca)
 - Loosely bound and play a role in structure

Cofactors are inorganic.

transition metals (Zn, Fe, Cu)
 - Play a functional role in catalysis as part of a functional group

Metals are good Lewis acids and effective electrophiles

58
Q

What are coenzymes? What are they derived from?

A

Coenzymes are a group of organic molecules that provide enzyme’s chemical diversity by containing functional groups that amino acid side chains do not. They can be tightly or loosely bound and their structures are often changed by the catalytic process. Most are derived from vitamins.

These are organic cogactors, simply cofactors are inorganic.

59
Q

What are the three groups of coenzymes?

A 
Electron transfer (NAD+)
Group transfer (coenzyme A)
High-energy transfer potential (nucleotides)
60
Q

What is the evolutionary consequence of ingesting a greater variety of food (metabolism wise)

A

The biosynthetic pathways for synthesizing nutrients are reduced and eventually disgarded as we ingest these nutrients instead. However, we (and many other mammals) can’t synthesizing ascorbic acid (vitamin C) making us vulnerable to scurvy

61
Q

What is the advantage of histidine on an enzyme active site?

A

Histidine is useful in acid/base catalysis because it has a pH around 7 at physiological pH. Because it has ionizable groups it can participate in both acid and base catalysis depending on the pH of the environment it’s in.

62
Q

What is Chymotrypsin?

A

A 27,000 D protein that belongs to the serine proteases

63
Q

What is special about the active site of serine proteases?

A

They contain a characteristic set of amino acid residues, often referred to as the serine protease triad. These are irreversibly inhibited by diisopropylfluorophosphate (DFP). It hydrolyzes peptide bonds adjacent to aromatic amino acid

64
Q

What are four aromatic amino acids?

A

phenylalanine
tryptophan
histidine
tyrosine

Bonda with these amino acids can be hydrolyzed by serine proteases

65
Q

What is the probable mechanism of action by chymotrypsin? (three steps)

A

An acyl-enzyme is formed making the first tetrahedral intermediate

The acyl-enzyme catalyzes the reaction and then the second tetrahedral intermediate is made

The enzyme product complex dissociates

66
Q

What are alcohol dehydrogenases? What do they use as a hydride ion acceptor?

A

Enzymes that can catalyze the reversible oxidation of alcohols to aldehydes or ketones

They use NAD+ as a hydride ion acceptor

67
Q

What is enzyme regulation necessary for? (3 things)

A

Maintenance of ordered state
Conservation of energy
Responsiveness to environmental changes

68
Q

What are 4 methods of enzyme regulation and control?

A

Genetic control
Covalent modification
Allosteric regulation
Compartmentation

69
Q

What are 4 types of covalent modifications (for enzyme regulation?)

A

Phosphorylation
Methylation
Acetylation
Nucleotidylatoin

70
Q

What are proenzymes and zymogens?

A

These are inactive enzyme precursors that are produced and stored by covalent interactions. Zymogens are converted into active enzymes by the irreversible cleavage of one or more peptide bonds.

71
Q

What is the difference between homotropic and heterotropic allosteric regulation of enzymes?

A

Homotropic allosteric regulation is where the effector is a substrate

Heterotropic allosteric regulation is where the ligand is not a substrate

72
Q

What four problems does compartmentation solve?

A

Divide and control
Diffusion barriers
Specialized reaction conditions
Damage control

Intro to Biochemistry (28 decks)

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