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Biochemical Structures > Enzymes > Flashcards

Enzymes Flashcards

1
Q

Enzyme definition

A

A globular protein that stabilises the transition state relative to the substrate, speeding up reactions. A biological catalyst

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2
Q

Catalysis definition

A

Lowering the energy barrier to reach the transition state, without the enzyme being used up at the end

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3
Q

Enzyme reaction in its simplest form

A

E+A ⇌ EA –> E + P. Where EA is the enzyme substrate complex.

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4
Q

Enzyme reaction in a more complicated form

A

E+A ⇌ EA ⇌ EA ⇌ EP ⇌ EP ⇌ E + P

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5
Q

Explain the more complicated reaction symbols and stages

A

Substrate A rapidly reacts with Substrate E to form a loose association enzyme substrate complex.

Interactions of the substrate with the resides of the catalytic centre yields a tight transition state complex.

This state is able to convert the tightly bound substrate into a tightly bound product.

This then turns to a loosely associated EP before dissociating into a free product and enzyme.

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6
Q

What is the transition state complex?

A

A chemical reaction undergoing when the enzyme and substrate are in contact, not simply the formation of an enzyme-substrate complex. Highest free energy and is extremely unstable due to the constant bond breaking and bond forming events.

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7
Q

Initial state definition

A

the total energy content of a system before a reaction takes place

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8
Q

Final state definition

A

Energy content after a reaction has taken place

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9
Q

When does a reaction occur?

A

If Gibb’s free energy is negative

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10
Q

What is Gibb’s free energy?

A

Fraction of energy released in a biochemical process available to do work of some kind.

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11
Q

6 classes of chemical reactions

A

Hydrolysis, condensation, ligation, group transfer, redox, isomerisation

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12
Q

Hydrolysis reaction + enzyme

A

Process of using water to break down a molecule into two parts. Hydrolase

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13
Q

Condensation reaction

A

Class of organic addition reaction with the release of a water molecule

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14
Q

Ligation reaction + enzyme

A

The joining of two nucleic acid fragments using DNA ligase.

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15
Q

Group transfer reaction + enzyme

A

Process where one or more groups of atoms is transferred from one molecule to another. Tranferase

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16
Q

Redox reaction + enzyme

A

Chemical reaction where the oxidation states of the atoms are changed. Oxidoreducatases- enzymes that are associated with coenzymes

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17
Q

Isomerisation reaction + enzyme

A

Process by which one molecule is transformed into another molecule which has exactly the same number of atoms but with different arrangements. Isomerase

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18
Q

How do enzymes catalyst chemical reactions in general terms?

A

Lower the activation energy barrier, converting a complex reaction into a number of simpler ones, where each step has a smaller activation energy barrier. Hastens the approach towards equilibrium, possibly accelerating the reactions in either directions.

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19
Q

Active site definition

A

A region of the enzyme that has both a binding and catalytic site. Substrate binds to the binding site. The position in which it binds strains the substrate, causing it to change. Often a cleft, crevice or pocket.

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20
Q

What play an essential role in binding?

A

Amino acid residues, cysteine, glutamate, aspartate, lysine, arginine, histidine, serine, threonine and hydrophobic residues.

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21
Q

What bonds form between the active site and substrate?

A

non covalent bonds: hydrogen bonds, ionic attractions, hydrophobic bonds, Van Der Waals and potentially transient covalent bonds.

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22
Q

What does enzyme specificity depend on?

A

The shape of the active site (caused by the different primary structures of polypeptides) that are only complementary to a given substrate.

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23
Q

Different types of specificity + explained and example

A

Absolutely specific- glucose oxidase. Will act on glucose alone

broad substrate specificity- hexokinase. Will act on a range of hexoses, not just glucose

Group specific enzymes- alcohol dehydrogenase. Enzyme catalyst selective in acting on specific groups. Will act on both primary and secondary alcohols.

Stereospecific enzyme- L-amino acid oxidase. Act only on one enantiomer.

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24
Q

Enzyme promiscuity definition

A

Enzymes with relaxed substrate specificity, catalyse distinctly different reactions, distinct catalytic activity under unnatural conditions (extreme temperature and pH).

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25
Q

What is a multimeric enzyme?

A

An enzyme formed of two or more polypeptide chains

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26
Q

Isoenzymes definition

A

Enzymes catalysing the same reaction from different genes. Enzymes with the same function but different structure

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27
Q

What differs between isoenzymes?

A

Kinetic parameters, regulatory proteins and amino acid sequence

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28
Q

Isozyme Example

A

Lactate Dehydrogenase (LDH) is a tetramer formed of two subunits, H form and M form. Exists in 5 forms. Found mostly in red blood cells and heart and indicate damage of diseased tissue

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29
Q

Multienzyme complex definition

A

Stable assemblies of more than one enzyme, generally involved in sequential catalytic transformations.

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30
Q

Multienzyme complex example

A

pyruvate dehydrogenase is a complex of three different enzymes that collectively catalyse the oxidation of pyruvate. Has two catalytic sites providing TPP and magnesium ion cofactor.

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31
Q

cAMP- dependent protein kinase explained

A

Protein kinase A activated by a rise in cAMP, causing the catalytic subunits to dissociate and become released- physical separation of catalytic and regulatory proteins in the enzyme. Dependent on allosterity (binding of cAMP.

32
Q

Co-factor definition

A

A non-protein chemical compound or metallic ion that is required for an enzyme’s activity as a catalyst. T

33
Q

Two types of co factors explained

A

prosthetic group- consists of a coenzyme with a permanently bound co factor.

Co-substrate- co factor is transiently bound

34
Q

Two classifications of cofactor

A

Inorganic- metal ions and organic- vitamins and derivatives.

35
Q

Holoenzyme definition

A

Complete enzyme with cofactor

36
Q

apoenzyme definition

A

An inactive enzyme without a cofactor

37
Q

Why are vitamins/vitamin derivatives often cofactors?

A

Contain an AMP structure, such as ATP, coenzyme A, FAD or NAD+.

38
Q

Which vitamins act as precursors?

A

B1, B2, B6 and B12

39
Q

Which vitamin acts as a cofactor?

A

Vitamin C

40
Q

What trace elements act as cofactors?

A

Fe3+, Zn2+, Ca2+. CO3+

41
Q

Metal ion functions

A

May determine the enzyme structure

help bind to the substrate, enhancing the action of the enzyme.

Can shield charge- such as Mg2+ which forms an Mg-ATP complex, orientating the phosphates on ATP to form the correct orientation and reduces the charge on the polyphosphate chain, preventing repulsion with the substrate

42
Q

What must occur for an ES complex to form?

A

The molecules must be in close proximity and correct orientation for the transient bonds to form between the active site and substrate.

43
Q

What is the regulator of a pathway?

A

The enzyme that catalyses the first step in a metabolic pathway.

44
Q

Two types of regulatory enzyme

A

Allosteric or regulated by covalent modification

45
Q

Allosteric enzyme definition

A

An enzyme with a different binding site (not just active site) where an effector can bind causing a conformational change which either activates or inhibits the enzyme

46
Q

What is the different binding site called?

A

Allosteric site

47
Q

Example of allosteric regulator explained

A

Feedback inhibition, where the final product of the metabolism pathway inhibits the enzyme, which can slow the rate of action of the enzyme if the products exceed the requirements.

48
Q

Allosteric effector definition

A

Regulatory molecule that binds to the allosteric site and modifies the rate. Positive if they stimulate enzyme activity and negative if they depress enzyme activity

49
Q

Two types of allosteric modulator explained

A

Homotropic- allosteric modulator is the substrate itself

heterotropic- allosteric modulator is different from the substrate.

50
Q

Explain mechanism of cooperativity

A

Most allosteric enzymes have many subunits with many allosteric sites. Long distance interactions between the sites causes a sigmoidal dose curve, becomes easier for substrate to bind.

This is due to the initial effector causing a conformational change in the other active sites so its easier to bind.

51
Q

Cooperativity rules

A
  1. Subunits of proteins are functionally related
  2. Each protein can exist in two functional states- T tense and R relaxed. These states are in equilibrium even if ligand is not bound
  3. Binding of ligand shifts the equilibrium towards either tense or relaxed changing the affinity for the ligand.
  4. inhibitors will bind to tense form and effectors to relaxed form.
52
Q

Allosteric enzyme response curve explained

A

Enzyme activity plotted against increasing concentrations of substrate a sigmoidal curve is formed. Binding of ligand creates a long distance change, altering the active sites. However, hard to bind final molecules as probability of colliding with the right orientation in the right place is lowered.

53
Q

Terms for binding the same/different molecule

A

Heterotropic- different

homotropic- same e.g oxygen in haemoglobin

54
Q

Two types of inhibition

A

Competitive and non competitive

55
Q

Competitive inhibition explained

A

Substrate and inhibitor occupy the same binding site on the enzyme or if binding of substrate changes the conformation of the enzyme so that the inhibitor cannot bind to an allosteric site.

56
Q

Non competitive inhibition explained

A

Both the free enzyme and enzyme-substrate complex can bind the inhibitor.

Substrate binding does not change the conformation of the enzyme that would change the affinity for the inhibitor.

affinity for the inhibitor is smaller than that of the substrate

Binding of the substrate reduces the affinity for binding the inhibitor

57
Q

What is the Monod-Wyman-Changeux model?

A

Formulated for oligomeric proteins with identical subunits, each with a ligand binding site.

Equilibrium of conformational states terminal relaxed and tense, which differ in affinity for ligand molecules.

T state has low affinity and R state has high affinity.

If an allosteric protein binds a target that has a higher affinity for R, the target binding further stabilises the R state, increasing that ligand’s affinity.

58
Q

What is ATCase?

A

Aspartate trans-carbamylase, catalyses the first step In the pyrimidine biosynthetic pathway.

59
Q

ATCase structure

A

Contains catalytic subunits that catalyse the carbamylation of the amino group of aspartate. Also has regulatory subunits containing allosteric sites. Formed of two catalytic dimers held together by three regulatory dimers.

60
Q

Inhibitors and activators OF ATCase

A

ATP binds to allosteric sites and activates the enzyme. (ASP and CP binding domains need to be together to work)

CTP binds to allosteric sites and inhibits the enzymes. CTP prevents the required conformational change for the enzyme to be activated

61
Q

Haemoglobin cooperativity explained

A

When oxygen binds to iron complex, the iron atom moves back into the centre of the porphyrin ring. Other conformational changes occur to expose the oxygen binding sites.

Binding of oxygen to one monomer also shifts the conformation from tense state to relaxed

62
Q

Inhibitors of haemoglobin

A

Competitive- carbon monoxide, cyanide and hydrogen sulfide.

Non-competitive- carbon dioxide (Bohr effect)

63
Q

Myoglobin cooperativity explained

A

Does not exhibit cooperativity as it is a monomeric protein with one binding site, therefore follows hyperbolic binding curves

64
Q

Lock and Key model explained

A

Proposed by E.Fischer who claimed that it is a direct fit between the rigid enzyme and substrate- very similar to strict specificity

65
Q

Induced fit model explained

A

Proposed by Koshland- enzyme structure is plastic. Enzyme modifies its conformation when in contact with a substrate, adapting to it and orientating essential residues to obtain maximal conformational change for catalysis.

66
Q

Where does the energy come from to form the ES complex assuming the induced fit model?

A

Activation energy derived from the binding energy between the enzyme and transition state.

67
Q

Drugs as allosteric ligands explained

A

Bind to allosteric site and can either upregulate the enzyme, such as those involved in immune responses that can target rapidly dividing cancer cells, or down regulate (shift sites to tense) such as those involved in the cell cycle, preventing neoplasia.

68
Q

How do covalent modifications regulate enzymes?

A

Post-translational covalent modification alters the activity of the enzymes, potentially for active or active.

69
Q

Main covalent modification?

A

Phosphorylation

70
Q

Explain phosphorylation cascade

A

OH functional group on serine, threonine or tyrosine of enzyme can undergo an addition of a phosphate from a protein kinase.

This forms a large negatively charged moiety which then undergoes a large conformational change, which in turn alters another protein and so forth

71
Q

Coagulation cascade

A

Zymogen of a serine protease and its glycoprotein cofactor are activated and catalyse the next reaction in the cascade, eventually forming cross linked fibrin.

72
Q

Zymogen definition

A

proenzymes that become catalytically active by hydrolysis.

73
Q

Function of HMG-CoA reductase

A

catalyses the conversion of HMG-CoA into mevalonic acid, in the biosynthesis of cholesterol

74
Q

What drug lowers cholesterol and how do they work?

A

HMG-CoA reductase inhibitors, known as statins. Prevent the formation of mevalonic acid, which thus lowers cholesterol levels. competitive inhibitor

75
Q

Explain how salt concentrations effect enzyme action

A

At 0mM of salt, enzymes bind to one another, thus do not function

As the salt increases, the solubility of the enzyme improves, so works faster

After the salt concentration exceeds a certain value, salting out occurs

This is where the alts bind to the enzyme, neutralising all the charges, preventing the enzyme from interacting with water- forming a precipitate containing enzyme

76
Q

What balances out the negative charge across the cell membrane?

A

Negative charge from DNA and RNA

Biochemical Structures (9 decks)

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