Metabolism Problem Set
Distinguish between cofactors and coenzymes. Give examples of each.
A cofactor is any nonprotein molecule or ion that is required for the proper functioning of an enzyme. Cofactors can be permanently bound to the active site or may bind loosely and reversibly, along with the substrate, during catalysis. A coenzyme is an organic molecule serving as a cofactor. Most vitamins function as coenzymes in metabolic reactions.
For this reaction: ATP --> ADP + Pi , ∆G =
-7.3 kcal/mol (-30.5 kJ/mol)
What is a catalyst?
A chemical agent that selectively increases the rate of a reaction without being consumed by the reaction.
In many cellular reactions, a phosphate group is transferred from ATP to some other molecule in order to make the second molecule less stable. The second molecule is said to be
phosphorylated intermediate.
When the terminal phosphate bond is broken, a molecule of inorganic phosphate Pi is formed, and energy is
released.
Transport Work
such as the beating of cilia, the contraction of muscle cells, and the movement of chromosomes during cellular reproduction
What is meant by a spontaneous process?
A process that occurs without an overall input of energy; a process that is energetically favorable
Explain the name ATP by listing all the molecules that make it up
ATP contains the sugar ribose, with the nitrogenous base adenine and a chain of three phosphate groups bonded to it, forming adenosine triphosphate.
What is allosteric regulation?
Allosteric regulation is the binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site.
What effect does an enzyme have on EA?
An enzyme catalyzes a reaction by lowering EA barrier.
For an exergonic reaction, is ∆G negative or positive?
An exergonic reaction proceeds with a net release of free energy. Because the chemical mixture loses free energy, ∆G is negative for an exergonic reaction.
Enzymes lower Ea by (2)
As the active site of an enzyme clutches the bound substrate, the enzyme may stretch the substrate molecules toward their transition-state form, stressing and bending critical chemical bonds that must be broken during the reaction.
What is meant by induced fit?
Caused by entry of the substrate, the change in shape of the active site of an enzyme so that it binds more snugly to the substrate. When the substrate enters the active site, it forms weak bonds with the enzyme, inducing a change in the shape of the protein. This change allows additional weak bonds to form, causing the active site to enfold the substrate and hold it in place.
Is cellular respiration an endergonic or an exergonic reaction? What is ∆G for this reaction?
Cellular respiration is an exergonic reaction. The ∆G for this reaction is: ∆G = -686 kcal/mol (-2,870 kJ/mol)
List the three main kinds of work that a cell does.
Chemical, Mechanical, Transport
Compare and contrast competitive inhibitors and noncompetitive inhibitors
Competitive inhibitors are substances that reduce the activity of an enzyme by entering the active site in place of the substrate, whose structure it mimics. Noncompetitive inhibitors are substances that reduce the activity of an enzyme by binding to a location remote from the active site, changing the enzyme's shape so that the active site no longer effectively catalyzes the conversion of substrate to product.
Enzymes lower Ea by (4)
Direct participation of the active site in the chemical reaction is another mechanism of catalysis.
Explain how protein structure is involved in enzyme specificity.
Enzymes are proteins, and proteins are macromolecules with unique three-dimensioal configuration. The specificity of an enzyme results from its shape, which is a consequence of its amino acid sequence. The specificity of an enzyme is attributed to a compatible fit between the shape of its active site and the shape of the substrate.
What is free energy? What is its symbol?
Free energy is the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell. Free energy is symbolized by the letter G, after Professor Willard Gibbs
Although it is not an enzyme, hemoglobin shows cooperativity in binding O2. Explain how hemoglobin works at the gills of a fish.
Hemoglobin is made up of four subunits, each of which has an oxygen-binding site. The binding of an oxygen molecule to one binding site increases the affinity for oxygen of the remaining binding sites. Thus, where oxygen is at high levels, such as in the lungs or gills, hemoglobin's affinity for oxygen increases as more binding sites are filled.
By what process will the ATP bond break?
Hydrolysis
If you could not regenerate ATP by phosphorylating ADP, how much ATP would you need to consume each day?
If ATP could not be regenerated by the phosphorylation of ADP, humans would use up nearly their body weight in ATP each day
What is energy coupling?
In cellular metabolism, the use of energy released from an exergonic reaction to drive an endergonic reaction.
Enzymes lower Ea by (1)
In reactions involving two or more reactants, the active site provides a template on which the substrates can come together in the proper orientation for a reaction to occur between them.
How is ∆G affected by the enzyme?
It cannot make an endergonic reaction exergonic.
How is allosteric regulation somewhat like noncompetitive inhibition? How might it be different?
It is like noncompetitive inhibition in that it may inhibit enzyme activity, but different in that it may also stimulate enzyme activity.
Contrast kinetic energy with potential energy
Kinetic energy is associated with the relative motion of objects, whereas potential energy refers to an object not presently moving; it is the energy that matter possesses because of its location or structure.
Name a human enzyme that functions well in pH 2. Where is it found?
Pepsin, found in the human stomach
Is photosynthesis endergonic or exergonic? What is the energy source that drives it?
Photosynthesis is an endergonic reaction. Plants get the required energy—686 kcal to make a mole of glucose—from the environment by capturing light and converting its energy into chemical energy.
Enzymes lower Ea by (3)
The active site may also provide a microenvironment that is more conducive to a particular type of reaction than the solution itself would be without the enzyme.
What is activation energy (EA)?
The amount of energy that reactants must absorb before a chemical reaction will start; also called free energy of activation.
Explain the difference between an allosteric activator and an allosteric inhibitor.
The binding of an activator to a regulatory site stabilizes the shape that has functional active sites, whereas the binding of an inhibitor stabilizes the inactive form of the enzyme
initial concentration of substrate affect on the rate of enzyme action
The more substrate molecules that are available, the more frequently they access the active sites of the enzyme molecules.
Recall that enzymes are globular proteins. Why can extremes of pH or very high temperatures affect enzyme activity?
Three-dimensional structures of proteins are sensitive to their environment. As a consequence, each enzyme works better under some conditions than other conditions, because these optimal conditions favor the most active shape for their enzyme molecule
temperature affect on the rate of enzyme action
Up to a point, the rate of an enzymatic reaction increases with increasing temperature, partly because substrates collide with active sites more frequently when molecules move rapidly. Above that temperature, however, the speed of the enzymatic reaction drops sharply.
Which type of energy does water behind a dam have? A mole of glucose?
Water behind a dam has potential energy. A mole of glucose also has potential energy, though more specifically, glucose has chemical energy, a term used by biologists to refer to the potential energy available for release in a chemical reaction.
pH affect on the rate of enzyme action
With some exceptions, the optimal pH values for most enzymes fall in the range of pH 6-8
Which reactions are considered "uphill"?
anabolic
Which reactions build up larger molecules
anabolic
Which reactions consume energy?
anabolic
Which reactions require enzymes to catalyze reactions?
anabolic,catabolic
What type of reaction is cellular respiration?
catabolic
What type of reaction is photosynthesis?
catabolic
Which reactions break down molecules?
catabolic
Which reactions release energy?
catabolic
Mechanical Work
the pumping of substances across membranes against the direction of spontaneous movement; possible examples include the sodium-potassium pump and proton pump
Chemical Work
the pushing of endergonic reactions that would not occur spontaneously, such as the synthesis of polymers from monomers
if energy is released, ∆G must be what?
∆G must be negative.
