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Biol 2700 > Enzymes > Flashcards

Enzymes Flashcards

1
Q

What is a catalyst? And what are the two types?

A

Catalysts are molecules that speed up reaction without being used themselves
1- biological molecules- Proteins and enzymes
2- RNA

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2
Q

Enzymes may require molecules. What are these molecules called? What are the two types?

A

Cofactors/coenzymes
Can be :
1- organic- biological molecules
2- inorganic| metal ions

Apoproteins- proteins
Holoenzyme- protein + coenzyme

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3
Q

What are the 6 classifications of enzymes?

A

Old - oxidoreductase
Tiger- transferase
Head butted - hydrolases
Little- lyases
Iguana - isomerase
Lamely - ligases

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4
Q

Explain

A

Oxidoreductase - transfer e as H
Transferase- transfers functional groups
Hydrolases - adds functional group to Water -cleaves cov bonds with water
Lysases- adds double bo;, clease covalent bond w/o water
Isomerase- isomerize by group transfer
Ligases- forms C-o,c-n,c-h,c-s . Coupled with ATP cleavage

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5
Q

Why are enzymes necessary

A

Accelerate
Regulate
Very specific , no side rxn
Main role in majority of rxn.
Provides an environment for easy bond form and breaking

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6
Q

ES and EP are cov or non-cov. Why?

A

Non Covalent
Because these complexes are reversible

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7
Q

Transition state theory

A

The energy required for substrate and reactant to reach the transition state

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8
Q

Describe ES stage

A
  • S to ES is called binding energy
  • S is bit distorted to look like product
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9
Q

Explain how s is distorted without needing extra energy.

A

1- E to ES is a energy releasing process, binding energy which is due to the formation of favourable interactions are formed- H bonds, hydrophobic bonds, VDW forces.
2- some of this binding energy is used for S distortion
3- ES start working from the ground level.

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10
Q

Compare the energy graphs
1- no enzyme
2- enzyme complementary to substrates
3x enzyme complimentary to transition state.

A
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11
Q

What are other affects of ES complex?explain?

A

-Reduce entropy of S -
-Dissolution - breaking the h2o shell around substrate
-Alignment of the groups that react
-induced fit- enzymes alter slightly to fit the transition S state, Affinity of S + is higher then S.
-strain reduction - steric / electrostatic are accommodated.

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12
Q

How and why does enzyme bind to only a few molecules?

A

1- shape consistency - 🔐
2- electrostatic consistency - correct matching of ionic and hydrogen bonds
3-thermodynamic consistency - the ability of substrate to flex to fit enzyme and vv.

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13
Q

Enzyme specificity is of two types?

A

1- optical specificity - different enzymes needed for D and diff for L
2- geometric specificity - different enzymes needed for cis and diff for trans.

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14
Q

Draw the two examples of the pervious specificity

A
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15
Q

Explain why metal ions are important ?

A
  • week interactions between metal ions and substrate stabilize charged transition state and orient and bind the substrate
  • megals accept and donate e in redox reactions
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16
Q

Describe the mechanism of carboxypeptidase

A

Carboxypeptidase use zinc as an alternate to amino acid to form an oxyanion hole

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17
Q

Draw the carboxypeptidase equation

A
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18
Q

Name the 3 types of enzyme inhibition

A

1- competitive
2- uncompetitive
3- non competeive

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19
Q

Explain competitive inhibitors and name a few examples.

A

Attach to the active site of the enzymes
Lipitor, viagra, protein inhibitors, VCT, LVV PETER
Malonic acid is an inhibitor of succinate dehydrogenase

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20
Q

Describe the changes of Vmax and kmax and why they occur.

A

Vmax is unchanged
- the rate decreases as the concentration of substrate increases, However at very high substrate concentration, the ability / prob of an inhibitor to bind to an enzyme is = 0. Substrate displaces I
Kmax increases
- kmax is apparently increased because now it takes more [S] to reach the vmax

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21
Q

Draw the MM and LB plots for competitive

A
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22
Q

Describe uncompetitive inhibitors

A

I binds to the allostseric site of ES complex only
Eg roundup

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23
Q

Dexcribe and explain the changes of Vmax and Kmax

A

Vmax is lower - inhibitor dec the active Etotal

Kmax is lower - higher affinity for (s) , the [s] to reach 1/2 Vmax is lower

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24
Q

Explain Non competivie

A

I binds to ES and E complex and prevent P formations

25
Q

Explain change in vmax and kmax

A

Vmax decreases
Bcz I decreases E tot (active Enzyme), Vmax =kcat(Etot)
Kmax unchanged
The affinity of I to E and ES is same

26
Q

Draw the two graphs for the other two inhibitors

A
27
Q

State the curve name of
1- v0 by (s) graph
2- m-m grap - v0 by (s)
3- draw them

A

1- sigmoidal
2- hyperbole

28
Q

Why are the curve different?

A

Sigmoidal is over a very narrow period of time therefore the enzyme acts as an in and off switch

29
Q

When does this Non M-M graph behaviour occurs (i think they are talking about sigmoidal graph curve)

A

1- due to cooperativity
2- the binding of S to an active site , make the binding of a subsequent S easier.

30
Q

What is cooperatiivity?

A

Occurs in a multi subunit enzyme
When the binding of an active site of one subunit, affects the binding of active site of other subunit.

31
Q

How does binding of one S to an active site affects the binding of the other S of the active site?

A

-in a multisubunit enzyme, Each subunit can occur in 2conformations
T-Etaut (low affinity) and R- Erelaxed (high affinity)
-when there are few S, The equilibrium favours T, low affinity
- when there is S and s binds, the equilibrium favors R phase - high affinity of S , and higher active sites so more S binds! Untill enzyme is saturated
-this causes the sigmoidal curve

32
Q

Draw what was explained regarding the non behaviour of mm curve

A
33
Q

What can affect the kinectic curves - the sigmoidal and hyperbole curve

A

Anything that affects the equilibrium
Eg - activators and inhibitors

34
Q

How do activators and inhibitors affect kinetic curve?

A

I and A bind to allosteric sites
Inhibitors bind to the T form and shift equilibrium to T form , bcz less S binds
Activators and substrates bind to R form and pull eq towards R

35
Q

Give an example of I and A binding and also draw the curve

A

Enzyme- phosphofructokinase
Substrate- fructose 6 p
Inhibitor - ATP
activators- AMP

36
Q

Give an example of allosteric enzyme /non enzyme and how it helps the human body

A

Allostericity helps extracts o2 from mothers blood
Hemoglobin isnt an enzyme however it binds to O2 with cooperatively, which affects how it responds to changes in o2 demands.

BGP and 2,3 DGP are inhibitors
Fetal hemoglobin has low affinity for BPH and higher affinity for o2 then adult haemoglobin
Therefore it has to absorb o2 from mothers blood.

37
Q

Explain the catalysed and uncatalysed reaction of carbonic anhydrase

A

Uncatalysed
The ocean water has co2 , which decreases its PH , makes it more acidic
H2O + CO2 —-> HCO3- + H+
Catalysed by carbonic anhydrase

H2O-E-CO2 <—-> E-HCO3- + H <—-> E +HCO3-
10^6 time s more faster

38
Q

Does a catalyst affect keq, why or why not?

A

The ratio of product conc to reactant conc
No
If the forward rxn increases, the backward rxn increases too because the free energy from the product to the transition state will also be lower

39
Q

Why is studying enzyme mechanism important?

A

Provides knowledge and understanding basis of life, for modern drug dev, medicine and agriculture

40
Q

Give an example of disease and drug that was made using protease studies/enzymes,proteins studies.

A

HIV RNA GENOME — > HIV polypeptide——HIV PROTEINASE—-> breaks them down , which become active and lead to virus formation
Structure based drug design and enzymology was used to made VIRACEPT, HIV proteinase inhibitors.

41
Q

What are the two ways rates are measured experimentally

A

Increase in [P] over time
Decrease in [S] over time

42
Q

What happens if we
1- lower the Ph from optimum
2-lower the temp from optimum
3- increase ph from optimum
4- increase Temp from optimum

A

1- enz inactive
2- enz inactive
3- enzyme denatured by ionic disruption
4- enzyme denatured by heat disruption

43
Q

What type of curve is a M-M curve ? Why does this curve occur?

A

Hyperbole
Rate is dependent on two vectors
1- the time taken for substrate molecule to reach the enzyme- varies with the conc of substrate
2- the time taken for the enzyme to process substrate to the product - fixed
-Rate inc (V) as [S] increases
However as the [S] increases a lot , the amout of time taken for the substrate to reach the enz is 0
And the rate is now dependent on the processing time only which is constant
At this stage we see a constant Vmax with inc substrate conc and enzyme is known to be saturated
This causes a hyperbole curve

44
Q

What are the assumptions made during the derivation of the mentis equation?

A

1- the k3»>K4, so k4 isnt a factor (this situations occur earlier in the reaction, when [P] =0)
2- K1 > k3, this make E+P formation the RDS( k3 - rate determining step)
3- rate of formations of E.S = k1[E][S]
4- rate of breakdown of E.S= k2[E.S] + k3[E.S]
5- in an equilibrium- the rate of forward formation=rate of backward breakdown
And equalize the above two equations.

45
Q

What are the 3 main reasons , that Km is important?

A

1- shows affinity of E for S
High km - fast dissociate- low Affinity -need for high [S]
Low km- slow dissociate- high affinity- need for low [S]
2- kx = [S] at 1/2 Vmax
High km , a need for high [S]= unfavourable reaction
Low km, need for low[S] - favoured reaction
3- km=[S] , [E.S]=[E]

46
Q

Why cant you ever calculate the Vmax from the M-M curve?

A

Vmax is a horizontal assimptote
The curve will come closer to Vmax , but never touch Vmax

47
Q

How can you accurately calculate Vmax from a graph?

A

Line weaver burke plot graph and its line equation
Bcz -, although Vmax is never reached , it can be extrapolated to straight line.
- very sensitive to variation

48
Q

Recall back , we mentioned the rate limiting step to be k3 (very slow). Why is rate limiting step important?

A

Helps us understand how many substrate convert to product in one second (turnover rate)
Quality control of vaccines
Help regulate optimum conditions in human bldy

49
Q

Explain and derive kcat = Vmax/[E.tot] using kcat=k3

A
50
Q

Kcat ranges from

A

5x10-1 —- 4x10^7/s

51
Q

Explain the use of kcat/km❓❓

A

It is the specificity constant - shows the efficiency of the enzyme
Higher sc higher efficiency
When km&raquo_space;>[S]
Then we can
V=kcat(etotal)(s)/km

52
Q

What are the advantages pf allosteric enzymes?

A

-REGULATION IN TWO WAYS
1- regulates enzymes using end product inhibition or feedback inhibitions
-Helps in regulation, where the final product inhibits Enz 1
For ex L-Ile inhibits threonine dehydratase
-it acts as inhibitors, by not resembling as the substrate for Enz1, so doesn’t attach to active site
2- tight regulation, because of high sensitivity of[S] over a narrow timeframe
Thats how- Remeber how we get the sigmoidal curve in it inital time , instead lf a linear straight line impn initial time in M-M curve

53
Q

What are other types of regulation ?

A

1-Covalent regulations
2-Zymogens
3-irreversible inhibitors

54
Q

What are the 4 types of covalent regulations?

A

1-PROTEIN KINASE - (adds P to amino acids)
phosphorylates ser
Phosphorylated ser attaches to allosteric site (causing allosteric conformation change) of glycogen phosphorylase
2- this above can be reversed by removing P from ser by PHOSPHATASE
1-2- phosphorykatio/deohophorylation - activates enzymes in metabolic control mechanism
3- protein ubiquitination- addition/removal of ubiquinin to influence its activity
Eg- analogous to protein phosphorylation

55
Q

What are zymogens

A

Zymogens are enzymes that are activated by proteolytic cleavages

56
Q

What zymogens does pancreas produces

A

Chymotripsinogen, tripsinogen, proelastase , procarboxypeptidase

57
Q

What enzyme carries out proteolytic cleavage of the zymogenes produced in pacreas

A

Enteropeptidase cleaves AA 1-6 of trypsinogen
Tripsinigen then activates other proenzymes that help in digestion of proteins on the duodenum

58
Q

What are irreversible inhibitor?

A

Irreversible I form cov bonds with the active site AA

59
Q

Give 3 examples of irreversible inhibition

A

1- penicillin reacts to serine in trans peptidase , inhibiting the bacterial cell wall synthesis
2- asperin acetylates ser in cox 2 enzyme ( that produces prostaglandins , a hormone that stimulates inflammation)
3- diisopropyl attaches ser 195, inactivating it

Biol 2700 (8 decks)

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