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z BIOC0001 > Enzymes > Flashcards

Enzymes Flashcards

1
Q

What do enzymes require?

what are they?

what are the 2 types of coenzymes?

A

cofactors

metal ions, coenzymes (organic)

co-substrates (transiently bound) & prosthetic groups (persistently bound)

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2
Q

What is the enzyme substrate reaction?

G<0 for a reaction to spontaneously occur, how does this happen?

kinetics———–

What is the velocity of the reaction?

What is k?

What’s the difference between ΔG‡, and ΔG?

What is the difference between ΔG‡ and ΔΔG‡?

so what is the rate enhancement equation?

A

E + S -> ES -> EP -> E + P

Free energy of P has to be less than S

V = k[S]

k = A exp (-ΔG‡/RT)

ΔG is free energy difference between P and S
ΔG‡ is the uncatalysed free energy between S + transition state (activation energy)

ΔΔG‡ is the catalysed free energy between enzyme transition state & substrate (lower activation energy)

rate enhancement = (ΔΔG‡uncat - ΔG‡cat)/RT

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3
Q

thermodynamics——–

what is K?

what happens between non covalent interactions between enzyme & substrate?

which interactions between enzyme & substrate also achieve this? what is the main concept behind this?

Who invented the lock & key model? Induced fit?

A

[P]/[S]

∆G = -RTlnK

releases small amount free energy- lowers activation energy

acid base
covalent
electrostatic
metal ion
- specificity & catalytic power

Fisher
Koshland

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4
Q

what are the 2 residues involved in the cleavage reaction in lysozymes? what is the substrate?

what type of catalysis is this?

what are the steps for the cleavage reaction?

A

glu35 & asp52, N-acetyl-D-glucosamine

general base & covalent

  1. Asp52 reacts with D ring & forms covalent bond
  2. Ring E protonated by Glu35 & leaves enzyme
  3. Glu35 acts as a base & accepts H+ from water & OH- reacts with ring D to release Asp52
  4. End up with both Glu35 & Asp52 with cleaved cell wall molecule
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5
Q

What are the 5 methods of regulating enzyme activity?

What is allosteric binding & cooperativity that happens as a result of it?

What factors affect enzyme activity?

What is G and K in an exergonic & endergonic reaction?

A
  1. enzyme concentration
  2. reversible covalent modification (turning enzymes on/off with phosphorylation)
  3. proteolytic cleavage of precursor (inactive enzyme molecules only active when N/C terminus cleaved)
  4. allostery/cooperativity
  5. inhibitor
Allo = binding of inhibitor/activator to allosteric/different site (from active site) which regulates the enzyme
Cooperativity = binding substrate in 1 subunit changes the affinity of another subunit & the substrate

temperature
concentration (enzyme, substrate, cofactor, inhibitor, activator)
pH

Exergonic: G<0 K>1
Endergonic: G>0, K<1

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6
Q

What’s the difference between reversible & irreversible inhibition?

What are the 2 types of irreversible inhibition?

4 types of reversible inhibition?

A 
Irreversible = slow dissociation of E-I complex
Reversible = fast dissociation of enzyme-inhibitor complex

Group-specific & suicide

Competitive, uncompetitive, non-competitive, mixed

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7
Q

What happens if you have many lines of different concentrations of [So] (initial substrate conc)?

What happens to [So] regardless of concentration over time? What are the reasons for this?

When [So] has reached infinity, what value is this?

What is the slope/gradient?

What are the concentrations of [S] and [P] at Vo? (initial velocity)

A

Higher conc, higher initial rate/reaction velocity (Vo) and higher concentration of [P]

Rate of reaction decreases/reaction velocity V

  1. [S] depleted
  2. enzyme may have denatured
  3. increased [P] means reverse reaction is possible
  4. high [P] could inhibit the enzyme

Vmax (straight perpendicular line after initial rate)

ΔP/Δt

[S] = {So]
[P] = 0
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8
Q

What are the x and y axis?

What do they 1st order & 0 order region look like?

What is Vmax/2?

What is the equation for Vo?

A 
x = [So]
y = Vo

1st order = initial linear-ish line when Vo is linear to [So]
0 order = max value/velocity (perpendicular line after reaching max velocity) Vmax

Km

Vmax[So] / [So] + Km

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9
Q

What is steady state kinetics?

What are the k involved in:
E + S <=> ES <=> E + P

What are the 3 assumptions for steady state kinetics?

what is the rate formation of ES?

what is the rate of breakdown of ES?

what is the equation for Km?

what is [ES] with respect to Km (Michaelis-Menten)?

What is Vo with respect to Km (Michaelis-Menten)? if [So] is small, what is the graph shape?

What is Vmax with respect to [Eo]?

A

Kinetics applied when [S] is greater than the [E]- hence there is no change in [E] only in [S] and [P]

E + S -> ES is k1
ES -> E + S is k-1
ES -> E + P is k2
E + P -> ES is k-2

  1. At beginning, [P] = 0 so k-2 is ignored
  2. At steady state [ES] is constant
  3. Vo is determined by [ES] so Vo = k2[ES]

[ES] = k1[E][S]

[ES] = (k-1 + k2)[ES]

hence k1[E][S] = (k-1 + k2)[ES]

(k-1 + k2)/k1

([Eo][So]) / ([So] + Km)

Vo = Vmax[So] / [So] + Km
linear

k2[Eo]

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10
Q

What is the x and y axis in a lineweaver-burk plot?

what is the gradient?

what is the y intercept?

what is the x intercept?

When plotting [So] vs [Vo] what is the difference between the hyperbolic curve & the cooperativity curve?

What is the Kcat equation?

A 
x = 1/[S]
y = 1/V

Km/Vmax

1/Vmax

-1/Km

Hyperbolic = classic Michaelis-Menten, 1 competitor inhibitor & 2 substrate binding events
Cooperativity = result of allostery

Vmax/[E]

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11
Q

What is Km a measure of?

What is the [So]:Km ratio in physiological conditions? Why is it important?

What is Kcat a measure of?

What is the specificity constant and what does it measure?

What does rate enhancement measure & what is the equation?

What is specific activity, its units & its equation?

What is Km never smaller than?

A

Associated binding of substrate to enzyme (E + S -> ES)

between 0.01-1.0. if [So] is too high the enzyme is at max velocity, if it’s too low there’s too many unoccupied enzymes (waste energy)
- need to be balance of no waste but change in [So] so enzyme reacts

Turnover number (s-1) ability for an enzyme to turn ES -> P

Kcat/Km efficiency (higher means enzyme prefers that specific substrate)

How much the enzyme speeds up the reaction: Kcat/Kuncat

Measure of enzyme purity- amount of enzyme catalyses a eraction of 1nml of substrate per min under standard conditions, U/mg, total activity/total protein

Kd

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12
Q

Where is the inhibitor/Ki added?

What happens to Vmax & Km? Why?

Where is the inhibitor/Ki added in uncompetitive inhibition?

What happens to vmax & Km?

What happens to vmax & Km in non-competitive?

What happens to vmax & Km in mixed?

A

To the enzyme (before E + S)

Vmax same
Km increases as increase in [S]

[E][I]/[EI]

at ES

Vmax decreases (more EI)
Km decreases (more I)

Vmax decreases
Km unchanged

Vmax decreases
Km changes

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13
Q

What is group specific inhibition?

What is suicide inhibition?

A

Substrate reacts with specific catalytic residues in enzyme- becomes inactivated as forms covalent bond

Inhibit binding to active site of enzyme

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z BIOC0001 (12 decks)

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