Tutorial - Week 9 - Enzymes Flashcards
________: catalyse and promote sequences of chemical reactions
Enzymes
___________: consecutive reactions catalysed by enzymes
The products of one reaction become the reactants of the next one
Pathways
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)
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.
___________: the overall network of enzyme catalysed pathways
(anabolic & catabolic)
Metabolism
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)
What are enzymes? Simple explanation
Enzymes are proteins that catalyse biochemical reactions by
lowering their activation energy
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 #$ )
Enzymes are classified according to…/
the type of reaction they catalyse
Name the type of reaction catalyzed by each enzyme class
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
What are the four parts required for enzyme catalyzation? Draw the process
Many enzymes require non-protein ________ for their ________ function
cofactors
catalytic
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
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.
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).
What is Apoenzyme
is an enzyme without the cofactor, and therefore is inactive.
What is holoenzyme
Holoenzyme = is an enzyme with cofactors attached and catalytically active
What are the three features that make a protein an enzyme?
Describe catalytic power
Give simple description and the difference between no enzyme in the reaction and an enzyme
What is the transition state?
highest energy
arrangement of atoms during a reaction
∆G‡ free energy of activation,
Activation energy (Ea): energy = ?
difference between the substrate and
the transition state.
Determines the rate of the reaction
∆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.
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
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)
