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Bichem > Enzymes yo > Flashcards

Enzymes yo Flashcards

1
Q

Enzyme definition

A
  • protein catalyst (usually) that increases the rate of reactions without being changed in the overall process
  • converts substrates into products and direct all metabolic events
  • increase rate,do not invent new reactions
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2
Q

Recommended or common name

A
  • usually have “ase” added to the name of the substrate in the reaction
  • or describe the action performed
  • or retain original trivial name
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3
Q

Systemic name

A
  1. Classification: divided into 6 major classes
  2. name: includes names of all substrates involved plus ase
  3. number: each enzyme is assigned a unique number
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4
Q

Systemic name classifications

A
  • oxidoreductases(oxidation/reduction)
  • transferases(transfer of C,N,P)
  • hydrolases(cleavage by addition of water)
  • lysase(cleavage of C-C,S,N bonds)
  • isomerases(racemization of isomers)
  • ligases(forms OSN bonds)
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5
Q

Synthase vs synthetase

A

synthase: no ATP required
Synthetase: ATP required

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6
Q

Phosphatase vs phosphorylase

A

Phosphatase: removes a P group
Phosphorylase: generate a P group

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7
Q

Oxidase vs oxygenase

A

oxidase: uses oxygen as an acceptor without incorporating it into a reaction
oxygenase: oxygen is incorporated

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8
Q

Arrow indication about reaction

A

Arrow pointing in both directions: it can catalyze either reaction
Arrow pointing in one direction: it can only catalyze in one direction (reverse might be possible, but not with that enzyme)

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9
Q

Enzyme structure: active site

A
  • special pocket that binds to the substrate
  • formed by folding of the protein that allows specific side chains to participate in binding
  • Binding makes Enzyme-Substrate complex which includes a conformational change
  • Enzyme-Product complex dissociates to enzyme and product
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10
Q

Enzyme Structure: allosteric site

A
  • any other part of the enzyme that is not the active site

- binds different regulatory molecules

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11
Q

Enzyme Efficiency

A
  • extremely high (10^14 times faster)
  • turnover number is the number of substrate molecules converted to product per enzyme molecule per second(kcat)(hella lot)
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12
Q

Enzyme Specificity

A
  • HIGHLY SPECIFIC
  • only one or few substrates
  • only one type of reaction
  • if there is more than one function, there are multiple binding sites
  • enzymes present in the cell determine the type of reaction that can happen
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13
Q

Coenzymes

A

organic molecules that are required by certain enzymes to carry out catalysis
-NAD+,FAD,NADP+

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14
Q

Cofactors

A

inorganic substances that are required for or increase rate of catalysis
-ZN2+, Mg2+

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15
Q

Holoenzyme

A

enzyme+nonprotein component=active

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16
Q

Apoenzyme

A

enzyme without nonprotein component=inactive

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17
Q

Regulation by inhibitors and activators

A

-the amount of the end product produced is regulated by its own concentration (feedback)

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18
Q

Post-transitional modifications

A

-regulation through covalent modulation of the enzyme molecule(phosphorylation)

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19
Q

Enzyme protein production

A

transcription and translation of enzyme genes

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20
Q

Regulation through specific local

A

-environment/ pH

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21
Q

Enzyme compartmentalization

A

-different metabolic pathways occurring in different cellular compartments

22
Q

Advantages of compartmentalization

A
  • isolates substrates and products from competing reactions
  • organizes enzymes into purposeful pathways that can proceed simultaneously
  • more precise regulation
23
Q

Free energy

A

-gibbs free energy (G)- quantitative measure of the energy transfers between chemical reactions

24
Q

Energy Barrier

A

energy difference between the reactant and a high energy intermediate

25
Q

Free energy activation

A

the difference in free energy between the reactants and intermediate

26
Q

Stabilization of transition state

A

(chemistry on the active state)

  • creates bonds in intermediate that are not like the ones in the substrates or products
  • increases the concentration of the reactive intermediates that can be converted to products
27
Q

Chemistry on the active site

A
  • provide chemical groups that participate in reactions with the substrate
  • enhance probability of transition state formation
  • enzyme is returned to its unaltered state before the release of the product
  • decrease the activation energy
28
Q

Factors that affect reaction velocity

A
  • substrate concentration
  • temp
  • pH
29
Q

Substrate concentration affect on reaction velocity

A
  • Rate of velocity-number of substrates converted to product per unit of time
  • VMax- the rate of an enzyme catalyzed reaction increases with the substrate until VMax is reached. represents saturation of all available binding sites
  • hyperbolic curve
  • sigmoidal curve is less common(no michaelis-menten)
30
Q

Temperature affect on reaction velocity

A
  • reaction velocity increases with temp until peak is reached
  • increases the amount of molecules that can overcome energy gap
  • After peak, velocity decreases with rising temp
  • human optimum is 37 degrees celcius
31
Q

pH affect on reaction veocity

A
  • Enzyme and substrate usually require certain things protonated/un so change in pH results in decreased velocity
  • protein structure requires certain pH so you can denature protein with change
  • pH optimum is specific for each enzyme
32
Q

Components of reaction model

A

-S,E,ES,P, rate constants

33
Q

Michaelis Menton

A
  • describes how reaction velocity varies with substrate concentration at a given concentration of enzyme
  • assumes concentration of substrate is much greater than enzyme concentration
  • assumes ES is in a steady state
  • initial velocity is used in analysis
34
Q

Michaelis Menton Km

A
  • characteristic of an enzyme and its particular substrate and reflects the affinity of the enzyme for that particular substrate
  • THE AMOUNT OF SUBSTRATE NEEDED TO HALF MAXIMAL VELOCITY (1/2 VMax)
  • Small Km=high affinity
  • high Km=low affinity
35
Q

Relationship of velocity to enzyme concentration

A
  • reaction rate is directly proportional to E a all concentrations of S
  • if E is halved, V0 and VMax are halved too
36
Q

Order of Reaction

A
  • when S is much lower than Km, velocity is proportional to the substrate concentration(first order)
  • when S is much greater, velocity is constant and equal to VMax and independent of S. (zero order)
37
Q

Lineweaver-burk plot purpose

A
  • uses 1/V0 vs 1/S

- results in a straight line which lets us determine Km and Vmax more accurately.

38
Q

Lineweaver-burk plot understanding

A
  • the intercept on the x axis is equal to -1/kM
  • intercept on the y axis is equal to 1/Vmax
  • double reciprocal plot
    - increase Km or Vmax, they will be closer to zero
    - decreasae km or vmax, they will be further from zero.
39
Q

Inhibitors

A
  • any substance that can diminish the velocity of an enzyme catalyzed reaction
  • irreversible and reversible
40
Q

Irreversible inhibitors

A
  • bind to E through convalent bonds
  • only way to recover E activity is to synthesize a new molecule
  • suicide inhibitor-enzyme converts inhibitor into a reactive form in its active site(product is inhibitor)
41
Q

Reversible inhibitors

A
  • bind through non covalent bonds which allows for full recovery of enzyme
    competitive: inhibitor competes with substrate for active site
    noncompetitive: inhibitor binds to allosteric site
42
Q

Competitive inhibition

A
  • the effect of the inhibitor can be overcome with large concentrations of S so NO EFFECT ON VMAX
  • lowers affinity so KM IS INCREASED
  • example:statin drugs
43
Q

Noncompetitive inhibition

A
  • cannot be overcome by substrate concentration so VMAX IS DECREASED
  • does not interfere with substrate binding so NO EFFECT ON KM
  • example: allopurinol
44
Q

Effectors

A
  • can affect KM or Vmax or neither or both

- can be negative or positive (inhibit or increase enzyme activity)

45
Q

Homotropic effectors

A
  • the substrate itself serves as an effector
  • most often positive
  • enhances catalytic activity
  • cooperativity effect
46
Q

Heterotropic effectors

A
  • the effector is different than the substrate molecule
  • feedback inhibition: an end product of a metabolic pathway inhibits upstream step
  • example:phosphofructokinase in glycolysis
47
Q

Regulation by posttranslational covalent modifications

A
  • most common is phosphorylation/dephosphorylation of hydroxyl group in ser,thr,tyr
  • protein kinase-phosphorylate
  • protein phosphatase-dephosphorylate
48
Q

Regulation by control of enzyme production

A
  • alter the rate of synthesis or degradation of the enzyme

- these enzymes are usually only needed under certain conditions and are not in constant use.

49
Q

timing of enzyme regulation

A

-gene expression regulation: take from hours-days
-covalent changes: immediate to minutes
allosteric control: immediate

50
Q

Blood vs plasma vs serum

A

blood=plasma+blood cells
plasma: fluid part of the blood without the cells
Serum: plasma without coagulating factors. not made in the body

51
Q

Plasma Enzymes

A

actively secreted: have certain function in plasma.small group of enzymes. do not play a role in diagnosis
-not actively secreted: function intracellularly not in plasma. released from cell lysis during normal turnover.levels are at a steady state. when there is an increase in these enzymes, it signifies tissue damage.

Bichem (9 decks)

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