8 Enzymes Flashcards
Protein catalysts that increase the rate of chemical reactions
Enzymes
Are enzymes altered or consumed in chemical reactions?
No, enzymes are neither altered nor consumed in the reactions
A protein that provide a means for regulating metabolic pathways in the body
Enzymes
What is catalytic power in enzymes?
Enzyme’s ability to accelerate the rate of noncatalyzed reactions by as much as 10^26 times
What does enzyme specificity mean?
Extreme selectivity to the substances it interacts with (substrate), and the reaction it catalyzes
Why enzyme activity regulation is important?
Activity can be regulated (increased or decreased) so that the rate of product formation responds to cellular need
How many classes of reactions are recognized?
Six classes (oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases)
Which class of enzymes catalyzes oxidation-reduction reactions?
Oxidoreductase
Which class of enzymes catalyzes transfer of moieties such as glycosyl, methyl, or phosphoryl groups?
Transferase
Which class of enzymes catalyzes cleavage of bonds by addition of water?
Hydrolase
Which class of enzymes catalyzes cleavage of C–C, C–S, and certain C–N bonds?
Lyase
Which class of enzymes catalyzes rearrangement of optical or geometric isomers?
Isomerase
Which class of enzymes catalyzes formation of bonds between two molecules coupled to the hydrolysis of high-energy phosphates?
Ligase
What is the difference between synthase and synthetase?
Synthase catalyzes the formation of a compound without ATP, while synthetase requires ATP
What enzyme uses water to remove phosphate group?
Phosphatase
What enzyme adds phosphate from inorganic phosphate to organic molecule acceptor?
Phosphorylase
What is the role of oxidase enzyme?
Oxidase enzyme use oxygen as the acceptor, but oxygen atoms are not incorporated into the substrate
How does oxygenase function in reactions?
Oxygenase enzymes incorporate one or both oxygen atoms into the substrate
Special cleft that provides the environment wherein chemical transformation takes place.
Active Site
True or False. Substrate able to bind through weak forces such as hydrogen bonds.
TRUE
The specific site on the enzyme where the substrate binds and catalysis occurs
Active site
The substance by which an enzyme acts
Substrate
What do you call the metal ions that participate directly in substrate binding or catalysis and extend the mechanistic capabilities of an enzyme?
Cofactor
What enzymes require a metal ion cofactor?
Metal Activated Enzymes
What enzyme contains metal ions that serve as prosthetic group?
Metalloenzymes
What organic molecules participate directly in substrate binding (catalysis) and extend mechanistic capabilities of an enzyme?
Coenzyme
_____ is permanently associated with the enzyme
Prosthetic group
What is the non-protein component that is transiently associated with the enzyme?
Cosubstrate
What is an enzyme without its nonprotein moiety and catalytically inactive?
Apoenzyme
Some enzymes require non-proteins for enzymatic activity. What is the term for an enzyme with its nonprotein moiety that is catalytically active?
Holoenzyme
What are the two models for enzyme specifity?
Lock and Key model & Induced fit model
What model describes enzymes as resembling a lock while the particular substrate acts as the key?
Lock and Key model
What model is being described when the active site of an enzyme is modified or altered upon binding of the substrate?
Induced Fit Model
What are the Enzyme Catalysis Strategies?
Catalysis by Proximity and Orientation, Acid-Base Catalysis, Catalysis by Strain, Covalent Catalysis, and Ribozymes
An Enzyme Catalysis Strategy where substrate molecules must come within bond-forming distance in order to interact?
Catalysis by Proximity and Orientation
An Enzyme Catalysis Strategy where the enzyme allow subtrates to bind in a manner that places reactive groups in appropriate orientations to chemically interact?
Catalysis by Proximity and Orientation
An Enzyme Catalysis Strategy where the acceleration of the reaction is achieved by the catalytic transfer of a proton?
Acid-Base Catalysis
What are the two types of Acid-Base Catalysis?
Specific Acid/Base Catalysis and General Acid/Base Catalysis
What are the only participating acids or bases in specific acid/base catalysis?
Protons or Hydroxide ions
Enzymes bind substrates in a conformation that weakens the bond targeted for cleavage through physical distortion and electronic polarization.
Catalysis by Strain
Involves formation of a covalent bond between enzyme and one or more substrate.
Covalent Catalysis
Residues on the enzyme that participate in Covalent catalysis are?
Cysteine or Serine, Histidine(occasionally)
An Enzyme Catalysis Strategy that follows a ping-pong mechanism
Covalent Catalysis
Consisted of Catalytic RNAs and most act in RNA processing
Ribozymes
Ribozymes satisfy several enzymatic criteria, what are these?
Substrate specific, Enhance reaction rate, Emerge from reaction unchanged
Performs the vitally important and highly complex process of synthesizing long polypeptide chains following the instructions encoded in mRNA molecules
Ribosomes
Enzymes are proteins except for?
Ribozymes
What are the three distinctive features of enzymes?
Catalytic power, specificity, and regulation
What are the non protein components that are essential for the catalysis to occur?
Cofactors and coenzymes
____ is the systematic study of the rate of reactions
Kinetics
____ is a transient, high-energy intermediate condition where bonds in the substrate are maximally strainedA
Transition State
Where does the transition state appear in the energy diagram of a chemical reaction?
At the apex of the energy profile in the energy diagram
Describes the direction in which the reaction will tend to proceed. It describes in quantitative form the direction and the concentration of the reactant and products present at equilibrium.
Free Energy Change/ ΔG
The energy input required to initiate a reaction is referred to as the ____
energy of activation
Enzymes lower the ________ energy required for a reaction by providing an alternate energetically favorable pathway.
activation
TRUE OR FALSE. Higher energy of activation, the faster the reaction will proceed
FALSE, the slower the reaction will proceed
Enzymes lower the ________ energy required for a reaction by providing an alternate energetically favorable pathway.
activation
Regardless in the presence or absence of enzymes, the overall concentration of reactants and products remain constant, thus, the ____ is unaffected.
equilibrium constant
Temprature increases the rate of uncatalyzed and enzyme-catalyzed reactions by increasing ___ and ___ of the reacting molecules.
kinetic energy and collision frequency
What is the “collision theory of capital kinetics”?
“For two molecules to react, they must collide and that they must have sufficient kinetic energy to overcome energy barrier”
However, further increase in temperature does not increase activity any more because at temperatures too high, heat energy can disrupt noncovalent interaction that maintains the ____ of proteins.
3D structure
The rate of almost all enzyme-catalyzed reactions significantly depends on ________ concentration, also known as pH.
hydrogen ion
This affects active site ionization, and enzyme denaturation
hydrogen ion concentration
pH at which maximal enzyme activity is achieved is ____
variable
What is the pH at which maximal enzyme activity is achieved for most intracellular enzyme?
5-9
What is the pH at which maximal enzyme activity is achieved for pepsin?
2
As substrate concentration increases, rate ____ until it reaches a maximum value
increases
What do you call the value where the enzyme is saturated and no further reaction can occur even as substrate concentration is increased?
Maximum Velocity (Vmax)
What do you call the behavior where the reaction velocity does not increase despite increase in substrate concentration?
Saturation Effect
____ kinetics is when the rate is independent of reactant (substrate) concentration
Zero-Order
What shape does the curve in an enzyme-catalyzed reaction typically exhibit in a plot of reaction rate versus substrate concentration?
Hyperbolic
Describes how reaction velocity varies with substrate concentration.
Michaelis-Menten Kinetics
This reflects the affinity of an enzyme for a substrate. Numerically, it is equal to the substrate concentration at which vi is half the maximum velocity
Michaelis Constant Km
TRUE OR FALSE. The lower the Km, the higher the affinity of an enzyme to a substrate.
TRUE
What is the reaction order when the substrate concentration [𝑆] is much less than the Michaelis constant (𝐾𝑚)?
The reaction velocity is approximately proportional to substrate concentration, exhibiting first-order reaction kinetics.
What is the reaction order when the substrate concentration [𝑆] is much greater than the Michaelis constant (𝐾𝑚)?
The reaction velocity is independent of substrate concentration, exhibiting zero-order reaction kinetics.
What is the linear form of the Michaelis-Menten equation used to determine enzyme kinetics, with the y-intercept representing 1/Vi, the x-intercept representing -1/Km, and the slope representing Km/Vmax?
Lineweaver-Burk Plot
What is the equation that is describing the enzymes with positive cooperativity, where the initial reaction velocity increases as the nth power of substrate concentration?
Hill Equation
What is the, ability to determine the kinetic mechanism of an enzyme inhibitor and inhibition constants by producing a straight line graph?
Lineweaver-Burk Plot Virtue
An empirical parameter denoted as ‘n’ in the Lineweaver-Burk Plot, representing the number, kind, and strength of interactions of multiple substrate-binding sites of an enzyme.
Hill Coefficient
What is the type of reversible inhibition where the inhibitor binds to the enzyme at a site distinct from the substrate-binding site, competing with the substrate for binding.
Competitive Inhibition
What is the sign when all binding sites of the hill coefficient behave independently?
n = 1
What is the sign when the hill coefficient exhibits positive cooperativity?
n > 1
What is the classification of inhibitor that interact with the enzyme through noncovalent association/dissociation reactions?
Reversible
What is the type of reversible inhibition where the inhibitor binds to the enzyme at a site other than the active site, not competing with the substrate for binding?
Noncompetitive Inhibition
What is the type of inhibition where inhibitors form covalent bonds with side chains or prosthetic groups in enzymes?
Irreversible Inhibition
Substrates and inhibitors compete for the same binding site on the enzyme. Therefore, there will be _____
slowing down of reaction.
Substrate shares a high degree of structural similarity to the inhibitor. Hence, it also follows that the inhibitor would bind to the substrate binding portion of the active site. However, the effect of competitive inhibitors can be overcome by _____
increasing the concentration of the substrate.
What is an example of a competitive inhibitor, are a group of medicines that can help lower the level of low-density lipoprotein (LDL) cholesterol in the blood?
Statin
Metabolite of Allopurinol, acts as a noncompetitive inhibitor of xanthine oxidase.
Oxypurinol
Drug requiring metabolism to its active form; Allopurinol is a prodrug metabolized to Oxypurinol, a xanthine oxidase inhibitor.
Prodrug
Form of arthritis causing joint pain and swelling due to high uric acid levels.
Gout
This contains a beta lactam ring that binds to enzyme serine residue, blocking cell wall synthesis in bacteria. What do you call this?
Penicillin
Sometimes irreversible enzymes are also termed as __ because even after removal of the remaining inhibitor, your enzymes are still inhibited
poison enzymes
Penicillin is able to exert its effect by covalently reacting with an essential serine residue on the active site of the enzyme ___, an enzyme responsible for cross-linking peptidoglycan chains
glycopeptide transpeptidase
Penicillin’s conformation resembles the transition state of glycopeptide transpeptidase’s normal substrate which is called
Transition State Analog
What kind of single displacement is an addition of substrates in a specific order?
Ordered
What kind of single displacement that either substrates may combine with the enzyme?
Random
A bimolecular reaction where both substrates must combine with enzyme to form a ternary complex for catalysis to occur
Single Displacement/Sequential reaction
A bimolecular reaction where one or more products released from enzyme before all substrates have been added. Ping-pong mechanism is the other term.
Double Displacement
Enzymes increase the rate of chemical reactions by ___
lowering the energy of activation.
3 factors that affect the rates of enzyme catalysis
Temperature, pH, and substrate concentration
Substrate analogs generating reactive groups during enzyme catalysis, irreversibly inhibiting the enzyme.
Suicide Inhibitors
This describes enzyme kinetics relating substrate concentration to reaction rate.
Michaelis-Menten Equation
Protein catalysts that increase the rate of chemical reactions without being changed in the overall process
Enzymes
T/F Almost all enzymes are proteins, except for ribozymes, which are ribosomal RNAs and a handful of other RNAs.
TRUE
T/F Enzymes are neither altered nor consumed in a reaction. They may be modified during a reaction sequence but return to their original form in the end
TRUE
How do enzymes regulate metabolic pathways?
By controlling the rate of product formation in response to cellular needs
It refers to the ability of enzymes to accelerate the reaction rates of non-catalyzed reactions by up to 10²⁶ times.
Catalytic power
T/F Enzyme activity cannot be regulated?
FALSE; Enzyme activity can be regulated, meaning it can be increased or decreased to ensure that the rate of product formation meets the cellular need.
How are enzymes traditionally named?
By adding the suffix “-ase” to the name of the substrate they act upon or by the reaction they catalyze
How many classes of reactions are recognized in the systemic naming of enzymes?
Six Classes
What type of reactions do oxidoreductases catalyze?
Oxidation-reduction reactions (where an oxidized compound loses electrons.)
Enzymes that catalyze the transfer of carbon, nitrogen, or phosphorus-containing groups.
Transferase
What enzyme catalyzes the cleavage of bonds by the addition of water?
Hydrolase
Which enzyme type catalyzes the cleavage of C–C, C–S, or certain C–N bonds without the use of water?
Lyase
What is the main difference between a lyase and a ligase?
Lyase cleaves bonds; Ligase forms bonds
What enzymes is responsible for rearranging optical or geometric isomers within a molecule?
Isomerase
What enzyme requires ATP to function?
Synthetase
What term describes an enzyme that is catalytically inactive because it lacks its non-protein moiety?
Apoenzyme
Organic molecules that participate directly in the enzyme’s catalytic process and can either be permanently associated as a prosthetic group or transiently associated as a co-substrate
Coenzymes
What enzyme catalyzes the removal of water from a molecule?
Dehydratase
Isomerases are involved in which type of reaction?
Rearrangement of molecular structure
Enzymes that are responsible for forming new covalent bonds between molecules, a process that is typically coupled with the hydrolysis of ATP to provide the necessary energy
Ligase
What enzyme type adds a phosphate group to a substrate using inorganic phosphate?
Phosphorylase
They are typically metal ions, such as zinc or iron, that help enzymes in binding substrates or catalyzing reactions. They can either be metal-activated enzymes or part of metalloenzymes.
Cofactors
A non-protein coenzyme or metal ion that is permanently attached to the enzyme, forming a stable complex.
Prosthetic Group
A coenzyme that binds transiently during the enzymatic reaction.
Co-substrate
A fully active enzyme composed of its protein component (apoenzyme) and its non-protein moiety (cofactor or coenzyme).
Holoenzyme
Specific site on the enzyme where substrate binds and catalysis occurs
Active Site
An unstable high energy complex intermediate between the reactants and products formed by activated substrates and enzyme
Transition-state complex
T/F Enzymes have extreme selectivity
TRUE
Model by Emil Fischer that implied that enzymes are rigid
Lock and Key Model
A more accepted model by Daniel Koshland that explains that the binding of a substrate to the enzyme induces a conformational change that is analogous to placing a hand to a glove
Induced Fit Model
T/F Substrate molecules must come within bond-forming distance to interact
TRUE
The ________ proximity of reactants, the higher the collision frequency, the faster the rate of reaction
Higher
Type of Acid/Base Catalysis that only participating acids or bases are protons or hydroxide ions
Specific Acid/Base Catalysis
Type of Acid/Base Catalysis that is responsive to all acids or bases present
General Acid/Base Catalysis
Enzyme catalysis strategy where enzymes bind substrates in a conformation that weakens the bond targeted for cleavage through physical distortion and electronic polarization
Catalysis by Strain
Enzyme catalysis strategy that involves formation of a covalent bond between enzyme and one or more substrate following a ping-pong mechanism
Covalent catalysis
Ability to maintain a constant internal environment despite changes in external surroundings at the cellular level
Homeostasis
2 Types of Mechanisms of Regulation
Passive & Active
This allows intermediates to be directly transferred from one enzyme’s active site to another, minimizing the loss of energy and information
Compartmentalization
Transfers electrons from NADPH to the next subunit
Cytochrome P450 Reductase
Transfers the electrons to oxygen
Cytochrome P450
In active regulation, one can increase or decrease the quantity of the enzyme via (2)
amount of enzyme being (1) synthesized and (2) degraded
In active regulation, one can increase or decrease the catalytic activity of the enzyme via (2)
(1) allosteric regulation & (2) covalent modification
Shutdown of enzyme synthesis through repressors
Repression
Pathway for the control of enzyme degradation catalyzed by E3 ligases
ubiquitin-proteasome pathway
2 prominent mechanisms of enzyme regulation to ensure a rapid response to meet the metabolic needs of cells
Allosteric Regulation & Covalent Modification
Refers to the regulation of an enzyme through the binding of an activator or inhibitor molecule at a site other than the active site
Allosteric Regulation
Allosteric effector that often bind to and either activate or inhibit one or more enzymes within their pathway
Feedback Effectors
Metabolic end products or intermediates with a secondary role as allosteric effectors or enzyme
Indicator Metabolites
Specialized allosteric ligands whose production or release is triggered in response to an external first messenger
Secondary Messengers
Mechanism of enzyme regulation that introduces a new covalent bond or cleaving an existing covalent bond alters the identity of the affected enzyme
Covalent modification
Type of Covalent modification where activated proteins retain their new form and properties until damaged, disposed, or degraded
Irreversible
Example of irreversible covalent modification where proproteins transform into its active, functionally competent form
partial proteolysis
Type of Covalent modification where one can restore modified protein to its modification-free precursor form
Reversible
Most prominent form of covalent modification in cellular regulation accomplished by protein kinases and protein phosphatases working in opp directions
Phosphorylation
Example of reversible covalent modification that involve histones, other nuclear proteins, and enzymes involved in core metabolic pathways
Acetylation
enzymes that catalyze similar reactions, but differ slightly in their amino acid composition
Isozymes
