Ch 11: Enzyme Catalysis
What type of forces bind substrates and other molecules to enzymes?
4 weak interactions
Which amino acid is most likely to act as a covalent catalyst in an enzyme active site? A. Ser B. Met C. Ala D. Ile
A. Ser
Convenient for everyday use and is often an enzymes previously used name
Accepted/Recommended name
catalyzes the oxidation of 1' and 2' alcohols to their corresponding aldehydes and ketones by removing H
Alcohol Dehydrogenase
Why have proteins fully eclipsed RNA as cellular catalysts?
Proteins have greater versatility having 20 types of amino acids with a greater variety of functional groups. Whereas nucleic acids consist of polymers of 4 types of chemically similar monomeric units
Path of minimum free energy, how reactants approach
Reaction coordinate
Catalyzes the formation of peptide bonds between amino acids during protein synthesis
Ribosomal RNA
An RNA molecule that has enzymatic activity
Ribozyme
proteolytic enzymes that include digestive enzymes from prokaryotes and eukaryotes as well as more specialized proteins that participate in development, blood coagulation and inflammation
Serine proteases
Explain how enzymes differ in geometric specificity ?
Some are absolutely specific for only one compound, but most enzymes catalyze the reactions of a small range of related compounds but with different efficiencies
Used when ambiguity must be minimized, name of substrate followed by -ase specifying the type of reaction
Systematic name
Explain how Aconitase exhibits stereospecificity?
The enzyme catalyzes the interconversion of citrate and isocitrate. Citrate is prochiral, therefore Aconitase can distinguish between the positions because citrate acts asymmetrically with the surface of the enzyme by making a 3 point attachment
The pH dependence of the rate of the RNase A reaction suggests what?
The involvement of 2 ionizable residues with pk values of 5.4 and 6.4
What makes enzymes effective catalysts?
Their specificity of substrate binding combined with their arrangement of catalytic groups
Why must coenzymes be regenerated?
They are chemically changed during the reaction and must return to its original state to complete the catalytic cycle. For transiently bound cosubstrate the regeneration may be catalyzed by another enzyme, but for a prosthetic group it occurs as part of the enzyme reaction
What do enzymes do to the transition state?
They reduce the free energy of the transition state, stabilizing the transition state of the catalyzed reaction
X-RAY studies indicate what happening to substrate binding sites when an enzyme binds?
They undergo a conformational change on (lock and key) substrate binding
Catalyze transfer of functional groups
Transferases
Stable molecules that geometrically and electronically resemble the transition state, are potent enzyme inhibitors
Transition state analogs
Developed by Henry Eyring, where much of understanding of how enzymes catalyze reactions
Transition state theory
The larger the delta G* the smaller the number of reactant molecules that have sufficient thermal energy to achieve transition state, T/F?
True
Catalyzes the hydrolysis of peptide bonds specific for a positively charged residue/ lysine
Trypsin
What are types of serine proteases?
Trypsin, chymotrypsin and elastase
How can enzymes catalyze oxidation-reduction reactions and types of group transfers?
With cofactors, they act as enzymes chemical teeth
In order to catalyze reactions, enzymes frequently require additional substances in their active site. What is the name for this family of substances? A. Coenzymes B. Prosthetic groups C. Essential ions D. Cofactors
cofactors
Enzymes that perform oxidation-reduction reactions are called: A. transferases. B. hydrolases. C. oxidoreductases. D. isomerases. E. lyases.
oxidoreductases
Trypsin, which prefers basic residues, is inactivated by tosyl-L-lysine chloromethylketone, T/F?
true
Chymotrypsin is activated when bound to tosyl-L-phenylalanine chloromethylketone (TPCK), because of the resemblance to a Phe residue, T/F?
False, it is inactivated
catalyze isomerizations
Isomerases
What are examples of cosubstrates?
NAD+, NADP+
How are transition state analogs used in the industry?
Some are naturally occurring antibiotics, others were designed to investigate the mechanism of enzymes or to act as specific enzyme inhibitors for therapeutic or agricultural use
a plot of free energy vs. reaction coordinate
Transition State Diagram/ Reaction coordinate diagram
point of highest free energy
Transition state
The rate enhancement of a catalyzed reaction is the ratio of the rates of the catalyzed reaction and the noncatalyzed reaction, T/F?
True
A catalyst lowers the free energy barrier for the forward reaction, but does not affect the rate of the reverse reaction, T/F?
false
Emil Fischer proposed what model for functionality of enzymes?
lock and key which shows complementarity between enzymes and substrates
What are 4 ways enzymes differ from ordinary chemical catalysts?
1) Higher reaction rates 2) Milder reaction conditions (under 100C and almost neutral pH) 3) Greater reaction specificity, barely have side products 4) Capacity for regulation
In an enzyme active site, what is the role of NAD+? A. To act as a cofactor. B. To act as a prosthetic group. C. To act as a coenzyme. D. A, B and C. E. A and C only.
A cofactor and coenzyme
Choose the best description of an enzyme: A. It increases the rate at which a chemical reaction approaches equilibrium relative to its uncatalyzed rate. B. It makes a reaction thermodynamically favorable. C. It allows a chemical reaction to proceed extremely fast.
A. It increases the rate at which a chemical reaction approaches equilibrium relative to its uncatalyzed rate.
Which of the following statements best explains the concept of geometric and electronic complementarity between enzyme and substrate? A. Molecules that differ from the substrate in shape or in distribution of functional groups cannot bind productively to the enzyme. B. Molecules that are similar to the substrate in shape or in distribution of functional groups cannot bind productively to the enzyme. C. Molecules that differ from the substrate in shape or in distribution of functional groups can bind productively to the enzyme. D. Molecules that differ from the substrate in shape or in distribution of functional groups can bind to the enzyme, but cannot function.
A. Molecules that differ from the substrate in shape or in distribution of functional groups cannot bind productively to the enzyme.
In studying the structure of a new enzyme, you find that side chains of Phe, Leu, and Ile are directed into the active site. Which of the following can logically be proposed on the basis of this observation? A. Some groups on the substrate are likely to be hydrophobic. B. This enzyme is likely to bind its substrate with induced fit to exclude water. C. The transition state intermediate in the reaction is likely to be small. D. The substrate for this enzyme is likely to be small.
A. Some groups on the substrate are likely to be hydrophobic
The difference in free energy between the substrate and product of a reaction catalyzed by Enzyme A is negative and small. What conclusions can be drawn about this reaction? A. The reaction is spontaneous and its speed is unknown from these data. B. The reaction is spontaneous and fast. C. The reaction is spontaneous but slow. D. The reaction is not spontaneous and is slow.
A. The reaction is spontaneous and its speed is unknown from these data.
What is the role of the active site His residue in the GAPDH reaction? A. To act as an acid-base catalyst. B. To act as a covalent catalyst. C. To covalently bind the cosubstrate NAD+. D. To bind a metal ion cofactor.
A. To act as an acid-base catalyst.
How are enzymes classified and named?
According to characteristics such as site of action, type of action, and substrate; according to the nature of the chemical reaction they catalyze, there is 6 major classes, each enzyme is assigned a name and a 4-part classification number
What are 5 types of catalytic mechanisms enzymes employ?
Acid-Base, Covalent, Metal Ion, Proximity and orientation effects, preferential binding of transition state complex
the region of an enzyme in which catalysis takes place
Active site
A substrate analog bearing a reactive group specifically binds at the enzyme's active site, where it reacts to form a stable covalent bond with a nearby susceptible group, the group can then be isolated and identified
Affinity Labelling
A well-designed enzyme active site provides which of the following features? A. Complementarity of shape and chemical nature to the substrate(s). B. Proximity and correct orientation of substrates and catalytic groups. C. Complementarity of shape and chemical nature to the transition state. D. Both A and B but NOT C are correct. E. A, B and C are all correct.
All are correct
How can digestive enzymes geometric specificity be described?
As preferences because they're so permissive in their range of acceptable substrates
What amino acid residues can act as acid/base catalysts?
Asp, Glu, His, Cys, Tyr and Lys
Which statement describes why enzymes can increase the rate of a reaction? A. Enzymes make non-spontaneous reactions spontaneous. B. Enzymes decrease the activation energy of the reaction they catalyze. C. Enzymes make thermodynamically unfavorable reactions favorable. D. Enzymes decrease the rate of the reaction. E. All of the above statements are correct.
B. Enzymes decrease the activation energy of the reaction they catalyze.
Which of the following is the BEST explanation for the frequent appearance of His side chains in enzyme active sites? A. The His side chain plays a major role in non-covalent binding interactions with substrates. B. The His side chain is able to act as both an acid and a base under physiological conditions. C. The His side chain is non-polar and therefore is typically located away from the surface of globular proteins. D. The His side chain is negatively charged.
B. The His side chain is able to act as both an acid and a base under physiological conditions.
Enzymes work by reducing the activation energy barrier of a reaction. Which of the following processes does NOT contribute to this? A. Specific amino acid side chains in the active site play a part in the catalytic mechanism. B. The enzyme binds the cosubstrate covalently. C. The enzyme binds the substrate specifically and with high affinity. D. The enzyme ensures appropriate proximity and orientation for substrates at its active site.
B. The enzyme binds the cosubstrate covalently.
Which of the following processes DOES NOT play a role in favouring formation of the transition state in enzyme catalyzed-reactions? A. The inclusion of additional chemical substances in the active site. B. The formation of covalent interactions between amino acid side chains and the co-substrate. C. Induced fit. D. The formation of non-covalent interactions between amino acid side chains and the transition state intermediate.
B. The formation of covalent interactions between amino acid side chains and the co-substrate.
What is the role of an enzyme in a biological reaction? A. To make the free energy change () of the reaction highly negative. B. To increase the rate at which substrate is converted to product. C. To preferentially bind the transition state intermediate such that it cannot be converted back to substrate. D. To ensure that the product has a lower free energy than the substrate. E. To ensure that all of the available substrate is converted to product.
B. To increase the rate at which substrate is converted to product.
Why would lysozyme exist in an organism?
Because organisms are susceptible to bacterial infection. In humans the lysozyme is found in the tears to protect the eyes from foreign invader. In eggs the lysozyme is found in the egg white to protect the growing chick from bacterial infection.
How do enzymes reduce free energy of the transition state (delta G*)?
By stabilizing the transition state
How can one determine where a bond gets broken?
By using an isotopically labelled compound
Which of the following statements about catalytic mechanisms of enzymes is TRUE? A. Enzyme catalytic mechanisms always require prosthetic groups and R groups. B. Enzyme catalytic mechanisms always require the use of acidic and basic R groups. C Enzyme catalytic mechanisms always require specific positioning of substrates and catalytic groups. D. Enzyme catalytic mechanisms always require the formation of covalent intermediates.
C Enzyme catalytic mechanisms always require specific positioning of substrates and catalytic groups.
The lower the delta G* the slower the reaction rate, T/F?
False, the greater the delta G*
The free energy of the transition state less than that of the reactants (delta G*)
Free Energy of Activation
A process in which proton transfer from an acid lowers the free energy of a reactions transition state
General Acid catalysis
If its rate is increased by proton abstraction by a base
General base catalysis
selective factor about the identities of the chemical groups on their substrates
Geometric specificity
The catalytically-active complex of a enzyme and its cofactor
Holoenzyme
catalyze hydrolysis reactions
Hydrolases
Enzymes that preferentially bind the transition state do what to the reaction?
Increase its concentration and therefore proportionally increase the reaction rate
What does a substrate binding site consist of?
Indentation or cleft on the surface of the enzyme that is complementary in shape to the substrate, the amino acid residues that form the binding site are arranged specifically to attract the substrate
catalyze bond formation coupled with ATP hydrolysis
Ligases
Catalyze group elimination to form double bonds
Lyases
Enzymes that perform group elimination reactions to form double bonds are called: A. isomerases. B. transferases. C. ligases. D. hydrolases. E. lyases.
Lyases
catalyze oxidation-reduction reactions
Oxidoreductases
Ethanol is called a _______ molecule because it can become chiral through the substitution of one of its methylene hydrogen atoms.
Prochiral
catalyzes the hydrolysis of peptide bonds specific for a small neutral residue
Elastase
Why can enzymes be regulated? A. Because they are proteins. B. Because they are highly specific. C. Because they work at physiological temperatures and pressures. D. Because they have greater catalytic power than industrial catalysts.
A. Because they are proteins.
Which of the following statements is TRUE? A. Catalysts work by lowering the activation energy of a reaction. B. The change in Gibbs free energy () for a reaction is positive when energy is released. C. The amount of energy released during a reaction determines the rate at which the reaction will occur. D. A reaction with a higher transition state energy will always occur more slowly than a reaction with a lower transition state energy. E. Enzymes speed up favorable reactions by inhibiting achievement of the transition state.
A. Catalysts work by lowering the activation energy of a reaction.
Which statement expresses the correct relationship between cosubstrates, coenzymes, and cofactors? A. Cosubstrates are coenzymes that transiently bind to enzymes, while coenzymes are cofactors that are organic compounds. B. Cosubstrates are coenzymes that transiently bind to enzymes, while cofactors are coenzymes that are organic compounds. C. Coenzymes are cosubstrates that transiently bind to enzymes, while coenzymes are cofactors that are organic compounds. D. Coenzymes are cosubstrates that transiently bind to enzymes, while cofactors are coenzymes that are organic compounds.
A. Cosubstrates are coenzymes that transiently bind to enzymes, while coenzymes are cofactors that are organic compounds.
Which term does not "belong" with the others given below? A. Denaturation B. Dehydration C. Phosphorolysis D. Reduction E. Dehydrogenation
A. Denaturation
Which of the following is FALSE with respect to an enzyme catalyzed reaction? A. Enzymes increase the kinetic and thermodynamic favorability of a reaction. B. Enzymes lower the activation energy of a reaction to increase the reaction rate. C. Enzymes increase a reaction rate by binding the transition state more tightly than the substrate(s). D. Enzyme catalyzed reactions are superior to chemically catalyzed reactions because they are more specific and they lack side products.
A. Enzymes increase the kinetic and thermodynamic favorability of a reaction.
Which statement explains why enzymes use cofactors in catalysis? A. Functional groups of protein side chains are less suitable for catalysis of certain reactions, such as oxidation-reduction reactions. B. Functional groups of protein side chains are less suitable for catalysis of certain reactions, such as acid-base reactions. C. Functional groups of protein side chains are incapable of participating in chemical catalysis. D. Functional groups of protein side chains are extremely limited in chemical catalysis.
A. Functional groups of protein side chains are less suitable for catalysis of certain reactions, such as oxidation-reduction reactions.
Which statement best describes the model of "induced fit"? A. Enzyme-substrate binding induces formation of the transition state, which reduces the free energy of the reaction. B. Enzyme-substrate binding induces enzyme specificity. C. Enzyme-substrate binding induces a conformational change in the enzyme, such that the binding site better conforms to the shape of the substrate. D. Enzyme-substrate binding induces an increase in the reaction entropy.
C. Enzyme-substrate binding induces a conformational change in the enzyme, such that the binding site better conforms to the shape of the substrate.
Which one of the following statements about enzyme catalyzed reactions is FALSE? A. Enzymes catalyze reactions at their active site. B. Many enzymes change shape upon substrate binding. C. Enzymes lower the free energy change for the reactions they catalyze. D. Enzymes form complexes with their substrates.
C. Enzymes lower the free energy change for the reactions they catalyze.
Why does heat inactivate enzymes? A. Heat breaks the peptide bonds that link the amino acid residues together. B. Heat causes dissociation of essential cofactors from the active site. C. Heat disrupts the weak, non-covalent interactions that determine protein 3-D structure. D. Heat decreases the free energy change of a reaction, making it less favourable.
C. Heat disrupts the weak, non-covalent interactions that determine protein 3-D structure.
3 invariant residues, ASP 102/HIS 57/ SER 195, forming a hydrogen bonded constellation
Catalytic triad
Catalyzes the hydrolysis of peptide bonds specific for the side chains flanking the to be cleaved bond and for aromatic R groups, the bond is cleaved on the C terminal side of the protein
Chymotrypsin
Required for catalytic activity , an organic molecule, can be a cosubstrate or prosthetic group
Coenzyme
May be metal ions such as Cu 2+, Fe 3+, or Zn 2+; can also be organic molecules required for catalytic activity of an enzyme
Cofactors
Reaction who is simultaneously subject to both acid and base processes
Concerted Acid Base Catalyzed Reaction
Which of the following is most likely true for an enzyme that displays maximal activity at pH 6.4? A. This enzyme does not act as an acid and/or base catalyst. B. This enzyme has a metallic cofactor. C. A Glu or Asp residue is required for enzymatic activity. D. A His residue is required for enzymatic activity.
D. A His residue is required for enzymatic activity.
Which of the following includes two characteristics of enzyme-catalyzed reactions? A. Without regulation, but with a broad degree of substrate specificity B. Capacity for regulation and a broad substrate specificity C. Without regulation, but with a high degree of substrate specificity D. Capacity for regulation and a high degree of substrate specificity
D. Capacity for regulation and a high degree of substrate specificity
The oxyanion hole in serine proteinases illustrates which of the following mechanisms of enzyme action? A. Reduction of the activation energy barrier. B. The role of serine side chains in proteolysis. C. Induced fit in substrate binding. D. Preferential transition state binding.
D. Preferential transition state binding.
Inhibits serine proteases (and other enzymes) by reacting with a serine at the active site
Diisopropylphosphofluoridate (DIPF)
Aconitase belongs to which one of the following six recognized mechanistic classes of enzymes? A. Isomerases B. Ligases C. Transferases D. Hydrolases E. Lyases
E. Lyases
Which of the following statements is true regarding enzymes? A.Histidine is not capable of acting as an acid or a base in general acid/base catalysis. B. Lyases require ATP to catalyze the formation of bonds. C. Isomerases are the most common enzyme class D. The binding energy is the energy associated with substrate binding. E. The rate of a reaction is inversely proportional to the activation energy for the reaction.
E. The rate of a reaction is inversely proportional to the activation energy for the reaction.
represented as E, a biological catalyst that increases the rate of chemical reactions by lowering the free energy barrier between reactants and products
Enzyme
Enzymes are stereospecific, how does this characteristic arise?
Enzymes by virtue of their inherent chirality form asymmetric binding sites
Explain how an enzyme binds to good or poor substrates?
Enzymes commonly bind to poor substrates with lower reaction rates better than good substrates. A good substrate doesn't bind with high affinity but it does so on activation to the transition site
Enzymes can typically bind several stereoisomers of a particular substrate, T/F?
False
The rates of enzymatically catalyzed reactions are typically 100 to 1000 times greater than those of the corresponding uncatalyzed reactions, T/F?
False
Catalysts act by raising the transition state free energy for the reaction being catalyzed, T/F?
False, by lowering
