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Cell Biology and Signalling > Enzyme Properties > Flashcards

Enzyme Properties Flashcards

1
Q

What are enzymes?

A

Biological catalysts which speed up the rate of a reaction, without altering the final equilibrium between reactants and products

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2
Q

What effect does an enz have as a catalyst on reaction?

A
  • help reaction to reach equ
  • permit cells to make/break covalent bonds at will
  • lowers Ea and inc reaction rate - allow larger prop of random collisions with surrounding mol to kick sub over energy barrier
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3
Q

What is free energy and why is it important?

A
  • Energy needed to do work/drive chem reactions
  • chem reactions proceed only in direction that leads to loss of free energy
  • There has to be release of free energy for reactions to occur
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4
Q

What has to be put in for reaction to occur and why?

A
  • energy e.g. heat as mol rel stable and can’t be changed to lower energy states without it
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5
Q

What is the effect of an enzyme on activation energy of reaction?

A
  • Free energy of activation normally quite high
  • Enz make it poss so less energy put in for reaction to progress
  • Quicker rate but not altering equ
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6
Q

What are enzymes responsible for when it comes to foodstuffs?

A

the controlled “combustion” (oxidation) of foodstuffs

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7
Q

What is the equation for the combustion of propane?

A

5 O2+ C3H8 —> 4 H2O + 3 CO2

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8
Q

What is equation for the combustion of glucose?

A

6 O2 + C6H12 O6 —> 6 H2O + 6 CO2

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9
Q

How do enz control comb/ox?

A

create series of steps by capturing change in energy (increases as its released from glucose) instead of going from start to finish in one step

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10
Q

Describe process of catalysis

A

S binds to enz active site
ESC formed
Catalysis occurs and EPC formed
P released from enz

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11
Q

Which is enz complementary to transition state and why?

A
  • more likely to get P formed as shape of intermediate has better fit for active site than S.
  • Enz stabilises TS
  • when S binds, enz stretch/distort key bonds + weaken it so less Ea needed to break bond at start of reaction
  • cond created in env of active site to lower Ea
  • lower Ea - more mol turned into P in given time
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12
Q

What is substrate specificity?

A

Enzymes will usually catalyse only one type of reaction. A few enzymes are so specific they will act on one substrate

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13
Q

What does alcohol dehydrogenase do?

A

oxidises primary alcohols e.g. methanol, ethanol, propanol etc to aldehydes

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14
Q

Where is alcohol dehydrogenase found?

A

In liver

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15
Q

What is group specificity?

A

enz will act on only a few related molecules/sub

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16
Q

What does an enz do if a natural compound can exist in two stereoisomer forms e.g. D-glucose and L-glucose?

A

the enzyme concerned with its metabolism in the cell will usually act only on one isomer.

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17
Q

What is specificity determined by?

A

presence of ‘active site’ into which only the substrate of the correct shape and charge can fit.

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18
Q

What is the active site?

A

a groove or cleft of defined shape in enz in which only the substrate of the correct shape and charge can fit.

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19
Q

What can a group of enzymes present together in one compartment of a cell give rise to?

A

complex and co-ordinated metabolic pathway in which the initial substrate e.g D-glucose is converted through a sequence of specific enzyme catalysed reactions to the product e.g. lactic acid.

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20
Q

How does the pathway in which group of enz convert initial S to P work?

A

Enz specific enough so in pathway – only mol it can work on is the one it needs to work on. e.g. Enz 1 only specific to glucose in that form, enz 2 only specific to B etc. Ability to pass on mol – p of 1 enz reaction s of another

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21
Q

What has specificity of enzymes has led to?

A

systematic classification scheme, established by the I.U.B. Commission on Enzymes

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22
Q

What is systematic classification scheme, established by the I.U.B. Commission on Enzymes?

A

Enzymes are divided into 6 main classes according to the type of reaction they catalyse
Six classes are then further divided into subgroups according to their substrate or source.
Each enzyme is identified by its own individual 4 digit number

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23
Q

What are 6 classes of enz?

A
  1. Oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases
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24
Q

What do oxidoreductases do + 3 e.gs?

A

catalyze the transfer of hydrogen atoms and electrons - add O2/remove 2Hs
lactate dehydrogenase
alcohol dehydrogenase
catalase

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25
Q

What do transferases do + e.g?

A

catalyse transfer of functional groups from donors to acceptors
alanine amino transferase

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26
Q

What is hydrolases do + e.g?

A

catalyze the cleavage of bonds by the addition of water (hydrolysis)
trypsin

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27
Q

What is lyases do + e.g?

A

catalyze the cleavage of C-C, C-O, or C-N
bonds - addition of groups to double bonds or formation of double bonds by removal of groups
ATP-citrate lyase

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28
Q

What do isomerases do + e.g?

A

catalyze the transfer of functional groups within the same molecule
phosphoglucose isomerase

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29
Q

What do ligases do + e.g?

A

use ATP to catalyze the formation of new covalent bonds

DNA ligase

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30
Q

What is IUB name and number for alcohol dehydrogenase?

A

alcohol : NAD oxidoreductase

E.C. 1.1.1.1

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31
Q

What is IUB no. for catalase?

A

E.C. 1.11.1.6

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32
Q

What does lactate dehydrogenase do?

A

Interconverts pyruvate to lactate

rev reaction – direction in which it goes depends on sub

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33
Q

What does alanine amino transferase do?

A

transfers NH2 group of glutamate to across C=O in py to form l-alanine and the C=O bond in py to bit where NH2 group is in glutamate

34
Q

What does ATP-citrate lyase do?

A

Catalyses Oxal (4C) accepting (2C) acetate to form citrate (6C)/breakdown of citrate to oxaloacetate + acetate

35
Q

What does trypsin do?

A

Hydrolyses peptide of gly-lys-val-ala to dipeptides of gly-lys + val-ala

36
Q

What does phosphoglucose isomerase do?

A

transfers C=O from C1 in glucose-6 phosphate to C2 in fructose-6 phosphate

37
Q

What does DNA ligase do?

A

Links hydroxyl and phosphate group in nucleotides to form phosphodiester bonds

38
Q

What bio mol are enz?

A

Proteins

39
Q

What determines shape of active site in enz?

A

one or more polypeptide chains folding into a complex 3- dimensional shape

40
Q

How is enzyme structure stabilised?

A

many weak bonds e.g. H-bonds, electrostatic salt links, hydrophobic interactions.

41
Q

What does it mean when enz inactive/denatured?

A

as weak bonds broken by changing env e.g. by heating/pH giving rise to a disorganised or tangled structure in which the enzyme no longer has any catalytic activity

42
Q

What problem does property of enz structure being stabilised by weak bonds cause but what is adv of this?

A

makes enzymes very sensitive to changes in their environment u can change enz activity by changing env

43
Q

What does active site of the enzyme contain?

A

functional groups that stabilize the transition state of the reaction

44
Q

What is “Lock and Key” model for enzyme catalysis?

A
  • enzyme = lock
  • sub = key
  • Only the correctly sized key (substrate) fits into the key hole (active site) of the lock (enzyme).
45
Q

What is problem with “Lock and Key” model for enzyme catalysis?

A
  • doesn’t explain stabilization of enzyme.
  • When an enzyme has a substrate enter into its active site, the enzyme will change its shape slightly to match the substrate.
  • If enzymes were to be specifically designed to fit a substrate, then there would be no need for it to have to adjust its shape.
  • Nothing much happens – sub just sits in active site
46
Q

What is Induced Fit model of enzyme catalysis?

A
  • amino acid side-chains that are a part of the active site are molded into a specific position.
  • This position allows the enzyme to start the catalyzing process. E.g. To remove phos from ATP – put ATP into active site – enz changes shape so opp charges meet to catalyse
  • Also poss change in shape to do with another active site to change shape of that part of mol to make it more/less active
47
Q

What is Modified Lock and Key model?

A

Enz constrains structure of mol – more likely to bring them into active site e.g. Changing orientation of S1 to bring it closer to S2

48
Q

What does chymotrypsin do?

A

Cleaves peptide bonds by hydrolysis on the carboxyl side of tyrosine, tryptophan and phenylalanine and of large hydrophobic residues such as methionine

49
Q

What is Phase 1 of chymotrypsin mech?

A

Enzyme creates nucleophile from serine side-chain.
Nucleophile attacks substrate.
Covalent intermediate is formed with second product ( PN ) bonded to serine, and first product ( PC ) is released.

50
Q

What is Phase 2 of chymotrypsin mech?

A 
Enzyme creates a nucleophile from a water molecule.
Nucleophile attacks covalent intermediate, breaking covalent bond to  serine.
Second product ( PN ) is released.
51
Q

What is effect of temperature on enzyme reactions?

A
  • v. Often Increase temp – increase energy of enz mol + sub – chance of them colliding increases
  • Some point – temp destabilises enz – breakdown of enz structure – enz no longer catalyses
  • Over normal phys range but enz can have own phys range – some work in boiling water/freezing cond
52
Q

Why is it Enz in cold cond don’t work v. well?

A

sub mol don’t have much energy – not colliding with active site

53
Q

What is optimum pH?

A

one where structure (various ionisation of aa) consistent with function

54
Q

What is effect of pH on enzyme reactions?

A

Diff proteins work at diff pH
To do with charges in enz and proteins/aa
Charges are to do with level to which proteins/aa protonated (accepted H+)
E.g. Something that relies on O- to interact when there’s high conc of H+ in sol – it will accept H+ to form OH and not be able to take part in the reaction or other way around

55
Q

What is Cu2+ cofactor for?

A

Cytochrome oxidase

56
Q

What is Fe2+/3+ cofactor for?

A

Cytochrome oxidase, catalase, peroxidase

57
Q

What is K+ cofactor for?

A

Pyruvate kinase

58
Q

What is Mg2+ cofactor for?

A

Hexokinase, G-6-phosphatase, pyruvate kinase

59
Q

What is Ni2+ cofactor for?

A

Urease

60
Q

What is Se cofactor for?

A

Glutathione peroxidase

61
Q

What is Zn2+ cofactor for?

A

Carbonic anhydrase, alcohol dehydrogenase

62
Q

What do cofactors do?

A

inorganic substances (non-protein chemical compound or metallic ion) that are required for, or increase the rate of, catalysis. Involved in moving e-s.

63
Q

What are coenzymes?

A
  • A specific type of cofactor - organic molecules that bind to enzymes and help them function. T
  • they bind to the active site of the enzyme to form active enzyme and participate in catalysis but are not considered substrates of the reaction.
  • Donate/accept e-s/H
64
Q

What are 3 e.g. of coenzymes?

A

NAD+, FAD, ATP

65
Q

What is e.g. of reaction NAD+ involved in?

A

CH3 CH2 OH + NAD+ —> CH3CHO + NADH + H+

catalysed by alcohol dehydrogenase

66
Q

What is e.g. of reaction FAD involved in?

A

succinate + FAD —> fumarate + FADH2 (catalysed by succinate dehydrogenase)

67
Q

What is e.g. of reaction ATP involved in?

A

glucose + ATP —> glucose-6-phosphate + ADP

catalysed by glucokinase

68
Q

What are isoenzymes?

A

enzymes with different protein structures which catalyse the same reaction

69
Q

What are 3 properties of isoenzymes?

A

Coded for by different genes
•Different isoenzymes often found in different cellular compartments (cytoplasm or mitochondria), or different amounts in different tissues
•Distinct biochemical roles – sometimes found in diff tissues/Respond diff to changes in substrate conc

70
Q

What are e.gs of isoenzymes?

A

e.g. hexokinase /glucokinase.

Lactate dehydrogenase

71
Q

What is reaction for conversion of py to L-lactate?

A

pyruvate + NADH + H+ L-lactate + NAD+

72
Q

Why are enz extremely efficient?

A

Speed up reactions by factor of m/more without themselves being changed
e.g. the enzyme catalase catalyses the breakdown of its substrate H2O2 to water at a rate 1014x faster than the uncatalysed reaction at 30C.

73
Q

In which direction do chem reactions proceed?

A

Direction that leads to loss of free energy which means as reaction progresses - change in free energy from R to P

74
Q

Why does energy have to be put in for a reaction to proceed?

A

Mol rel stable and can’t be changed to lower energy states without initial input of energy

75
Q

What is activation energy?

A
  • Min energy required to start reaction
  • Energy that boosts mol over energy barrier before it can undergo chem reaction that moves it to lower energy (more stable) state
  • Normally quite high
76
Q

How do enz lower activation energy?

A

Bind tightly to substrates + hold them in way that red activation energy

77
Q

Why are enz catalysts?

A

Lower activation energy of reaction and inc rate of reaction

78
Q

How do enz inc rate of chem reactions?

A

Allow larger proportion of random collisions with surrounding mol to kick sub over energy barrier

79
Q

What is reaction rate like when there’s no enz and why?

A
  • takes long time
  • activation energy needs to be overcome
  • energy needs to be put in so stick bends and breaks
80
Q

Why is not much P formed when enz comp to sub?

A
  • sub has to be distorted in particular shape (transition state) for enz to occur
  • to distort sub - lots of energy needed from random mol collisions
  • energy almost never exceeds Ea so reaction occurs slowly if at all
81
Q

What is transition state?

A

Where atoms around bond have altered geometry + e- distribution

  • state corresponding to highest energy along reaction (at peak of curve) on free energy graph
  • has more free energy compared to S/P
  • least stable state

Cell Biology and Signalling (7 decks)

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