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Protein Structure & Function > Enzymes > Flashcards

Enzymes Flashcards

1
Q

How do enzymes alter reactions?

A

Higher reaction rate under milder reaction conditions
Greater reaction specificity
Capacity for regulation
Lowers activation energy needed

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2
Q

What do enzymes not alter?

A

Don’t alter equilibrium point of reaction
Don’t alter overall free enery

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3
Q

What makes up an enzyme?

A

Protein molecules
And sometimes cofactors

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4
Q

What can the cofactors in enzymes be?

A

Inorganic molecules = metal ions
Coenzymes
Organic molecules = vitamins or derivatives

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5
Q

What are cofactors?

A

A non-protein chemical compound that is bound or unbound to the enzyme and is required for the enzymes catalytic activity

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6
Q

What happens to cofactors during reaction?

A

May be chemically changed by the reaction, so must by REGENERATED

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7
Q

What is a prosthetic group?

A

Bound cofactors to a protein

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8
Q

What’s a protein called with and without its prosthetic group?

A

Holoenzyme = active protein with prosthetic group

Apoenzyme = inactive protein because doesn’t have its prosthetic group

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9
Q

Describe what cytochrome and heme group relationship is

A

Heme is a prosthetic group of all cytochromes and is associated with Histidine residues

It is a prosthetic group because it is a tightly bound cofactors of cytochrome

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10
Q

Describe what G3PDH and NAD+ relationship is

A

NAD+ is the cofactor of glyceraldehyde 3-phosphate dehydrogenase

It is not bound to dehydrogenase permenantly = when reaction takes place is can then unbind and be used by another DH

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11
Q

What are the effects of pH on enzymes?

A

pH affects the ionization of polar groups on enzymes

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12
Q

What is the initial velocity and how is it measured?

A

Initial velocity is measured at the beginning of a reaction when the reverse reaction is insignificant

When starting out the products are 0 so probability of reversing the reaction is lower

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13
Q

What is the graph to calculate initial velocity?

A

Time = x axis
Product = y axis

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14
Q

What is the Michaelis-Menten equation?

A

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

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15
Q

What are the axis for Michaelis-Menten plot?

A

x axis = [S]
y axis = Vo

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16
Q

How are Vmax and Km calculated from the Michaelia-Menten plot?

A

V max = max velocity, where it plateaus
Km = conc of substrate at half Vmax

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17
Q

When are initial velocity (Vo) and [S] proportional and independent of one another?

A

Vo is proportional to [S] when [S] is small = can see in graph there is a stright line

Vo is independent of [S] when [S] is large = graph starts curving

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18
Q

What are the axis for Lineweaver-Burk plot?

A

x axis = 1/[S]
y axis = 1/Vo

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19
Q

What are the important intersection on the Lieweaver-Burk plot?

A

y intercept = 1 / Vmax
x intercept = - 1 / Km

Gradient = Km / Vmax

20
Q

What is the equation for 1/Vo?
(lineweaver-burk plot)

A

1/Vo = 1/Vmax + Km / Vmax [S]

21
Q

What is the Km?

A

Concentration of a substrate at which the reaction velocity is half the maximal

Reflects the affinity of the enzyme for the substrate

22
Q

What does having a higher Km mean?

A

The value of KM is inversely related to the affinity of the enzyme for its substrate.

High values of KM correspond to low enzyme affinity for substrate and vice versa

23
Q

Define Vmax

A

Maximal rate of reaction (velocity)
Under saturation substrate conditions

24
Q

What can we calculate from Vmax?

A

kcat (k_2)

25
Q

What is kcat?

A

Catalytic constant = the number of maximum substrate molecules converted by the enzyme into a product per unit time when enzyme is fully saturated with substrate

ES&raquo_space;> E + P

26
Q

What is the catalytic constant also known as?

A

kcat is also known as the turnover number

27
Q

What is the equation to calculate kcat?

A

Vmax = kcat x [ET = total enzyme concentration in our reaction]

28
Q

What makes up total enzyme concentration in a reaction? [ET]

A

[ET] = [E] + [ES]

29
Q

Describe the saturation conditions in terms of enzymes and substrates

A

All catalytic sites are saturated with substrate [ES] so no free enzyme [E] = 0

Thus, [Et] = [ES]

30
Q

What does high kcat tell us?

A

The highest kcat shows the most catalytically efficient enzyme

kcat units = per second

31
Q

What are the physiological conditions within the cell and what is calculated instead?

A

[S] is much lower than Km so kcat does not apply

kcat / Km is used to measure enzyme’s catalytic efficiency instead

32
Q

Define diffusion-controlled limit

A

The frequency at which two molecules can collide

Enzymes which attain kcat/Km within the diffusion-controlled limit are considered to have attained kinetic perfection

33
Q

What is the value of diffusion-controlled limit?

A

10^8 - 10^9 per M per s

34
Q

What does Vo - [S] relationship look like for allosterically regulated enzymes?

A

Sigmoidal curve

35
Q

What is the allosteric effect?

A

Binding of a ligand at one site affects the binding of another ligand at ANOTHER site of the same protein

Allosteric enzymes have two or more substrates

36
Q

Define allosteric effectors

A

Ligands which bind to allosteric site and modulate the enzyme activity
Positive effectors = activation
Negative effectors = inhibition

37
Q

What is a homotropic effector?

A

The substrate is itself

38
Q

What subunit interactions usually occur in allosteric effects?

A

Interactions among subunits of OLIGOMERIC proteins (composed of more than one subunit)

39
Q

What are the two forms of allosteric enzymes?

A

Taut = less active
Relaxed = more active

40
Q

Name the two models of allosterism

A

Symmetry/Concerted model
Sequential induced-fit model

41
Q

What is the symmetry/concerted model?

A

The ligand can bind to a subunit in either T or R conformation = molecular symmetry of the protein is conserved during the conformational change

Subunits must all exist at T or R conformation = no oligomers with both T and R state subunits

42
Q

What is the sequential induced-fit model?

A

Ligand binding progressively induces conformational changes in the subunits, the greatest changes occur in those subunits that have bound ligands

Symmetry of oligomeric protein = not preserved

Cooperatively interactions = influence that binding of ligand to subunit has on neighbouring subunits

43
Q

When is haemoglobin in T form?

A

No oxygen = Fe(II) is situated out of the plane of the heme because
1. doming of porphyrin skeleton
2. Fe-N (porphyrin) bonds are too long to allow Fe to lie in plane of porphyrin

44
Q

When is haemoglobin in R form?

A

Interaction with oxygen
1. reduces doming
2. F-N bond shortens = Fe moves to centre of heme plane dragging along His and causing tertiary changes in polypeptide

As other subunits are closely coupled, structural change within one subunit will influence the structure of the other subunits

45
Q

Give example of symmetry/concerted model enzyme

A

Aspartate transcarbamoylase (ATCase from E/coli) to make CTP

CTP is allosteric regualted of ATCase = assures that when there is a lot of product enzyme is inhibited so no more is made

Protein Structure & Function (11 decks)

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