Chapter 2: Enzymes Flashcards

Question

What is the name for the site within and enzyme where a substrate is held?

Answer 1

Active site

Answer 2

They both act as activators of enzymes. They regulators induce a conformational change in the enzyme that promotes its activity. Cofactors are generally inorganic molecules or metal ions and are often ingested as dietary minerals. Coenzymes are small organic groups like vitamins or derivatives of vitamins such as NAD+, FAD, and coenzyme A.

Answer 3

Tightly bound cofactors or coenzymes that are necessary for enzyme function are known as prosthetic groups. Heme group in hemoglobin is an examine of a prosthetic group. Heme is a porphyrin ring containing a ferrous iron ion (Fe2+).

Answer 4

They both act as activators of enzymes. Cofactors tend to be inorganic (minerals), while coenzymes tend to be small organic compounds (vitamins). They both induce conformational change in the enzyme thus promoted its activity. Tightly bound cofactors or coenzymes that are necessary for enzyme function are termed prosthetic groups.

Answer 5

A, D, E, K

Answer 6

Saturation refers to the maximum capacity of a group of enzymes to act. When the amount of enzyme is the limiting factor, the reaction will reach saturation where the enzymes are working at maximum velocity, called Vmax.

Answer 7

Increasing the concentration of enzyme is the only way to increase Vmax.

Answer 8

As the amount of substrate increases, the enzyme is able to increase its rate if reaction until it reaches a maximum enzymatic reaction rate (Vmax). Once Vmax is reached, adding more substrate will not increase the rate of reaction.

Answer 9

Under constant concentration of enzyme, we can calculate the velocity of the enzyme to substrate concentration using the Michaelis Menten equation.

Answer 10

Km=concentration of substrate at 1/2(Vmax)

Answer 11

Km is a measure of affinity of the enzyme for its substrate. Km is the Michaelis Menten constant and is often used to compare enzymes. High Km means the enzyme has low affinity for its substrate. Low Km means the enzyme has high affinity for its substrate.

Answer 12

A low Km reflects a high affinity for the substrate (low [S] required for 50% of enzyme saturation) A high Km reflects a low affinity for the substrate (high [S] required for 50% of enzyme saturation).

Answer 13

Yes. It cannot be altered by changing the concentration of enzyme or substrate. Recall that Km=[S] at 1/2(Vmax)

Answer 14

The variable Vmax represents maximum enzyme velocity and is measured in moles of enzyme per second. Vmax can be mathematically related to Kcat which has units of s^-1. Kcat measures the number of substrate molecules “turned over” to product, per enzyme molecule per second.

Answer 15

The units of Kcat are s-1. Kcat measures the number of substrate molecules converted to product per enzyme molecule per second.

Answer 16

Most enzymes have Kcat values between 101 and 103.

Answer 17

LW-B plots are handy because they give us an easier and more accurate approximation of Vmax. The M-M plot forces us to guess Vmax as it appears asymptotic. LW-B is a double inverse plot of the Michaelis Menten equation.

Answer 18

Lineweaver burn plot is a double reciprocal plot of the Michaelis Menten equation. It allows us to determine the type of inhibition that an enzyme is experiencing because Vmax and Km can be compared without estimation.

Answer 19

Some enzymes show a sigmoidal (S-shaped) kinetics owing to cooperativity among substrate binding sites. The cooperative binding of hemoglobin, which acts as a transport protein rather than an enzyme, results in the characteristic sigmoidal curve.

Answer 20

Cooperative enzymes have multiple subunits and multiple active sites. Subunits and enzymes may exist in one of two states: T : low affinity tense state R : high affinity relaxed state

Answer 21

Binding of the substrate encourages the transition of other subunits from the T state to the R state, which increases the likelihood of substrate binding by these other sub units. Conversely, loss of substrate can encourage the transition from the our state to the T state, and promote dissociation of a substrate from the remaining subunits.

Answer 22

As more people start arriving, the atmosphere becomes more relaxed in the party seems more appealing. But as people start going home, the party dies down and more people are encouraged to leave so the tense hosts can clean up.

Answer 23

Increasing [S] has different effects: when [S] is low, and increase in [S] causes a proportional increase in enzyme activity. At high [S], increasing [S] has no effect on Vmax because Vmax has already been attained. Increasing [E] will always increase Vmax regardless of starting [E].

Answer 24

Km is a measure of an enzymes affinity for its substrate and is defined as the substrate concentration at which an enzyme is functioning at half of its maximal velocity. As Km increases, an enzymes affinity for its substrate decreases. As Km decreases, an enzymes affinity for its substrate increases.

Answer 25

X intercept: -1/Km Y intercept: 1/Vmax

Answer 26

They are all the same thing.

Answer 27

T, pH, salinity

Answer 28

Usually double activity per increase in 10°C in temperature up to an optimal T where activity falls off due to denaturation. 37°C, 98.6°F, 310K in humans.

Answer 29

Most enzymes depend on pH in order to function properly as it can affect the ionization of the active site as well as denature the protein. Enzymes in the blood operate best at pH=7.4. pH less than 7.35 is considered acidemia.

Answer 30

Blood: 7.4 Stomach (pepsin): 2 Duodenum (trypsin): 8.5

Answer 31

Increasing levels of salt in vitro (in glass) can disrupt H and ionic bonds, causing a partial change in the confirmation of an enzyme. Can also cause denaturation.

Answer 32

Feedback regulation regulates enzymes by products further down a metabolic pathway. Feed forward regulation: less common. enzymes regulated by intermediates that precede the enzyme in the pathway. Negative feedback (feedback inhibition): far more common. Helps maintain homeostasis, once we have enough of a given product, it turns off the pathway that creates the product.

Answer 33

Enzymology and endocrine system. Hormonal feedback loops are also inhibited by negative feedback.

Answer 34

Competitive inhibition: involves occupancy of the active site. Substrates cannot access enzymatic binding sites if there is an inhibitor in the way. Non-competitive inhibition: binds to an allosteric site instead of the active site, which induces a change in enzyme confirmation. Mixed inhibition: results when an inhibitor combined to either the enzyme or the enzyme substrate complex, but has different affinity for each. Uncompetitive inhibition: bind only to the enzyme substrate complex and essentially lock the substrate in the enzyme.

Answer 35

Competitive inhibition simply involves occupancy of the active site. Substrates cannot access and enzymatic binding sites if there is an inhibitor in the way. Can be overcome by adding more substrate so that the substrate inhibitor ratio is higher. Competitive inhibitors decrease the value of Km because the substrate concentration has to be higher to reach half the maximum velocity in the presence of the inhibitor. Adding a competitive inhibitor does not alter the value of Vmax because if enough substrate is added, it will out compete the inhibitor and be able to run the reaction at maximum velocity.

Answer 36

Non-competitive inhibitors binds to an allosteric site instead of the active site, which induces a change and enzyme conformation. Because the two molecules do not compete for the same site, inhibition is considered non-competitive and cannot be overcome by adding more substrate. Once the enzyme’s comformation is altered, no amount of extra substrate will be conducive to forming an enzyme substrate complex. No competitive inhibitors do not change Km because any copies of the enzyme that are still active, maintain the same affinity for their substrate. Adding a non-competitive inhibitor decreases the measured value of Vmax because there is less enzyme available to react.

Answer 37

Mixed inhibition results when an inhibitor combined to either the enzyme or the enzyme substrate complex, but has different affinity for each. If the inhibitor had the same affinity for both, it would be a non-competitive inhibitor.

Answer 38

Depends on the preference of the inhibitor for the enzyme versus the enzyme substrate complex. If the inhibitor preferentially binds to the enzyme, it increases the Km value (lowers affinity). If the inhibitor preferentially binds to the enzyme substrate complex, it lowers the Km value (increases affinity) In either case, Vmax is decreased. The curve for the activity with and without the inhibitor intersect at a point that is not on either axis.

Answer 39

Uncompetitive inhibitors bind only to the enzyme substrate complex and essentially lock the substrate in the enzyme, preventing its release. Uncompetitive inhibitors lower Km and Vmax. On a Lw-B plot, the curves for activity with and without an uncompetitive inhibitor are parallel.

Answer 40

Irreversible inhibition is when the active site is made unavailable for a prolonged period of time, or the enzyme is permanently altered. This type of inhibition is not easily overcome or reversed. Aspirin is good example. Acetylsalicylic acid irreversibly modifies cyclooxygenase-1. The enzyme can no longer bind substrate to make its products (prostaglandins) which are involved in modulating pain and inflammatory responses. To make more prostaglandins, new cyclooxygenase-1 we have to be synthesized through transcription and translation. Irreversible inhibition is a prime drug mechanism, and something you will come across often in medical school.

Answer 41

Allosteric. Enzymes that are allosteric have multiple binding sites. Covalently modded enzymes. Enzymes can be activated or deactivated through covalent modification such as phosphorylation or dephosphorylation. Zymogens. Enzymes are sometimes secreted as inactive zymogens like trypsinogen.

Answer 42

Enzymes that are allosteric have multiple binding sites. The active site is present, as well as at least one other site that can regulate the availability of the active site. Allosteric enzymes alternate between an active and an inactive form. The inactive form cannot carry out enzymatic reaction. An activator will result in a shift that makes the Active site more available for binding to the substrate. An inhibitor will make the active site less available. Michaelis Menten plots of cooperative, allosteric enzyme kinetics often have a sigmoidal curve.

Answer 43

Enzymes are often subject to covalent modification such as being activated or deactivated by phosphorylation or dephosphorylation. Glycosylation is the covalent attachment of sugar moieties to enzymes. Glycosylation prepare enzyme for transport within the cell, or can modify protein activity.

Answer 44

Certain enzymes are particularly dangerous if they are not tightly controlled. These include the digestive enzymes like trypsin, which if released from the pancreas in an uncontrolled manner would digestive the organ itself. Zymogens are inactive forms of enzymes. They contain a catalytic (active) domain and a regulatory domain. The regulatory domain must be either removed or altered to expose the active site. Most Zymogens have a suffix -ogen.

Answer 45

Feedback inhibition refers to the product of an enzymatic pathway turning off enzymes further back in the same pathway. This helps maintain homeostasis: as product levels rise, the pathway creating that product is appropriately down regulated.

Answer 46

A competitive inhibitor increases Km because the substrate concentration has to be higher to reach half the maximum velocity in the presence of the inhibitor. A mixed inhibitor will increase Km only if the inhibitor or preferentially binds to the enzyme over the enzyme substrate complex.

Answer 47

Irreversible inhibition refers to the prolonged or permanent and activation of an enzyme, such that it cannot be easily re-natured to gain function.

Answer 48

Example of transient modifications include allosteric activation or inhibition. Example of covalent modifications include phosphorylation and glycosylation.

Answer 49

Zymogens are precursor of active enzymes. It is critical that certain enzymes remain inactive until arriving at their target site. Digestive enzymes of the pancreas or a great example (trypsinOGEN and chymotrypsinOGEN)

Answer 50

An enzyme devoid of its necessary cofactor is called an apoenzyme.

Answer 51

When Km equals the [S], then the enzyme is working at 1/2 Vmax.

Answer 52

This is a good question to reading Lw-B plots.

Chapter 2: Enzymes Flashcards

(106 cards)