Tutorial - Week 9 - Enzymes Flashcards by Levi Stringer

________: catalyse and promote sequences of chemical reactions

Enzymes

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___________: consecutive reactions catalysed by enzymes
The products of one reaction become the reactants of the next one

Pathways

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Describe Catabolic pathways:

pathways that degrade organic nutrients into
simple end products to extract chemical energy and convert it into a
form useful to the cell (e.g. ATP, NADH, NADPH, FADH2)

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Describe Anabolic pathways:

pathways that start with small precursor
molecules and convert them into more complex molecules (e.g.
proteins, nucleic acids). These require the use of energy.

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___________: the overall network of enzyme catalysed pathways
(anabolic & catabolic)

Metabolism

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What are enzymes? (4 points)

Under biologically relevant conditions, uncatalysed reactions tend to be slow (for example reactions required to
digest food would take a very long time if not catalysed)
Life depends on powerful and specific catalysts: Enzymes
Almost every biochemical reaction is catalysed by an enzyme
Most enzymes are proteins (a few exception are RNA molecules: ribozymes)

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What are enzymes? Simple explanation

Enzymes are proteins that catalyse biochemical reactions by
lowering their activation energy

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Enzymes affect the _______________, not the_____________

The reaction equilibrium is dependent on…?

rate of the reaction

equilibrium

the thermodynamics of the
reaction (remember ∆G !” = −RT ln K #$ )

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Enzymes are classified according to…/

the type of reaction they catalyse

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Name the type of reaction catalyzed by each enzyme class

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How enzymes work:

Enzymes have an _______:
* It provides a specific…?
* It binds and recognises a…?

active site

environment that helps accelerate the reaction

specific substrate(s

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What are the four parts required for enzyme catalyzation? Draw the process

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Many enzymes require non-protein ________ for their ________ function

cofactors

catalytic

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What is a cofactor?

Cofactor = a non-protein chemical component needed for the biological activity of an enzyme. Cofactors can
be inorganic ions, Fe 2+ , Mg 2+ , or complex organic molecules, also referred to as coenzymes

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What is a coenzyme?

Coenzyme = are cofactors that are organic molecules and bind loosely to the active site of an enzyme to help
with the catalysis, such as NADH and vitamins.

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What is a prosthetic group?

Prosthetic group = are cofactors that are tightly bound, or even covalently bound, to the enzyme (e.g. FAD in
flavoproteins).

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What is Apoenzyme

is an enzyme without the cofactor, and therefore is inactive.

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What is holoenzyme

Holoenzyme = is an enzyme with cofactors attached and catalytically active

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What are the three features that make a protein an enzyme?

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Describe catalytic power

Give simple description and the difference between no enzyme in the reaction and an enzyme

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What is the transition state?

highest energy
arrangement of atoms during a reaction

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∆G‡ free energy of activation,
Activation energy (Ea): energy = ?

difference between the substrate and
the transition state.
Determines the rate of the reaction

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∆G‡ free energy of activation (Ea)
catalysed: explain

When the enzyme is
complementary to the transition
state, it helps destabilise the
substrate (bend stick), reduces the Ea
and accelerates the reaction.

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Enzymes catalyse reactions: how?

substrates bind to the active site
of the enzyme, which accelerates the chemical reaction,
products are formed, and then allow products to dissociate

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The function of enzymes is to...?

lower the activation energy (Ea) to accelerate the reaction

Enzymes selectively recognise specific _________ * Substrates bind to the __________ of the enzyme via __________ bonds (______________________) * Specificity is controlled by __________ and ____________ in the active side.

substrate (s). active site non-covalent H-bonds, van der Waals and ionic interactions the 3D structure specific amino acids

The substrate binds to the __________. * The active site is...? * The active site of an enzyme is the place where...?. * The active site provides...?

active site (or binding site) a region in the enzyme uniquely suited to bind specific substrate(s) a reaction is catalysed catalytic groups to facilitate the chemistry that stabilises the formation of the transition state

Enzymes act as...?

a template for the reaction to occur, they bind to specific substrate (s), stabilise the transition state, lower the activation energy and accelerate the reaction.

What are the two models of enzyme specificity?

Explain the Lock and key model

Explain the induced fit model

Weak bonds (non-covalent) between the substrate and binding site of an enzyme normally involve:

Interactions between the enzyme and substrate, optimised in the _________ * Reduction of _______ by constraining the substrate(s) in the proper orientation to react in the active site * Desolvation of the substrate(s) (many organic molecules are surrounded by...? * Change in the enzyme conformation when the ...? * The induced fit serves to...?

transition state entropy a shell of water molecules that can reduce interactions between substrates) substrate binds (induced fit). bring specific functional groups on the enzyme into the proper position to catalyse the reaction

Inhibitors: describe

inhibit the activity (i.e. interfere with the kinetics of the reaction catalysed by the enzyme)

Activators: do what?

Increase the activity of the enzyme

Enzyme inhibitors: are...?

molecules that interfere with the catalysis, by slowing or stopping enzymatic reactions

Type of enzyme inhibitors?

Describe what the competitive inhibitor does?

Competitive inhibitor: competes with the substrate for the active site. If the inhibitor occupies the active site, the substrate cannot bind

Uncompetitive inhibitor: what does it do?

Binds to a different site, but binds only to the ES complex.

What are Noncompetitive (or mixed) inhibitor also referred to as? What do they do?

Allosteric inhibitors Binds to a different site, it can bind to the E or to the ES complex.

Irreversible inhibitors bind _________ with, or ________, a functional group that is essential for the enzyme’s activity, or they form a...?

covalently destroy highly stable noncovalent association.

Label these types of activation

What do allosteric inhibitors do?

Allosteric inhibitor: induces a conformational change that reduces the enzyme's affinity for its substrate. Noncompetitive and uncompetitive inhibitors are examples of allosteric inhibition. Vmax is reduced

What do allosteric activators do?

Allosteric activators: bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme’s active site(s) for its substrate(s). Vmax is increased

Describe Product accumulation:

excess of product, might inhibit the enzyme activity.

Describe Substrate availability:

if no substrate is available, the reaction does not occur; increased concentration accelerates the enzyme activity

Describe Genetic control:

it can induce more or reduce the expression of enzymes

Describe Covalent modification:

attachment of a chemical group by covalent bond can modify the enzyme activity (e.g. phosphorylation of specific amino acid residues can activate or inactivate enzymes)

Describe Expression of enzymes as Zymogens:

inactive enzyme precursors that only become active after specific proteolytic cleavage

Describe Expression of several isoenzymes:

enzymes with similar function and overall 3D structure, that differ in the primary sequence of the polypeptides that make up their quaternary structure (e.g. LDH1, LDH2, LDH3, LDH4, LDH5)

Modulator proteins:

proteins that bind to enzymes and influence the activity of the enzyme

Most enzymes have certain _________ properties in common: Substrate concentration, [S], affects...?

kinetic the rate of the reaction

The rate of an enzymatic reaction depends on....? which depends on...?

the formation of enzymesubstrate complex (ES) the concentration of substrate, until all the enzyme binding sites are occupied with substrate

As we increase the amount of substrate there is a higher rate of?

Product production

The rate of an enyzmatic reaction depends on...?

the concentration of substrate we have when we first start the reaction

The reaction is faster at the beginning when there is more...?

substrate (initial rate, V0)

T/F: As the reaction proceeds and substrate(s) is(are) consumed, the rate slows down

True

The ___________________ can be determined by the variation of product produced over time

rate of an enzymatic reaction

The initial rate of an enzymatic reaction, V0, can be determined by...?

the variation of product produced over time, at the beginning of reaction (as shown in the figure, is the tangent at the beginning of the reaction/linear part of the curve)

Label the arrows

What is this yellow arrow pointing to?

The initial rate (Vo)

Describe the Michaelis-Menten enzymatic reaction:

a model that describes the kinetics of many enzymatic reactions

In the Michaelis-Menten enzymatic reaction, the Vmax represent? Km is? (2 points)

Kinetic parameters (KM and Vmax) are used to compare...?

enzyme kinetics

Kinetic parameters: A traditional approach to determine these parameters is by using the _________________ to linearise the MichaelisMenten plot, an approach that takes the reciprocal of both sides of the Michaelis-Menten equation

Lineweaver-Burk plot

Label

Competitive inhibitor: Explain

competes with the substrate for the active site. If the inhibitor occupies the active site, the substrate cannot bind

List what happens to Km and Vmax

The lines in the Lineweaver Burk representation intersect at the...?

Y-axis

We need a lot more substrate to overcome the inhibitor and obtain the _______

Vmax

Describe what happens to the Km and Vmax when there is an uncompetitive inhibitor

Km^App decreases Vmax^App decreases

Define Uncompetitive inhibitor:

Binds to a site different from active site, but binds only to the ES complex.

Describe what happens to the lines in the Lineweaver Burk representation when uncompetitive inhibitors are binding?

The inhibition cannot be overcome by increasing the [S], Vmax is lower

Non-competitive (or mixed) inhibitor: Define What happens to the Km and Vmax, and the lines and their intersections

Binds to a site different from Binds to a site different from active site , but binds to E or to the ES complex

How fast an enzyme molecule convert a substrate into a product?

The higher the Kcat, the faster the enzyme at catalyzing the reaction Specificity constant (kcat/KM): is the best way to compare the catalytic efficiencies of different enzymes

Types of enzyme reaction, based on the number of substrates: * True unimolecular reaction: Explain

A single substrate rearranges to a single product (e.g. isomerases catalyse reactions that normally are true unimolecular)

Pseudo unimolecular reaction: What is it?

A single substrate molecule is separated into two or more products (e.g. hydrolases that break a chemical bond; water is a substrate, but is in large excess, and is not a limiting substrate)

Describe bimolecular reactions

Describe sequential bimolecular reactions

Describe Non-Sequential biomolecular:

Mechanisms of enzyme catalysis: Describe general acid and base catalysis

Describe covalent catalysis

Describe metal ion catalysis

Give example of general base catalysis

Give an example of covalent catalysis

Give an example of metal ion catalysis

Key concept: What are enzymes?

Enzymes are proteins that catalyse biochemical reactions by lowering their activation energy

Key concept: The active site, cofactors, and how enzymes work: (3 points)

Key concept: Features that distinguish enzymes from other proteins: (3 points)

Key concept: Enzyme regulation and types of enzyme inhibitors (2 types and explain)

Key concept: Enzyme kinetics, initial rate, Michaelis-Menten model, and kinetic parameters (explain 4 points)

Key concept: Lineweaver-Burk plot and their use to determine kinetic parameters and type of enzyme inhibitor (explain)

To linearise the Michaelis-Menten plot, an approach that takes the reciprocal of both sides of the Michaelis-Menten equation, comparison of kinetics with and without inhibitor

Key concept: List the different types of enzyme reaction, based on number of substrates

Key concept: Mechanisms of enzyme catalysis (3 points)