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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
Explain change in vmax and kmax
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
Draw the two graphs for the other two inhibitors
27
State the curve name of 1- v0 by (s) graph 2- m-m grap - v0 by (s) 3- draw them
1- sigmoidal 2- hyperbole
28
Why are the curve different?
Sigmoidal is over a very narrow period of time therefore the enzyme acts as an in and off switch
29
When does this Non M-M graph behaviour occurs (i think they are talking about sigmoidal graph curve)
1- due to cooperativity 2- the binding of S to an active site , make the binding of a subsequent S easier.
30
What is cooperatiivity?
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
How does binding of one S to an active site affects the binding of the other S of the active site?
-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
Draw what was explained regarding the non behaviour of mm curve
33
What can affect the kinectic curves - the sigmoidal and hyperbole curve
Anything that affects the equilibrium Eg - activators and inhibitors
34
How do activators and inhibitors affect kinetic curve?
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
Give an example of I and A binding and also draw the curve
Enzyme- phosphofructokinase Substrate- fructose 6 p Inhibitor - ATP activators- AMP
36
Give an example of allosteric enzyme /non enzyme and how it helps the human body
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
Explain the catalysed and uncatalysed reaction of carbonic anhydrase
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
Does a catalyst affect keq, why or why not?
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
Why is studying enzyme mechanism important?
Provides knowledge and understanding basis of life, for modern drug dev, medicine and agriculture
40
Give an example of disease and drug that was made using protease studies/enzymes,proteins studies.
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
What are the two ways rates are measured experimentally
Increase in [P] over time Decrease in [S] over time
42
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
1- enz inactive 2- enz inactive 3- enzyme denatured by ionic disruption 4- enzyme denatured by heat disruption
43
What type of curve is a M-M curve ? Why does this curve occur?
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
What are the assumptions made during the derivation of the mentis equation?
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
What are the 3 main reasons , that Km is important?
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
Why cant you ever calculate the Vmax from the M-M curve?
Vmax is a horizontal assimptote The curve will come closer to Vmax , but never touch Vmax
47
How can you accurately calculate Vmax from a graph?
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
Recall back , we mentioned the rate limiting step to be k3 (very slow). Why is rate limiting step important?
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
Explain and derive kcat = Vmax/[E.tot] using kcat=k3
50
Kcat ranges from
5x10-1 —- 4x10^7/s
51
Explain the use of kcat/km❓❓
It is the specificity constant - shows the efficiency of the enzyme Higher sc higher efficiency When km >>>[S] Then we can V=kcat(etotal)(s)/km
52
What are the advantages pf allosteric enzymes?
-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
What are other types of regulation ?
1-Covalent regulations 2-Zymogens 3-irreversible inhibitors
54
What are the 4 types of covalent regulations?
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
What are zymogens
Zymogens are enzymes that are activated by proteolytic cleavages
56
What zymogens does pancreas produces
Chymotripsinogen, tripsinogen, proelastase , procarboxypeptidase
57
What enzyme carries out proteolytic cleavage of the zymogenes produced in pacreas
Enteropeptidase cleaves AA 1-6 of trypsinogen Tripsinigen then activates other proenzymes that help in digestion of proteins on the duodenum
58
What are irreversible inhibitor?
Irreversible I form cov bonds with the active site AA
59
Give 3 examples of irreversible inhibition
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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