biocatalysis 1

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    15.1 PROPERTIES OF ENZYME AND MECHANISM

    OF ACTIONS

    15.2 COFACTORS

    15.3 INHIBITION

    15 0 BIOCATALYSIS

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    15.1 PROPERTIES OF ENZYME

    a) State the properties of enzymes

    b) State the six classes of enzyme according

    to IUB classificationc) Explain the mechanism of enzyme action

    (lowering activation energy)

    d) Describe the hypotheses related to its

    mechanism of action: Induced fit model,

    lock and key model

    e) Explain factors that affect the enzymatic

    reaction

    Learning Outcomes

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    Enzyme is a biocatalyst

    Bio = life

    Catalyse = speed up the rate of reaction.

    Definition

    Enzyme is a globular proteins which act as

    biological catalyst that speed up the rate ofbiochemical reaction in living things by lowering

    the activation energy.

    Learning Outcomes:

    15.1 a) State the properties of enzymes

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    Structure of enzyme

    Mostly are globularproteins.

    Consist of one or several

    polypeptide chain with

    unique amino acids

    sequence.

    R groups of amino acids

    interact with each otherto form hydrogen bonds,

    ionic bonds &

    hydrophobic interaction.

    Learning Outcomes:

    15.1 a) State the properties of enzymes

    Structure of Enzyme

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    PROPERTIES OF ENZYME

    1. Enzymes are highly specific One enzyme acts only on a

    specific reactions or a few

    related reactions.

    Since each enzyme has aunique amino acid sequence,

    different interactions between

    R groups are formed.

    These interactions cause the

    polypeptide to fold into a

    unique 3 dimensional shape.

    Learning Outcomes:

    15.1 a) State the properties of enzymes

    Structure of Enzyme

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    1. Enzymes are highly specific

    The shape are highly specific especially at smallpart of enzyme called active site which binds to a

    specific substrate.

    Learning Outcomes:

    15.1 a) State the properties of enzymes

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    2. Enzymes remain unchanged at the end of reaction

    Enzymes are not altered, destroyed or used by the

    reaction it catalyses.

    Some enzyme can be used repeatedly.

    3. Enzymes are highly efficient

    Only smallamount of enzyme is needed to react with

    large amount of substrate.

    Learning Outcomes:

    15.1 a) State the properties of enzymes

    Properties of Enzyme

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    4. Most catalysed reaction are reversible

    An enzyme can catalyse both the forward and reverse

    reactions.

    5. Does not influence the direction of reaction and final

    concentration of products

    It only speeds up the rate of reaction.

    6. Enzymes activity is influenced by temperature, pH,

    substrate & enzyme concentration and inhibitors.

    Enzyme activity are maximum at optimum temperature

    or PH

    can be denatured by extreme temperature or extreme

    pH.

    Learning Outcomes:

    15.1 a) State the properties of enzymes

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    15.1 PROPERTIES OF ENZYME

    a) State the properties of enzymes

    b) State the six classes of enzyme according

    to IUB classificationc) Explain the mechanism of enzyme action

    (lowering activation energy)

    d) Describe the hypotheses related to its

    mechanism of action: Induced fit model,

    lock and key model

    e) Explain factors that affect the enzymatic

    reaction

    Learning Outcomes

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    1. In 1964, IUB (International Union of Biochemistry)

    introduced a classification guide of enzymes to

    differentiate enzymes.

    2. Before it is introduced, it is hard to recognize enzyme

    according to traditional way of naming.

    3. Eg: pepsin, renin, trypsin

    4. Enzymes are classified into 6 main classes according

    to the general reaction it catalyses.

    ENZYME CLASSIFICATIONLearning Outcomes:

    15.1 b) State the six classes of enzyme according to IUB classification

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    The Classification of Enzyme

    1. Common naming of enzyme usually has 3parts

    1) name of substrate

    2) type of reaction3) suffix ase

    Eg: Alcohol dehydrogenase, RuBP

    carboxylase

    2. Sometimes, they are named based on the

    substrate they act on

    3. Eg: sucrase, amylase, lipase, protease

    Learning Outcomes:

    15.1 b) State the six classes of enzyme according to IUB classification

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    Enzyme ClassificationEnzyme group Type of reaction

    catalysedEnzyme

    examples

    1. Oxidoreductase Transfer of O or H atoms or

    electrons between

    substances, i.e. all

    oxidation-reductionreactions.

    Dehydrogenase

    Oxidase

    2. Transferase Transfer of a chemical

    group from one substance

    to another

    Transaminase

    Phosphorylase

    3. Hydrolase Breaking a molecule into

    simpler molecules by

    hydrolysis reactions

    (addition of water

    molecule)

    Peptidase

    Lipase

    Sucrase

    Learning Outcomes:

    15.1 b) State the six classes of enzyme according to IUB classification

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    Enzyme

    group

    Type of reaction

    catalysed

    Enzyme

    examples

    4. Lyase Breaking of a chemical bonds

    without the addition of water

    (other than by hydrolysis)

    Decarboxylase

    (remove CO2)

    5. Isomerase The rearrangement of atoms

    within a molecule converting

    from 1 isomer to another

    Isomerase

    Mutase

    6. Ligase Formation of bonds between

    two molecules using energyfrom the breakdown of ATP

    Synthetase

    Learning Outcomes:

    15.1 b) State the six classes of enzyme according to IUB classification.

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    15.1 PROPERTIES OF ENZYME

    a) State the properties of enzymes

    b) State the six classes of enzyme according

    to IUB classificationc) Explain the mechanism of enzyme action

    (lowering activation energy)

    d) Describe the hypotheses related to its

    mechanism of action: Induced fit model,

    lock and key model

    e) Explain factors that affect the enzymatic

    reaction

    Learning Outcomes

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    Before any chemical reactions can occur, reactants

    must absorb energy to break the existing bonds

    before new bonds can be formed.

    Definition

    The minimumenergy required to break the existing

    bond for a chemical reaction to take place is calledactivation energy.

    Learning Outcomes:

    15.1 c) Explain the mechanism of enzyme action (lowering activation energy)

    Activation Energy (Ea)

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    The existing bonds start to

    break when enough energy isabsorbed.

    Reactants become unstable

    and very reactive.

    This condition is calledtransition state.

    By lowering the activation

    energy, less energy can be

    absorbed to start a reaction.

    More reactants can reachtransition state and converted to

    products within a short time.

    Learning Outcomes:

    15.1 c) Explain the mechanism of enzyme action (lowering activation energy)

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    Learning Outcomes:

    15.1 c) Explain the mechanism of enzyme action (lowering activation energy)

    Activation Energy (Ea)

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    Learning Outcomes:

    14.1 c) Explain the mechanism of enzyme action (lowering activation energy)

    Activation Energy (Ea)

    L i O

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    Substrate binds to enzymes active site to form an

    enzyme substrate complex

    Bring substrate molecule closer to each other / in

    a correct orientation Enzyme stretch / distort the existing bonds

    Learning Outcomes:

    15.1 c) Explain the mechanism of enzyme action (lowering activation energy)

    How Enzyme Lowers the Activation Energy

    L i O t

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    R group of active sites interact with substrates to

    increase the reactivity of the substrate.

    These make it easier for substrate to be changed

    into product.

    Thus, activation energy is reduced without

    increasing the temperature in living cells.

    Learning Outcomes:

    15.1 c) Explain the mechanism of enzyme action (lowering activation energy)

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    15.1 PROPERTIES OF ENZYME

    a) State the properties of enzymes

    b) State the six classes of enzyme according

    to IUB classificationc) Explain the mechanism of enzyme action

    (lowering activation energy)

    d) Describe the hypotheses related to its

    mechanism of action: Induced fit model,lock and key model

    e) Explain factors that affect the enzymatic

    reaction

    Learning Outcomes

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    1. Proposed by Koshland

    (1959).

    2. Suggested that theactive site is not exactly

    complementary to the

    shape of substrate.

    3. The active site is

    flexible and can change

    its shape.

    Learning Outcomes:

    15.1 d) describe the hypotheses related to its mechanism of action: Induced fit model, lock and key model

    Induced fit model

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    4. When collisions occur between

    enzyme and substrates,substrate can bind to the active

    site of the enzyme.

    5. The binding of the substrateinduces the enzyme to change

    its shape slightly.

    6. To enable the substrate to fit

    precisely to the active site.

    7. An Enzyme-Substrate complex

    is formed.

    Learning Outcomes:

    15.1 d) describe the hypotheses related to its mechanism of action: Induced fit model, lock and key model

    O

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    8. Enzyme stretched the existing

    bond to facilitate the reaction tooccur.

    9. Activation energy is reduced,

    so it is easier to achieve

    transition state.

    10. Product is formed and

    released from the active site.

    11. Enzyme changes back to

    original conformation.

    Learning Outcomes:

    15.1 d) describe the hypotheses related to its mechanism of action: Induced fit model, lock and key model

    L i O t

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    Learning Outcomes:

    15.1 d) describe the hypotheses related to its mechanism of action: Induced fit model, lock and key model

    L i g O t

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    Induced fit model

    Learning Outcomes:

    15.1 d) describe the hypotheses related to its mechanism of action: Induced fit model, lock and key model

    L i g O t

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    Induced fit model

    Learning Outcomes:

    15.1d) describe the hypotheses related to its mechanism of action: Induced fit model, lock and key model

    Learning Outcomes

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    1. Enzyme is very specific because its active site

    had a specific shape that fits exactly to a

    specific substrate.

    2. The shape of active site is rigid.

    3. This is called lock and key hypothesis which is

    proposed by Fischer (1890).

    4. Enzyme is bigger and act as lock.

    5. Substrate is smaller and act like a key.

    Learning Outcomes:

    15.1 d) describe the hypotheses related to its mechanism of action: Induced fit model, lock and key model

    Lock & Key model

    Learning Outcomes:

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    Lock & key model

    Learning Outcomes:

    15.1 d) describe the hypotheses related to its mechanism of action: Induced fit model, lock and key model

    Learning Outcomes:

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    Lock & key model

    1. The shape of active site isexactly complementary to the

    substrate.

    2. Substrate binds to the active site

    of enzyme to form an enzyme-substrate complex (ES complex).

    3. The shape of substrate slightly

    changed.

    4. Existing bonds are broken.

    5. Transition state is achieved,

    reaction occurs.

    Learning Outcomes:

    15.1 d) describe the hypotheses related to its mechanism of action: Induced fit model, lock and key model

    Learning Outcomes:

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    6. Products are formed.

    7. The shape of products differ from substrates.8. Thus, products no longer fit into active site.

    9. Products are released from active site.

    10. Free active site binds with other substrate.

    Learning Outcomes:

    15.1 d) describe the hypotheses related to its mechanism of action: Induced fit model, lock and key model

    Learning Outcomes:

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    Lock & key model

    Learning Outcomes:

    15.1 d) describe the hypotheses related to its mechanism of action: Induced fit model, lock and key model

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    15.1 PROPERTIES OF ENZYME

    a) State the properties of enzymes

    b) State the six classes of enzyme according

    to IUB classificationc) Explain the mechanism of enzyme action

    (lowering activation energy)

    d) Describe the hypotheses related to its

    mechanism of action: Induced fit model,lock and key model

    e) Explain factors that affect the enzymatic

    reaction

    Learning Outcomes

    Learning outcome:

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    1. Substrate concentration

    2. pH

    3. Temperature

    4. Cofactors

    g15.1 e) explain factors that effect the enzymatic reaction

    Factors affect the enzymatic reaction

    Learning outcome:

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    Substrate Concentration

    At low substrate

    concentration, the rate of

    enzyme reaction

    increases as substrateconcentration increase.

    There are many enzyme

    molecules compared to

    substrates, not all active

    sites are occupied.

    g15.1 e) explain factors that effect the enzymatic reaction

    Learning outcome:

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    As substrate concentration

    increase, more active sites

    are occupied until all of them

    bind to its substrate.

    The rate of reaction reaches

    the maximum rate.

    Increasing substrate

    concentration does not affect

    the rate of reaction since allactive sites are saturated with

    the substrate.

    The graph reaches a plateau.

    15.1 e) explain factors that effect the enzymatic reaction

    Learning outcome:

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    15.1 e) explain factors that effect the enzymatic reaction

    Learning outcome:

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    Most enzyme are effectiveover a narrow PH range.

    Maximum enzymes are

    effective over a narrow PH

    range.

    Different enzyme has

    different optimum pH value.

    Changes in pH above orbelow the optimal pH value

    will change the hydrogen

    ion (H+) concentration.

    pH

    15.1 e) explain factors that effect the enzymatic reaction

    Learning outcome:

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    15.1 e) explain factors that effect the enzymatic reaction

    Learning outcome:) f ff

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    This ion changes the ionic

    charge of the acidic & basicgroups of amino acids of the

    enzyme.

    The ionic & hydrogen bonds

    that hold the specific 3D

    shape of enzyme are

    disrupted.

    It changes the conformation ofactive sites.

    15.1 e) explain factors that effect the enzymatic reaction

    Learning outcome:15 1 ) l i f t th t ff t th ti ti

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    Substrate cannot fit into the

    active site to form Enzyme-Substrate complex.

    Therefore, the rate of reaction

    decreases quickly. If the changes of pH is too

    high or too low, the active

    sites are destroyed causing

    the enzyme to denature.

    Therefore the rate of reaction

    decreases quickly.

    15.1 e) explain factors that effect the enzymatic reaction

    Learning outcome:15 1 ) l i f t th t ff t th ti ti

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    Enzyme Optimum pHPepsin 2.00

    Sucrase 4.50

    Enterokinase 5.50

    Salivary amylase 7.80

    Trypsin 8.00

    Pancreatic lipase 9.00

    15.1 e) explain factors that effect the enzymatic reaction

    Learning outcome:15 1 ) l i f t th t ff t th ti ti

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    All enzymes work withina range of temperaturespecific to organism.

    Increases intemperature generallylead to increases inreaction rates.

    At low temperatures, anenzyme-catalysedreaction takes placeslowly.

    Temperature

    15.1 e) explain factors that effect the enzymatic reaction

    Learning outcome:15 1 ) l i f t th t ff t th ti ti

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    Hydrogen bond andhydrophobic interactionare not flexible enough.

    Induced fit mechanism

    is not optimum

    Movement of moleculesslow

    15.1 e) explain factors that effect the enzymatic reaction

    Learning outcome:15 1 ) l i f t th t ff t th ti ti

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    15.1 e) explain factors that effect the enzymatic reaction

    As temperature increase, themovement of molecules

    increases.kinetic energy ofthe enzyme & substrateincreases.

    More collisions occurbetween enzyme andsubstrates to form EScomplex.

    The rate of reactionincreases until it reachesoptimum temperature

    (usually 35

    0

    C-40

    0

    C).

    Learning outcome:15 1 e) explain factors that effect the enzymatic reaction

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    When temperature

    exceeds optimumtemperature, thebonds which hold thespecific 3D shape of

    enzyme are broken.

    Active sites are

    destroyed, enzymedenatured.

    15.1 e) explain factors that effect the enzymatic reaction

    Learning outcome:15 1 e) explain factors that effect the enzymatic reaction

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    Resulting from the

    breakdown of the weakbond such as hydrogenbond, hydrophobicinteraction,disulphide

    bridge and Van derWaals

    Substrates can nolonger fit into the activesites of the enzyme.

    The rate of reactiondecreases quickly.

    15.1 e) explain factors that effect the enzymatic reaction

    Learning outcome:15 1 e) explain factors that effect the enzymatic reaction

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    15.1 e) explain factors that effect the enzymatic reaction