Macromolecules and Enzymes - GRE Subject Test: Biochemistry, Cell, and Molecular Biology

An enzme is a biological catalyst that increases the rate of a reaction. This is accomplished by lowering the activation energy necessary to start the reaction. The equilibrium of the reaction, however, is not affected. This means that enthalpy and entropy are not affected by an enzyme's presence.

The correct answer is lyases. This class of enzymes only requires one substrate for the forward reaction.

Ligases catalyze the formation of a bond between two molecules, isomerases rearrange the atoms of a molecule, kinases phosphorylate molecules, and transferases transfer or join functional groups from one molecule to another.

Kinases are enzyme that catalyze the transfer of a phosphate group from ATP to a substrate molecule. The phosphorylation of fructose-6-phosphate to fructose-1,6-phosphate is mediated by a kinase phosphofructokinase.

If the reaction rate has plateaued, this indicates that the enzyme has reached saturation. At this point, every active site on every molecule of enzyme is actively catalyzing the reaction as quickly as it can. The only way to change the reaction rate, at this point, would be to increase the concentration of the enzyme in the solution. Further increasing substrate concentration will have no effect.

We know that the enzyme has not become denatured because the reaction is still occurring. The rate of the reaction is constant during the plateau, and does not drop to zero.

A Lineweaver-Burk plot is a way to graphically represent enzyme kinetics. It is convenient because several portions of the graph readily display important information, such as rate constants. The y-intercept in particular is useful because it represents the reciprocal of the maximum velocity. The x-intercept describes the negative reciprocal of the Michaelis constant. The slope is the quotient of the Michaelis constant over the maximum velocity.

The two plots contain the same information. A Michaelis-Menten plot shows the relationship between initial reaction rate concentration of substrate ( versus ). A Lineweaver-Burk plot shows the relationship between the inverses of these same two variables, however, it is much easier to visualize important data on a Lineweaver-Burk plot. The x-intercept, the y-intercept, and the slope all contain points of interest. A downside of the Lineweaver-Burk plot, however, is that it is more susceptible to inaccuracy if there is some flaw in the accumulated data.

The only option that will alter the is to add a non-competitive inhibitor. The addition of this inhibitor will affect the amount of free enzyme available to catalyze the reaction, and thus lower the by reducing the effective enzyme concentration.

Addition of a competitive inhibitor will alter the , but not the . Increasing the substrate concentration will have no effect once saturation has been reached.

During a reaction, the reactants must pass through high-energy transition states before they evolve into the products. The catalyst reduces the free energy of this transition state, thus making it 'easier' for the reactant to undergo the chemical reaction since the activation energy has been lowered.

The correct answer is uncompetitive inhibition. The formation of a enzyme-substrate complex creates an alternative site on the enzyme for an inhibitor to bind. This mechanism is considered uncompetitive because the inhibitor and substrate are not competing for the same binding site on the enzyme.

Enzymes exert their effect on the reaction rate by decreasing the energy needed for the reaction to proceed. As a result, the enzyme will decrease the activation energy. It should be noted that the forward reaction rate and reverse reaction rate are both increased by an enzyme. If this were not the case, more product would be made compared to the uncatalyzed reaction, and enzymes do not affect equilibrium constants for reactions.

The difference between the binding of cAMP and phosphorylation is that the latter is a covalent modification. Covalent modifications are a different way to regulate proteins, and do not fall under the category of allosteric regulation. Allosteric regulation only occurs outside of the active site, often simply called an allosteric site. The non-covalent binding of cAMP to a region of an enzyme outside of the active site thus qualifies as allosteric regulation.

Ligases are enzymes that catalyze the formation of new bonds between molecules. A classic example is DNA ligase, an enzyme that synthesizes phosphodiester bonds in the DNA backbone.

Transferases move small molecules from one molecule to another, sometimes altering the functional groups of a compound. Isomerases convert molecules from one isomer to another. Lyases are enzymes that break bonds through a means other than hydrolysis (typically by formation of a double bond).

Since chymotrypsin uses a water molecule in order to cleave the polymer, it is considered a hydrolase enzyme.

Since the enzyme has changed the shape of the molecule without altering its chemical formula, the enzyme has simply made a new isomer of the molecule. This action is accomplished by isomerase enzymes.

All answer choices fit the description. Epigenetics (above the gene) are heritable modifications of chromatin and DNA that affect gene expression. Pioneer transcription factors are able to bind DNA in heterochromatin and recruit enzymes that promote euchromatin formation which allows other transcription factors to bind and effect gene expression. Histone methyltransferases and acetyltransferases methylate and acetylate histones, respectively, to alter gene expression. DNA methyltransferases are also enzymes that confer epigenetic changes to DNA by methylation, which usually represses gene expression.

The correct answer is acetylases. DNA can be directly methylated by methylases, mended during DNA repair by ligases, uncoiled by topoisomerases, and replicated by polymerases. However, DNA cannot be acetylated. Epigenetic associated-acetylation occurs only on histones to determine the chromatin state of a specific region.

Flippases use ATP to permit membrane lipids to reorient themselves in the cellular membrane, specifically in the direction from extracellular to intracellular facing. Floppases catalyze the reverse movement: intracellular to extracellular. Migratases are not a class of enzyme. Phospholipases and kinases catalyze other types of reactions and certainly can act on lipids, but not this particular lipid movement.

Because the inhibitor binds at the active site, it is actively competing with the ligand for access to the enzyme. This type of inhibitor displays competitive inhibition. Competitive inhibition can be overcome by adding excessive amounts of substrate. If the amount of substrate greatly out-measures the amount of inhibitor, then the substrate will still bind the enzyme very frequently and allow the reaction to proceed.

Noncompetitive inhibitors bind an enzyme at a spot that is not the active site. Uncompetitive inhibitors bind the enzyme-substrate complex, once the substrate has already entered the active site. Suicide inhibitors "kill" enzymes, typically by making permanent modifications to amino acids in the active site.

Plotting the concentration of the inhibitor versus the concentration of the substrate will not give you any useful information because the reaction rate is essential in determining the type of inhibitor present.

Plotting initial reaction rate versus substrate concentration, or plotting the inverses, describes the graphical representation of Michaelis-Menten kinetics and a Lineweaver-Burk plot, respectively. Both of these are excellent methods to visually determine the type of inhibition displayed. On the graph, the line representing the inhibited enzyme will shift in predictable fashions depending on the type of inhibition.