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Cellular biology and biochem > Energetics and dynamics of protein action > Flashcards

Energetics and dynamics of protein action Flashcards

1
Q

Hydrolase

A

hydrolytic cleavages

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2
Q

polymerase

A

polymerisation reactions

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3
Q

synthase

A

synthesis

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4
Q

kinase/phosphatases

A

add/remove phosphates

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5
Q

isomerases

A

rearrangements

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6
Q

oxide-reductases

A

oxidise/reduce substrates

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7
Q

ATPases

A

use ATP

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8
Q

What is BRENDA?

A

a database that tells you about proteins

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9
Q

What are the stages of an enzyme substrate reaction?

A

S+E=>ES=>EP=>E+P

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10
Q

What is an endergonic reaction?

A

When ΔG is greater than 0

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11
Q

What is an exergonic reaction?

A

When ΔG is less than 0

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12
Q

What reactions tend to be spontaneous?

A

exergonic

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13
Q

How can you make an endergonic reaction spontaneous?

A

by coupling to with a highly exergonic reaction

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14
Q

What is the induced fit model?

A

proposes distortion of enzyme and substrate is important in catalysis

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15
Q

What is catalysis dependant on?

A
  • localisation of substrate
  • orientation of substrate
  • binding energy of substrate
  • catalytic residues on protein framework
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16
Q

What is the activation energy?

A

the energy required to reach the transition state (bent stick)

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17
Q

When a protein binds to an enzyme why does ΔG initially fall?

A

because the enzyme will displace some water molecules which will increase disorder

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18
Q

What does the enzyme need to be complimentary to?

A

the transition site

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19
Q

How can a structural change provide activation energy?

A

in hexokinase, when in open form it is unlikely to react. When glucose binds it changes its conformation to closed form which allows ATP to bind.

20
Q

How can conformational changes affect ΔG?

A

allow compensation between ΔH and ΔS to minimise ΔG

21
Q

What is K2?

A

ES => E + P

Kcat

22
Q

What is Kcat?

A

turnover number of the enzyme (how good it is) (rate that ES is converted to E + P

23
Q

What is the steady state assumption?

A

the concentration of ES stays the same (rate of formation of ES=rate of degradation of ES)

24
Q

What are the assumptions of M-M scheme?

A
  1. assume that the reverse reaction is negligible (while its favourable we can establish experimental conditions that preclude or minimise the reverse reaction)
  2. assume only a single central complex (ES) exists (ES breaks down directly to +P
  3. Assume that [S}&raquo_space;[E] interaction of S with E does not significantly affect the concentration of S
25
Q

What is Vmax?

A

the max velocity that can enzyme can work at

26
Q

What is the equation for Vmax

A

Vmax=Kcat[E]

27
Q

What is the Km?

A

the substrate conc when the reaction rate is half maximal (michaelis constant)
(measure of affinity of the enzyme for the substrate)

28
Q

What is the Michaelis menten equation?

A

velocity = Vmax[S]
————-
Km+[S]

29
Q

How do you measure enzyme efficiency?

A

cat/kM

30
Q

Why do you have to be careful when using Michaelis-Menton?

A
  • does not explain kinetic properties of many enzymes

- example of sigmoidal curves for proteins with multiple subunits such as allosteric enzymes

31
Q

What is the upper limit of enzyme efficiency and why is there an upper limit?

A

1x10^8M^-1.s^-1

limited by time taken for substrate to diffuse into active site

32
Q

What is a problem of the michaelis menten equation?

A

you can’t work out Vmax because infinite amounts of substrate are needed

33
Q

How do you get the Lineweaver-Burk equation?

A

by flipping the michaelis-menton equation over (which changes michealis-menten equation into a straight line)

34
Q

What are the components of the y=mx+c equation?

A

y= 1/v0
m=km/Vmax
x= 1/[S]
c= 1/Vmax

35
Q

What is the x intercept in a Lineweaver-Burk plot?

A

-1/Km

36
Q

What is the y intercept?

A

1/Vmax

37
Q

What is the limitation of the Lineweaver-Burk plot?

A

its highly sensitive to measurements at low [S]

38
Q

If it is 1/v 1/[S] graph where is high substrate conc?

A

At the bottom close to both axis

39
Q

What happens in competitive inhibition?

A
  • Km increases because less substrate is binding so affinity is lower
  • Vmax is unaltered because if you increase [S] you can outcompete the inhibitor
40
Q

How do non-competitive inhibitors work?

A
  • molecule binds to site on enzyme other than the active site
  • modifies the enzyme conformation to slow/prevent product formation
  • high affinity for second binding site
41
Q

What happens to the Km of non-competitive inhibition?

A
  • Km is unaltered (substrate can still bind but can’t be converted as quickly into products Tham without the inhibitor)
  • Vmax is reduced (product formation slows down
42
Q

Give one example of naturally occurring non-competitive inhibitors?

A

-caffeine

43
Q

Give an example of a synthetic non-competitive inhibit?

A

haloperidol

44
Q

Give an example of a naturally occurring competitive inhibitor?

A

digitalis

45
Q

Give an example of a synthetic competitive inhibitor?

A

ibuprofen

46
Q

Explain why non-competitive inhibition is common in feedback inhibition, using threonine as an example.

A
  • biosynthesis of isoleucine from threonine in bacteria involves 4 steps and 4 enzymes
  • first reaction is catalysed by threonine deaminase
  • this reaction is noncompetitvely inhibited by isoleucine, the end product of the pathway
  • as the product increases the first reaction rate decreases
  • this leads to less product and a reduction in the inhibition as the isoleucine dissociates from the enzyme
  • the cycle begins again

Cellular biology and biochem (11 decks)

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