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Cellular Biology and Biochemistry > Energetics and Dynamics of Protein Action > Flashcards

Energetics and Dynamics of Protein Action Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

Why should we study energetics and dynamics of protein action?

A

Study enzyme function in health and disease

Understand complex behaviour of enzymes

Design pharmacological agents to inhibit target enzymes

Understand impact of natural and engineered gene mutations on enzyme function

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2
Q

What do Hydrolases do?

A

Hydrolytic cleavages

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3
Q

What do Polymerases do?

A

Polymerisation reactions

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4
Q

What do Synthases do?

A

Synthesis

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5
Q

What do Kinases and phosphatases do?

A

Add or remove phosphate groups

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6
Q

What do Isomerases do?

A

Rearrangements of proteins

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7
Q

What do Oxido-reductases do?

A

Oxidise / reduce substrates

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8
Q

What do ATPases do?

A

Uses ATP

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9
Q

What is BRENDA?

A

a database that tells you about proteins

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10
Q

What are the stages of an enzyme substrate reaction?

A

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

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11
Q

What is the active site cleft?

A

Structural scaffold of each enzyme providing an active site.
Has catalytic activity
Has residues to interact with the substrate

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12
Q

What is the transition state of an enzyme?

A

The point with the highest amount of free energy where catalysis occurs

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13
Q

What is an endergonic reaction?

A

A reaction which requires energy and is not spontaneous since ΔG > 0

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14
Q

What is an exergonic reaction?

A

A reaction which is spontaneous and does not require energy input since ΔG < 0

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15
Q

How can you make an endergonic reaction spontaneous?

A

by coupling to with a highly exergonic reaction

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16
Q

How can we determine the ΔG of a reaction?

A

If the reaction is spontaneous or not.

How reversible the reaction is.

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17
Q

How does coupling an endergonic reaction with an exergonic reaction help in a metabolic pathway?

A

The 2 reactions can occur spontaneously
Energy is released from exergonic reaction
Used to hlp drive the endergonic reaction

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18
Q

What is the induced fit model?

A

proposes distortion of enzyme and substrate is important in catalysis

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19
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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20
Q

What is the activation energy?

A

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

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21
Q

What is important about an enzymes active site?

A

Enzyme is complementary to the substrate when it is in its transition state

Enzyme binding brings the substrate towards its transition state

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22
Q

When a protein binds to an enzyme why does ΔG initially fall creating a lowered free energy of the ES*?

A

because the enzyme will displace some water molecules which will increase disorder (entropy) and lower the free energy

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23
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

24
Q

How can conformational changes affect ΔG?

A

allow compensation between ΔH and ΔS to minimise ΔG

25
Q

What is the michaelis menten scheme and what should be considered?

A

E + S <==K1==> ES ==K2==> E + P

Consider that the slowest step determines the overall rate of reaction

26
Q

What is K2?

A

ES => E + P

Kcat

27
Q

What is Kcat?

A

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

28
Q

What is the steady state assumption?

A

rate of formation of ES=rate of degradation of ES so the concentration of ES stays the same.

29
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
30
Q

What is Vmax?

A

the max velocity that can enzyme can work at

31
Q

What is the equation for Vmax

A

Vmax=Kcat[E]

32
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)

33
Q

What is the Michaelis menten equation?

A

V0 = Vmax[S] / Km + [S]

34
Q

How do you measure enzyme efficiency?

A

cat/kM

35
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

36
Q

What is the limit of enzyme efficiency and why is

there an upper limit?

A

Allostery

limited by time taken for substrate to diffuse into active site

37
Q

What is V0?

A

Initial Rate of reaction

38
Q

What is a problem of the michaelis menten equation?

A

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

39
Q

How do you get the Lineweaver-Burk equation?

A

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

40
Q

How do catalysts lower the activation energy?

A

By stabilising the transition state

41
Q

What are the components of the straight line in a line weaver burk plot and what are the axis??

A

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

Y axis = 1/Vo
X axis = 1/[S]

42
Q

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

A

-1/Km

43
Q

What is the y intercept?

A

1/Vmax

44
Q

What is the slope/gradient of the lineweaver-Burk plot?

A

Km / Vmax

45
Q

What is the limitation of the Lineweaver-Burk plot?

A

its highly sensitive to measurements at low [S]

46
Q

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

A

At the bottom close to both axis

47
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
48
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
49
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
50
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
51
Q

How does the lineweaver-Burk plot show non-competitive inhibitory activity?

A

-1/Km stays the same (same x intercept)

1/Vmax is reduced (higher y intercept)

52
Q

How does the lineweaver-Burk plot show competitive inhibitory activity?

A

Vmax stays the same (same Y intercept)

-1/Km increases (closer to origin)

53
Q

Give a natural and synthetic non-competative inhibitor example

A

Natural - Caffine

Synthetic - Trichostatin

54
Q

Give a natural and synthetic competative inhibitor example

A

Natural - Tetradotoxin

Synthetic - Ibuprofen

55
Q

Explain the neuraminidase enzyme example for drug design?

A

Neuraminidase - essential for viral proliferation.
Sailidase - cleaves sialic acid

Sial acid held in AS cleft through a few bonds

Zanamivir (relenza) - Designed drug with a higher affinity and a competitive inhibitor binds with more bonds.

56
Q

What are most drugs that inhibit enzymes?

A

Transition state analogues.

Cellular Biology and Biochemistry (22 decks)

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