Enzymes Flashcards
What is an enzyme?
A biological catalyst that increases the rate of a reaction and is chemically unchanged by the reaction
T/F:
Enzymes are mostly protein or DNA
False
Protein and RNA
What would happen if we didn’t have enzymes
Chemical reactions would not occur on a useful timescale and life cannot be sustained
Life would not be possible
Why are proteins better than RNA as enzymes?
Greater scope with a protein than with an RNA molecule
In 1897, Eduard buchner ……
Showed that extracts from year cells could ferment sugar to alcohol
In 1926, James Summer ……
Isolated and crystaized urease, finding that the crystals consisted of proteins
In 1930s, John Northrop and Moses Kunitz…
crystalyzed digestive enzymes and found all were proteins
In 1930, J.B.S Haldane suggested that …
weak bonding interactions between an enzyme and its substrate might allow reactions to be catalyzed
Enzymes act in ordered sequences of chemical reactions known as …
Biochemical Pathways
What is Krabbe Disease?
Genetic disease
Deficient in enzyme galactosyleramidase
Impairment in growth and maintenance of myelin
Which industry are enzymes mostly used in?
Food and beverage industry
Loss of an enzyme’s _________ causes loss of activity
Native Structure
T/F:
Simple proteins require additional chemical groups for activity
False
They do not require additional chemical groups for activity
What is a holoenzyme?
Catalytically active enzyme with its bound metal ion and/or co-enzyme
What is an apoprotein/apoenzyme?
The protein part of the holoenzyme
How are enzymes classified?
According to the reactions that they catalyze
What are the six class names?
Oxidoreductases Transferases Hydrolases Lysases Isomerases Ligases
T/F:
Enzymes size range from 15, 20, 40 kDa
True
T/F:
The active site takes up the majority of the enzyme
False
It is a tiny part
What allows the active site to bind to the substrate?
The amino acid residues with R groups
Why is the active site structured so that it is closed during the reaction?
This excludes water
Most reactions take a long time with water present or don’t proceed at all
Define equilibrium
When there is no net change in the CONCENTRATIONS o REACTANTS OR PRODUCTS
T/F:
The enzyme affects the equilibrium
False
Just increases the rate of reaction
What is the ground state?
The contribution to the free energy of the system by an average molecule
What does a negative deltaG mean?
The reaction is favourable
The transition state is the _____ energy state as you go from substrate to product
Highest
T/F:
The transition state is a reaction intermediate
False
What is the rate of reaction dependent on?
The difference between the free energy of the transition state and the ground state
Activation energy= AG++
Determined by the reaction step with the highest activation energy (rate-limiting step)
What is a reaction intermediate?
A chemical species on the reaction pathway that has a lifetime longer than a molecular vibration
What is a reaction step?
Interconversion of two sequential reaction intermediates
What is Keq?
Equilibrium constant
=[P]/[S]
A large negative value for deltaG reflects an equilibrium that favours ____ over ____
Products over Reactants
What information does this formula provide?
V=k[S]
Rate of reaction (V)
k= rate constant
[S]= substrate concentration
Basically the rate of a reaction is determined by the concentration of the reactions and by the rate constant
The rate constant is ____ and _____ related to deltaG++
Inversely and exponentially
What is the role of non-covalent interactions in enzyme catalyzed reactions?
Non-covalent interactions are critical for the formation of complexes between enzyme and substrate
What is the role of covalent interactions in enzyme catalyzed reactions?
Lower the activation energy by providing an alternative lower-energy reaction path
What is deltaGB and how does it affect deltaG++
deltaGB= binding energy
When the enzyme and substrate bind, there are weak interactions that release small amounts of energy to stabilize the interaction
Enzymes use this energy to lower the activation energy for the overall reaction
T/F:
The enzyme with a completely complementary active site to its substrate would be a really good enzyme
False
bad enzyme
needs to be good at binding the intermediate/transition state
Is binding energy positive or negative?
Negative
It is favourable
What happens when you sum together the deltaG and deltaGB?
Results in a lower net activation energy
activation energy is unfavourable= positive
binding energy is favourable= negative
How much energy does a single weak interaction provide?
4-30 kJ/mol of energy
Why is it difficult to experimentally distinguish between enzyme specificity and enzyme catalysis?
Because they both arise from weak interactions between E and S (ie deltaGB)
What kinds of barriers does deltaGB overcome?
– Entropy of molecules in solution
– Solvation shells of Hbonded water
– Need for distortion of substrates in many reactions
– Need for alignment of catalytic functional groups on the enzyme.
What is induced fit?
When E interacts with S through multiple weak interactions, E itself usually undergoes a change in conformation.
The conformation changes may involve small motions near the active site or large motions of entire protein domains.
Typically, a network of coupled motions occurs throughout the enzyme structure that ultimately brings about the required changes in the active site
Once S is bound, ________________ aid in the formation and cleavage of bonds during the reaction
properly positioned catalytic functional groups
How do unstable charged intermediates affect biochemical reactions?
They can rapidly break down back into reactants –> unfavourable, reaction moves towards substrate rather than products
This problem can be fixed by transferring protons to or from the substrate/intermediate that will rapidly break down into products
Why does hexokinase favour the reaction with glucose rather than water?
When the enzyme binds to glucose, it undergoes a conformational change to become active
when glucose is not present, it won’t be active
Provide an example of how a metal ion can stabilize a reaction intermediate
Enolase acid-base reaction
Enolase= enzyme
Uses 2 Mg ions to stabilize the intermediates to allow the reaction to proceed
How does lysozyme act as an antibacterial agent?
Found in tears and egg whites
Cleaves the glycosidic bond between the two types of sugar residues in the peptidoglycan cellular wall
T/F:
There is usually equal amounts of enzyme and substrate concentration
False
Enzyme concentration is usually way less than substrate concentration
What is V0?
Rate of the reaction at the very beginning of the experiment
Generally reflects the steady state
Michaelis-Menten Equation:
V0= Vmax[S]/Km+[S]
What is Vmax?
maximum velocity the enzyme can work at under given conditions
Occurs when all the enzyme is in the form of ES (enzyme is saturated with substrate)
What is Km?
[S] that gives a rate of 1/2Vmax
T/F:
E+S –> ES is slower than ES –> E + S
False
Breakdown of ES into E and S is slower than the formation of ES
(it is rate limiting)
What occurs during the steady state?
[ES] and [other intermediates] remain approximately constant over time
V0 generally reflects this state
What occurs during the pre-steady state?
[ES] builds up over time, lasts only microseconds
What are some limitations of Michaelis Menten equation?
o The real meaning of Vmax and Km differ between enzymes.
o Vmax and Km by themselves provide little information about the number, rates or chemical nature of steps in the reaction.
o Regulatory enzymes do not exhibit Michaelis-Menten behaviour.
What can the MM equation be converted into to generate?
Lineweaver-Burk plot
Makes it easier to identify the Vmax and Km
Y=intercept= 1/Vmax
X intercept= -1/Km
What happens to Km in two step reactions when K2 is less than k-1?
Km equation becomes k-1/k1
This is the dissociation constant Kd ie measure of the affinity of the enzyme for its substrate
Therefore Km= measure of the affinity of the enzyme for its substrate
What is Kcat?
describes the limiting rate of any enzyme-catalyzed reaction that is saturated with substrate
also called the turnover number, which means the number of substrate molecules converted to product per second when the enzyme is saturated with substrate
What are the three types of reversible inhibition of an enzyme?
Competitive
Uncompetitive
Mixed
Many ________ inhibitors combine with the enzyme to form an EI complex and prevent catalysis
competitive
What is alphaKm?
Km observed in the presence of an inhibitor
What is KI?
Inhibition constant
[I] required to give half maximum inhibition
When a competitive inhibitor is present, how can you make the reaction be favoured?
Add more substrate
What do uncompetitive inhibitors bind to?
They only bind to the ES complex
What do mixed inhibitors bind to?
Can bind to E or ES
Uncompetitive and mixed inhibition are observed only for enzymes with ____ substrates
2 or more
