Chp 8: Enzymes as Catalysts Flashcards
- Define catalytic power
The rate of an enzyme-catalyzed reaction divided by the rate of the uncatalyzed reaction
- What is meant by substrate specificity of an enzyme?
The ability of an enzyme to select one or a few substrates from a group of similar substrates.
Most catalysts, unlike enzymes, are not specific. They react with many substrates and help to produce many products.
- What is the active site?
A cleft, an indentation, or crevice on the enzyme where a substrate binds, a transition state complex is formed, and products are released.
The enzyme usually changes conformation due to the interactions between the amino acid side chain groups of the enzyme and the functional groups of the substrate, so that the outside solution can’t take part of the reaction.
- Explain the Induced Fit Theory Model for Substrate Binding.
- The enzyme changes its conformation when it binds to a substrate.
- This “induced” conformation is due to the interactions between the amino acid side chains of the active site and the functional groups of the substrate.
- The substrate also changes conformation in response to the enzyme.
- What was the major shortcoming of the Lock-and-Key Model for Substrate Binding?
The major shortcoming of the lock-and-key model was that it lacked the idea of a change in conformation – instead it originally thought that a rigid substrate would slide into a rigid active site of the enzyme and a reaction would take place
- Explain catalytic power in terms of the transition state and activation energy.
An enzyme’s catalytic power increases the rate of a reaction by lowering the activation energy required to reach the transition state
- What is a transition state?
State during an enzyme reaction when an intermediate exists that resembles both substrate and product while containing the most free energy.
The enzyme stabilizes the transition state by lowering its activation energy
- What is activation energy?
Energy required to achieve the transition state
- What is a coenzyme?
Any organic cofactor that binds to the enzyme and is necessary for the reaction (usually derived from vitamins)
- What is a cofactor?
Any non-protein molecule that binds to the enzyme and is necessary for the reaction
- What is a prosthetic group?
Any cofactor (metal ion or coenzyme) that binds tightly to an enzyme, many by covalent bonding.
These are difficult to remove without denaturing the enzyme.
- What does an activation-transfer coenzyme do?
Forms a covalent bond with a portion of the substrate that contains a lot of free energy, thereby activating the substrate for transfer. This way the transfer of the group is exergonic.
- Thiamine pyrophosphate always attacks which group on substrate? Which bond is broken?
The alpha-keto group on alpha-keto carboxylic acids is the group that is always attacked by the coenzyme thiamine pyrophosphate
The C-C bond between the ketone carbon and the carbonyl carbon is broken. CO2 is released as a result.
- Which vitamin is thiamine pyrophosphate synthesized from?
Vitamin thiamine (B1)
- What is Coenzyme A’s functional group on the coenzyme?
Sulfhydryl group
- What kind of bond does Coenzyme A form with the activated group?
Thioester bond with the carboxylic acids
- What types of groups on Coenzyme A are activated?
The acyl group is activated.
This is what the “A” in CoA stands for
- Which vitamin is Coenzyme A synthesized from?
Vitamin panthothenic acid (or pantothenate, B5)
- Define catalytic power.
The rate of an enzyme-catalyzed reaction divided by the rate of the uncatalyzed reaction
- Is biotin a prosthetic group?
Yes, because there is a covalent bond between the carbon of the cofactor and the nitrogen of a lysine residue in the carboxylase enzyme
- Which kind of enzyme uses the coenzyme biotin and what does it do?
Carboxylase enzymes.
These covalently bind to CO2 and transfer them onto other substrates.
- Which vitamin is biotin synthesized from?
Biotin is both the vitamin AND the coenzyme
- What type of group does the cofactor pyroxidal phosphate react with?
The amino group of an amino acid
- Which vitamin is pyroxidal phosphate synthesized from?
Vitamin B6
- Concerning NAD+, what is the other reaction product besides pyruvate and acetaldehyde?
H+ is made along with acetaldehyde and pyruvate.
Whenever NADH is made, an H+ is also produced.
- What does NAD stand for?
Nicotinamide Adenine Dinucleotide
- What is the function of the ADP portion of NAD+?
The ADP portion of the NAD+ molecule binds tightly to enzymes such as lactate/alcohol dehydrogenases, causing conformational changes to the enzyme-substrate complex.
- When lactate dehydrogenase or alcohol dehydrogenase oxidize their substrates, what is transferred to NAD+?
A hydride ion
- Which vitamin is NAD+ synthesized from?
Niacin
- Be able to draw a probable plot of activity versus pH for an enzyme that functions at pH=7.0
The plot of activity is usually a bell-shaped curve with a maximum rate of reaction between pH 7-9.
Whenever the pH strays far from the enzyme’s optimal pH (maximum rate), whether in the acidic or basic direction, the enzyme’s ability to function is decreased
- Be able to draw a probable plot of activity versus temperature for a human enzyme.
Usually rises from 0 to 37°C and then drops rapidly at temps of 45-55°C. The rise is due to increased vibrational energy of substrates. The rapid decrease is due to denaturation of the native conformation
- Explain how diisopropylphosphofluoridate causes symptoms associated with acetylcholinesterase.
Diisopropyl phosphofluoridate (DFP aka nerve gas) inhibits acetylcholinesterase, thus preventing the degradation of the neurotransmitter acetylcholine and abnormally increasing the degree of muscle contraction.
- Is DFP an irreversible inhibitor? Why?
DFP is an irreversible inhibitor because it binds covalently to serine at the active site. Thus acetylcholinesterase activity can only be recovered as new enzyme is synthesized, which does not occur quickly.
- What is the normal function of acetylcholinesterase?
To hydrolyze acetylcholine into acetate and choline, degrading acetylcholine so that it is no longer active at the neuromuscular junction.
Acetylcholine binds to receptors on muscle and causes a contraction:
- Increased acetylcholine → increased muscle contraction
- Decreased acetylecholine → relaxation of muscles
- How does aspirin inhibit cyclooxygenase?
- By transferring its acetyl group to a serine hydroxide at the active site of cyclooxygenase and forming a covalent bond.
- Aspirin binds to the active site because it resembles the normal substrate.
- This is irreversible inhibition of prostaglandin synthesis from arachadonic acid.
- Cyclooxygenase is also known as COX or prostaglandin endoperoxide synthase
- Is penicillin an irreversible inhibitor?
Yes, after binding it forms a covalent bond with serine at the active site
- Is penicillin a suicide inhibitor? Why?
- Yes, because it binds to the active site and undergoes a partial reaction to irreversibly inhibit the enzyme.
- Partial reaction means that the inhibitor is not released from the enzyme (i.e., a full reaction would have released the inhibitor and returned the enzyme to its active state).
- So the enzyme necessary for bacterial wall synthesis commits suicide by reacting with penicillin
- Why does penicillin bind so readily to the active site of the enzyme?
Because a portion of the molecule resembles the transition state of the normal enzyme reaction
- What is the normal function of xanthine oxidase?
Catabolizes/converts purine nucleotides into uric acid/urate
- In general terms, why are heavy metals toxic?
Because they bind to proteins, change their conformation, and inhibit their function
- Alcohol dehydrogenase is an example of which class of enzyme?
Oxidoreductase
- Aldolase is an example of which class of enzyme?
Lyase
- Be able to name the 6 major classes of enzymes.
- Oxidoreductase
- Transferase
- Hydrolase
- Lyase
- Isomerase
- Ligase
- Chymotripsin is an example of which class of enzyme?
Hydrolase
- Glucokinase is an example of which class of enzyme?
Transferase
- Match this reaction with a class of enzyme: ATP + C2CO3 + Pyruvate → ADP + Pi + oxaloacetate
Ligase - joins together two molecules by hydrolyzing a high-energy bond
- Match this reaction with a class of enzyme: CH3CH2OH + NAD+ → CH3CHO + NADH + H+
Oxidoreductase - one substrate is oxidized while the other is reduced
- Match this reaction with a class of enzyme: Dihydroxyacetone phosphate → Glyceraldehyde-3-phosphate
Isomerase
- Match this reaction with a class of enzyme:
Fructose 1,6-bisphosphate → Dihydroxyacetone phosphate + glyceraldehyde 3-phosphate
Lyase - splits or combines molecules without H2O, oxidation, or ATP hydrolysis
- Match this reaction with a class of enzyme: RCONHR +H2O → RCOOH +H2NR
Hydrolase - cleaves a bond by adding H2O, producing two compounds
- Match this reaction with a class of enzyme: Glucose + ATP → Glucose-6-P + ADP
Transferase - transfers a group from one molecule to another
- Pyruvate carboxylase is an example of which class of enzyme?
Ligase
- Triosephosphate isomerase is an example of which class of enzyme?
Isomerase
- Which class of enzymes catalyze group transfer reactions, meaning they transfer a group from one molecule to another?
transferase
- Which class of enzymes catalyze reactions that cleave a bond by adding H2O, producing two compounds? This can be the reverse reaction where two compounds come together by removing H2O.
hydrolase
- Which class of enzymes is recognizable by one substrate being oxidized and another being reduced?
oxidoreductase
- Which class of enzymes join together two molecules coupled with the hydrolysis of a high energy bond (such as the diphosphate bond in ATP or similar triphosphate)?
ligase
- Which class of enzymes split or combine molecules without H2O, oxidation, or ATP hydrolysis being involved?
lyase
- Which class of enzymes rearrange the atoms of a molecule to form an isomer?
isomerase
- What is the difference between a synthase and a synthetase?
• Synthase is a lyase, does not use ATP or other high energy equivalent when splitting or combining molecules • Synthetase is a ligase that does use ATP or another high energy equivalent when combining molecules as it requires the energy from the high energy bond to form the covalent bond
- Is malathione a suicide inhibitor? Why?
The product of malathion binds to the enzyme and is converted into an enzyme-substrate complex that does not dissociate from the enzyme.
It is converted by the enzyme into an irreversible inhibitor, which fits the definition of a suicide inhibitor (a compound that binds to the active site and is converted by the enzyme into an irreversible inhibitor).
- Is the inhibition of acetylcholinesterase by malathion irreversible?
Malathion gets converted to malaoxon by the liver, which then binds to acetylcholine esterase in a manner similar to diisopropylphosphofluroidate (DFP, nerve gas).
At first the binding is reversible, but with time becomes irreversible
- What are the symptoms associated with malathion?
- Malathion gets converted to malaoxon by the liver, which then binds to acetylcholinesterase in a manner similar to diisopropylphosphofluroidate (DFP, nerve gas).
- Inhibition of acetylcholinesterase prevents the hydrolysis of acetylcholine, so the concentration of it in the synapse builds up to abnormally high levels with abnormally high muscle contraction.
- Explain why allopurinol is used to treat gout.
- Gout is a disease characterized by high concentrations of sodium urate that precipitate out of solution in the joint of the big toe/ankle and causes pain.
- Allopurinol is used to treat gout because it inhibits the xanthine oxidase reactions, lowering the concentration of urate in the system.
- Is allopurinol a suicide inhibitor? Why?
Yes, because it binds to xanthine oxidase specifically and is converted into a form that is bound irreversibly.
Irreversible = suicide.
- What normal reaction is inhibited by allopurinol?
Hypoxanthine → Xanthine → Urate
Both the above reactions are inhibited by allopurinol, which prevents the formation of urate ions that precipitate into urate crystals.
These are the last reactions in the catabolism of purine AMP and GMP.
- What is the coenzyme of the alcohol dehydrogenase reaction?
NAD+
- What is the common vitamin deficiency seen in alcoholics?
Thiamine (b1) deficiency, which occurs because alcohol inhibits the transport of thiamine through the intestinal mucosal cells. Also, many alcoholics have poor diet and thus ingest very little thiamine.
- What is the equation for the first step for alcohol metabolism in humans?
CH3CH2OH + NAD+ → CH3CHO + NADH + H+
Ethanol is oxidized to acetaldehyde while NAD+ is reduced to NADH
- Which vitamin is the coenzyme of the alcohol dehydrogenase reaction synthesized from?
Niacin
