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Biochemistry > Enzyme structure and functioning > Flashcards

Enzyme structure and functioning Flashcards

1
Q

What are enzymes?

A

Biological catalyst that lowers the activation energy

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2
Q

What kind of proteins are most enzymes?

A

Globular

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3
Q

What are all metabolic processes catalysed by?

A

Enzymes

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4
Q

Are enzymes specific catalysts?

A

Yes

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5
Q

What is the substrate?

A

The molecule or atom that an enzyme acts on

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6
Q

What is substrate transformed into?

A

Product

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7
Q

Why are biocatalysts better than inorganic catalysts?

A

More effective
Greater specificity (avoids side products)
Milder reaction conditions
Higher reaction rate
Capacity for regulation

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8
Q

Can active sites of enzymes recognise stereoisomers?

A

Yes

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9
Q

What do proteolytic enzymes do?

A

Catalyse the hydrolysis of peptides and also the hydrolysis of an ester bond

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10
Q

Do different enzymes have different degrees of specificity?

A

Yes they do

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11
Q

What are cofactors?

A

Small molecules that some enzymes require for activity

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12
Q

Two main classes of cofactors

A

Coenzymes (organic molecule derived from vitamin)
Metals

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13
Q

What are tightly bound coenzymes called?

A

Prosthetic group

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14
Q

What are holoenzymes?

A

Enzymes with its cofactor

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15
Q

What are apoenzymes?

A

Enzymes without its cofactor

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16
Q

Are there any disorders and deceases that are caused by deficiency of one enzyme or excessive activity of an enzyme?

A

Yes both

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17
Q

Can enzymes be used therapeutically?

A

Yes

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18
Q

Do many drugs act through interactions with enzymes

A

Yes

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19
Q

What are isoenzymes?

A

Same catalytic action and same name (like exokinese) but there are more variants (like I II III …) which are produced by different organs

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20
Q

6 major classes of enzymes

A

Oxidoreductases
Transferases
Hydrolases
Lyases (synthases)
Isomerases
Ligases (synthetases)

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21
Q

What do transferases do?

A

Transfer groups

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22
Q

What do hydrolyses do?

A

Use water to break proteins

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23
Q

What do lyases?

A

Fuse two molecules to form one molecule

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24
Q

What do isomerases do?

A

Transfer isomers, move groups

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25
Q

What are ligases?

A

Uses energy to fuse two molecules together

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26
Q

5 types of enzyme regulations

A

Allosteric regulation
Reversible covalent modifications
Proteolytic cleavage
Feedback regulation
Regulation by isoenzymes

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27
Q

What is the allosteric site?

A

Site that is different from the binding site

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28
Q

Can feedback regulation be positive or negative?

A

Both

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29
Q

Can allosteric regulation be positive or negative?

A

Both

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30
Q

What is the rate of enhancement?

A

How much the enzymes enhances the reaction compared to without the enzymes

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31
Q

Is the tertiary structure of a protein destabilised by the hydrophobic effect?

A

No

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32
Q

Where does the strength of alpha kreatin protein come from?

A

Cross-linking alpha helices by disulfide bonds

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33
Q

The motif in the glycolysis enzyme hexokinase could contain what?

A

Beta turn
Beta sheet
Alpha helix
Disulfide bonds

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34
Q

What feature is not associated with globular proteins?

A

Alpha and beta classification

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35
Q

What characteristics of protein is associated with proteostasis?

A

Synthesis
Refolding
Degradation

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36
Q

What does denaturing followed ny renaturing of a protein demonstrate?

A

That primary structure dictates tertiary structure

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37
Q

Are chaperones always required?

A

No

38
Q

What does gibbs free energy provide information about?

A

Spontaneity and not the rate of reaction

39
Q

What does the Gibbs free energy have to be for a reaction to occur?

A

Negative

40
Q

What is a reaction called when the gibbs free energy is negative?

A

Exergonic reaction

41
Q

What is Gibbs free energy when the reaction is at equilibrium?

A

0

42
Q

What is a reaction called if Gibbs free energy is positive?

A

Endergonic reaction

43
Q

Do enzymes affect the equilibrium?

A

No

44
Q

Can enzymes effect the Gibbs free energy of a reaction?

A

No

45
Q

What is the velocity of a reaction?

A

Product/time

46
Q

Which has the highest activation state:
Product to substrate
or
Substrate to product

A

Product to substrate

47
Q

What does enzymes do to lower the activation energy?

A

Organise the reactive groups into close proximity and proper orientation

48
Q

What do enzyme bind best?

A

Transition states

49
Q

Does speed matter when it comes to enzymes?

A

Yes speed matters a lot

50
Q

What is binding energy?

A

Major source of free energy used by enzymes to lower the activation energies of reactions

51
Q

Common features of active sites of enzymes

A

3d cleft or crevice created by AA from different parts of the primary structure
Active site constitutes a small portion of the enzyme volume
Unique microenvironment
Multiple weak interactions take place between enzyme and substrate
specificity depends on the molecular architecture at the active site

52
Q

Does the specificity of an enzyme effect the rate of reaction?

A

Not necessarily

53
Q

Is the ligand binding site and active site the same?

A

Yes, both connect with substrate and change into a product
The ligand binding site is a part of the active site

54
Q

4 factors contributing to the barrier to reaction

A

Entropy of molecules in solution
Salvation shell of hydrogen bonded water
The distortion of substrates that must occur in many reaction
The need for proper alignment of catalytic functional group

55
Q

What kind of energy can be used to overcome all the barriers contributing to the reaction barrier?

A

Binding energy

56
Q

What is the desolvation of the substrate?

A

Removing of molecules surrounding substrate

57
Q

What is acid-base catalysis?

A

Give and take protons

58
Q

What is covalent catalysis?

A

Change reaction paths

59
Q

What is metal ion catalysis?

A

Use redox cofactor, pKa, shifters

60
Q

3 kinds of catalysis

A

Acid-base
Metal ion
Covalent

61
Q

Are enzymes specific for a particular substrate?

A

Generally yes

62
Q

Difference between number of products produced by an enzyme and a nonbiological catalyst

A

An enzymes yields a specific product where nonbiological catalyst may produce more than one product because of side reactions

63
Q

Effects of enzymes on reaction

A

Activation energy lowered
Formation of transition state is promoted
Rate constant for reverse reaction increases

64
Q

2 ways enzymes increase the rate of reaction

A

Lower the activation energy of the reaction
Promote the formation of a transition state

65
Q

Difference between lock and key and induced fit model

A

In induced fit the conformation changes when the substrate binds where in lock and key the structure is rigid

66
Q

2 things both the induced fit and lock and key model have in common

A

The substrate binds at the active site, forming an enzyme-substrate complex
The substrate binds to the enzyme through non covalent interactions

67
Q

What inorganic ion does not serve as a cofactor?

A

Ca2+

68
Q

What is an apoenzyme?

A

An enzyme that requires a cofactor for its activity

69
Q

What is the inorganic ion called when it is very tightly or covalently bound by the enzyme?

A

A prosthetic group

70
Q

Is polymerases one of the 7 EC classes of enzymes?

A

No

71
Q

What is the free energy starting point for a reverse reaction designated as?

A

Ground state

72
Q

Why is the conversion of sucrose to CO2 not spontaneous?

A

Because it has a very large activation energy barrier

73
Q

What does an enzyme change relative to an uncatalyzed reaction?

A

The rate of the reaction

74
Q

Can small changes in free energy lead to large changes in the equilibria?

A

Yes

75
Q

What a reaction where the rate depends on the concentration of two molecules called?

A

Second-order reaction

76
Q

Binding energy is defined as

A

The energy derived from non covalent enzyme-substrate interaction

77
Q

What is the primary source of the energy enzymes used to reduce activation energies?

A

Noncovalent enzyme-substrate intercation

78
Q

How does the induced fit mechanism of enzyme catalysis work?

A

The enzyme undergoes a conformational change to maximise weak interactions to the substrate

79
Q

Which amino acid has the least effect on the function of an enzyme if it replaces a Glu residue in the enzyme?

A

Asp

80
Q

True or false: does covalent catalysis by enzymes never involve coenzymes?

A

False

81
Q

What does it mean that enzymes can be stereoselective?

A

They can be so elective they distinguish L-amino acids and D-amino acids

82
Q

What do proteolytic enzymes catalyse?

A

The hydrolysis of peptide bonds

83
Q

2 bonds proteases bread

A

Peptide bonds
Ester bonds

84
Q

2 proteolytic enzymes

A

Trypsin
Thrombin

85
Q

Do trypsin and thrombin have the same specificity?

A

No

86
Q

During which state does the enzymes bind most tightly?

A

Transition state

87
Q

Which amino acid residue is especially agressive in acid-base catalysis?

A

Serine

88
Q

What does covalent catalysis require on the enzyme?

A

A nucleophile

89
Q

Examples of nucleophiles used in covalent catalysis

A

Serine
Thiolate
Amine
Carboxylate

90
Q

What is chymotrypsin?

A

A peptidase

91
Q

Can one enzyme use multiple enzymatic mechanisms?

A

Yes

Biochemistry (28 decks)

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