Enzymes Flashcards
One method to increase the amount of CO2 in sodas would be to pump CO2 into the cans. What method do companies do instead?
Utilize the H2O + CO2 = H2CO3 (carbonic acid) method instead as this allows CO2 to be dissolved into the the liquid itself and therefore much more CO2 can be fit inside the can
The fizz you see on the top of the soda can is due to CO2. However as you drink it, you notice the bubbles are dramatically more. What is causing this increase in bubbles?
Carbonic anhydrase found in the mouth causes an increase in CO2 through H2O + CO2 H2CO3 backwards reaction. The enzyme helps facilitate the reaction to occur much more quickly than it would naturally on its on (seen on/in the can)
Enzymes have many mechanisms to function. Name them all.
Acid-Base Catalysis, Proximity-Orientation, Covalent Catalysis, Electrostatic Catalysis
Mnemonic: CAPE
An enzyme facilitating the transfer of a hydrogen from one species to another. What type of mechanism of action is the enzyme committing to? A. Proximity - Orientation B. Electrostatic Catalysis C. Covalent Catalysis D. Acid - Base Catalysis
D. Acid-Base Catalysis
A newly discovered protein is transferring an oxygen from a carbonyl to an inole. What mechanism of action is this protein committing to?
None of knowledge yet. The ones required to know are: Acid-Base Catalysis, Proximity-Orientation, Covalent Catalysis, Electrostatic Catalysis
An enzyme facilitating the transfer of an electron from one species to another. What type of mechanism of action is the enzyme committing to? A. Proximity - Orientation B. Electrostatic Catalysis C. Covalent Catalysis D. Acid - Base Catalysis
B. Electrostatic Catalysis. It is acting like a carrier or an electron sink
True or false: Electrostatic Catalysis is a mechanism of an enzyme in which the enzyme will act as a mediator to hold electrons temporarily and even transfer it from one molecule to another.
False. Electrostatic catalysis is a when a cofactor of an enzyme such as magnesium, functions in stabilizing the reactants. Ex: DNA Polymerase uses Mg2+ to stabilize the negatively charged DNA in order to replicate it
What is the purpose of an enzyme utilizing the proximity and orientation mechanism of action?
These enzymes bring the needed molecules closer together to increase collision, and orient molecules in appropriate angles to allow a reaction to occur.
What are the requirements from reactants in order for a reaction to occur?
In order for molecules to react, they need to collide at the right angles
Carbonic Anhydrase catalyzes a reaction involving which molecules to form carbonic acid? A. H2O and CO2 B. H2 and CO2 C. H2O and CO D. H2 and CO
H2O and CO2
CO2 is not as readily carried by hemoglobin or any protein in the body. How does this increase the importance of carbonic anhydrase?
This enzyme allows the addition of CO2 and H2O into a soluble form (bicarbonate in blood). This process is important to allow the excretion of CO2 in the lungs, which can’t be done in the tissues.
True or False: CO2 is 10 times as soluble as O2 in water.
False, CO2 is 20 times as soluble than water, therefore CO2 can be carried in the blood stream while O2 needs a special carrier. CO2 is soluble because water molecules are attracted to these polar areas. The bond between carbon and oxygen is not as polar as the bond between hydrogen and oxygen, but it is polar enough that carbon dioxide can dissolve in water. In blood, 85% of CO2 is carried as HCO3-
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The production of carbonic acid from carbon dioxide and H2O occurs… A. In the tissues B. In the bloodstream C. In the blood cells D. In the lungs
C. Occurs in the blood cells, and diffuses out to dissolve into the bloodstream as bicarbonate. At the lungs, catabolize carbonic acid into H2O and CO2
True or false: After the generation of carbonic acid, another enzyme catalyzes the acid into bicarbonate and acid
False. This is a spontaneous event that occurs very quickly after the formation of carbonic acid. Therefore once it is shuttled out, the molecule is a bicarbonate already
Bicarbonate ends up in the bloodstream once it is produced. Describe the mechanism of its travel there. What is the importance of this mechanism
It binds onto a chlorine/bicarb shuttle at the membrane of the RBC. As Cl- from the ECM is taken into the cell, bicarbonate is shuttled out. This mechanism preserves the electrical charge both in the plasma and the red blood cell.
While the acid buffer system of bicarbonate anabolism is seen in RBC, where else in the body is this system also seen in?
In the kidneys as well as the lungs
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HCO3- is used to adjust the H+ concentrations in the blood. What happens to the pH at the lungs when CO2 is exhaled?
Some HCO3–, which helps to adjust H+ concentrations, is lost from the body when CO2 is expelled from the lungs. As a result the H+ concentration also decreases as well because it is converted into H2O and the pH increases. [Note: Lung pH is around 7.4]
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The efficiency of carbonic anhydrase’s conversion of CO2 to H2CO2 is A. 100,000 CO2/ min B. 1,000,000 CO2/ min C. 100,000 CO2/sec D. 1,000,000 CO2/sec
D. 1,000,000 CO2/sec. Therefore this enzyme is very good at its job in lowering the toxic CO2 levels in the blood
Of the following, which is not a fact about enzymes:
A. They have the ability to transform energies
B. Apoenzymes are dependent on cofactors for function
C. Enzymes limit the number of unwanted products
D. All enzymes are proteins
D. Not all enzymes are proteins, some are RNA molecules that have the ability to catalyze reactions as well.
B. Enzymes without their cofactors are called apoenzymes, and with interaction between the two, these are called holoenzymes
C. Enzymes limit the number of unwanted products by having a high specificity for substrates and conducting only one or related sets of reactions
Enzymes bound to their cofactors are called: A. Apoenzymes, B. Vitamins C. Coenzymes D. Holoenzymes
D. Holoenzymes are produced when apoenzymes bind their cofactors.
B and C: Vitamins tend to be the composition of coenzymes (which are organic cofactors)
Compare and contrast metal ions and coenzymes
Metal ions and coenzymes are both cofactors to an enzyme to allow efficient and effective function. However, both differ as metal ions are metals, or metal compounds while coenzymes are made organic molecules usually made of vitamins
Compare and contrast prosthetic groups and coenzymes
Prosthetic groups are a specific class under coenzymes. While coenzymes refer to all organic cofactors, prosthetic groups are cofactors that are tightly/covalently bound to the protein itself which means that this group is essential for the function of the enzyme
Two molecules, CO2 and H2O are bound by carbonic anhydrase and are converted into H2CO3. What prevents a CO2 and H2O from converting into other types of substrates such as glucose?
The enzymes innate property of commiTting to one or related sets of reactions (it’s specificity) leads to specific orientation and combination of molecules
Trypsin, an protease cleaves carboxyl groups of…
(1) cleaves peptide bonds on the carboxyl side of lysine (2) binds and cleaves the carboxyl side of arginine amino acid. [demonstrates its specificity for related reactions
In an experiment, you throw in an unknown enzyme into its substrates. After a reaction, you momentarily see change to its structure. You conclude this is not an enzyme. Is your conclusion correct?
Maybe not, if this is a true enzyme, the structure and shape may change, however, it will assume its original shape and structure once the reaction is completely over.
Identify the correct definition
A. Enzymes lower the standard free energy of a reaction
B. Enzymes consume the substrate to produce product
C. Enzymes lower the free energy of activation
D. Enzymes lower the E_rcn
C. Enzymes lower the free energy of activation aka the reaction’s activation energy (ΔG‡). They don’t change the standard free energy of a reaction (E_rcn/ΔG°) and don’t change the products or reactants. They simply change the pathway from reactant to product.
Compare and contrast the two catalytic strategies enzymes can take on: Covalent and electrostatic.
Both are strategies by enzymes. However, covalent catalysis is the covalent bond of an enzyme to the substrate, while the electrostatic catalysis is the enzyme using molecules such as metal cofactors to stabilize big positive or negative charges
While conducting an experiment, you analyze a reaction from a reaction coordinate diagram. The graph shows the substrate with a higher energy state compared to the product and the free energy of activation, to be bigger compared to the standard free energy. Which molecule is more stable?
The product is more stable compared to the reactants as it has a decreased energy state. Molecules with increased energies are more reactive and unstable.
Where on a reaction coordinate graph can you find the transition state?
This will be the highest peak along the pathway of a substrate’s conversion to its product.
Compare and contrast free energy of activation and the standard free energy.
Delta G Double Dagger - (ΔG‡) - this is the free energy of activation - amount of energy substrate needs to have in order to break the reaction barrier to get to point B. Standard Free Energy (ΔG°) the net change between our reactant and product. This is the energy released into the environment once the reaction is over. This includes ΔG‡ in its equation as well
What will determine how fast a reaction occurs?
Its innate free energy of activation (the energy difference from substrate to transition state)
You are working on a biochem problem and the calculate that the reaction has a negative Gibbs free energy. Is this reaction in equilibrium?
No, negative Gibbs free (Energy of products - energy of reactants) demonstrates a spontaneous, exergonic reaction and therefore is still taking place. When Gibbs free energy (ΔG) has reached 0, the reaction is said to have reached equilibrium
Describe what Gibbs free energy is.
Gibbs free energy is how much energy is inputted or released into the chemical reaction. It relies only on the energy of the product - reactant. The pathway in which it takes to achieve this, does not matter.
During your attempt to combust an ATP, you discover the standard free energy of your reaction is positive. What has gone wrong with your experiment?
You have created ATP rather than combust. Creating this high energy molecule requires energy (endergonic reaction/nonspontaneous reaction). OR your math could be wrong
Your intern is calculating how much energy is released as you force a GTP molecule to release a phosphate by calculating the transition state energy and the substrate energy level. What should you tell him?
Gibbs free energy is the energy released/inputted into a reaction and does not rely on the pathway of a reaction.
K1 = K2. What does this mean in terms of G?
Q represents a quantity of a species of a reaction. When Q changes to K, this entails that the substrate/product has reached equilibrium, therefore K is the numerical values of Q at the end of the reaction. Therefore when K1 = K2, equilibrium has been reached. And therefore Gibbs is 0 (also mean equilibrium)
Compare and contrast activation energy and gibbs free energy
Activation energy = the free energy of activation. This is the required energy needed for a substrate to enter into its transition state. Changing the pathway in which the substrate gets converted into its product, such as addition of an enzyme, will lower this value.
Gibbs free energy is the standard free energy, or the energy released with a substrate changing into its product. Changes to the pathway will ont change this value
Describe the role of an enzyme and the transition state of a substrate.
As the substrate enters into its transition state (the most unstable state) the enzyme stabilizes it to allow it to enter this stage much more quickly. In the active site, there exists and environment which allows the stability of the bonds creating and forming, decreasing the activation energy. Remember, a reaction is dependent on the activation energy.
The x axis of a reaction coordinate diagram of a chemical reaction is …
The reaction progress of the chemical reaction. This is not time!!! Time cannot be determined by the reaction progress
You are comparing two scenarios of the same reaction: One with a catalysis and another without. They both reach equilibrium. What key things do both share at this point?
Both scenarios should have the same quantity of products and reactants and they should have the same amount of gibbs free energy released/consumed.
You have 10 enzymes and add 3 substrates into the mixture. What is its activity?
The enzymes are functioning at 30% of its maximum velocity. Activity of enzymes are measured based on all the same enzymes’s activity. When all enzymes of the same type are functioning (meaning all substrates have binded to the active site), then it has reached its max capacity.
You are solving a problem and you read that the enzyme has reached its max velocity with 100 mg of bicarbonate. What does max velocity represent?
The maximum velocity of the enzyme represents the activity of the active site. Keep in mind that enzymes will never reach this, but simply an estimation
Compare and contrast the binding of a substrate to an enzyme when it is done initially, and when it is in its induced fit.
The Initial binding of an enzyme and a substrate occurs when theses two molecules first interact. This binding leads to strong interactions, however the fit of another is not the strongest quite yet. As the substrate and enzyme conform to one another’s shape, they develop the strongest interaction - this process is called induced fit. This interaction is the point in which the substrates enter into their transition state in order to be cleaved into their products.
