Biology chapter 8

Catabolic Pathway

degradative process that generates energy as an end product

Anabolic Pathway

energy consuming process that builds more complex molecules from simpler ones

What is energy?

the capacity to do work, and capacity to cause change.

Kinetic Energy

energy associated with movement (includes thermal energy)

Potential energy

stored energy that can potentially be converted to another form of energy and do work

Chemical Energy

may be stored as form of potential in a molecule

Thermodynamics

Study of the energy transformations within a defined system vs. surroundings

First Law of Thermodynamics

Energy can be transferred or transformed but neither created nor destroyed (Conservation of Energy)

Second of Thermodynamics

every energy transfer or transformation increases the disorder of the universe

The stability of matter is greatest

At the lowest energy state

Spontaneous (Gibbs)

the process will run without an outside input of energy (Delta G is negative)

Gibbs free energy of a system

delta G= G (final)-G(initial)

In a spontaneous change

the system becomes more stable, the released free energy can be harnessed to do work

ATP (Adenosine Tri-phosphate)

produced by cellular respiration (breaking down of glucose leads to energy release that drive ATP synthesis which is endergonic)

Hydrolysis of ATP

Exergonic reaction

How does ATP power cellular work

Energy coupling mechanism (the use of an exergonic process to drive an endergonic one) Hydrolysis of ATP releases energy that can drive endergonic reactions (breaking of high energy bond between phosphates in ATP releases energy)

What type of things do cell use energy for?

Mechanical work, Transport work, and chemical work

Catalyst

a chemical agent that speeds up a reaction without being consumed by the reaction

Enzyme

(biological catalysts) speed up metabolic reactions by lowering energy barrier, enzymes are not consumed by the reaction itself, very selective in the reactions that they catalyze, can ONLY lower the activation energy barrier they CANNOT change the delta G for a reaction nor it cannot make an endergonic reaction exergonic. Mostly proteins, each enzyme has an optimal temperature and pH that favor the most active conformation of the protein molecules, many require non-protein helper that binds to the enzyme for catalytic activity

Activation Energy Barrier

chemical reaction involves bond breaking and bond forming. A major factor in determining the rate of a particular reaction

Substrate

the molecule that an enzyme acts on.

Coenzyme

organic such as vitamins

Cofactors

inorganic such as metals

Enzyme inhibitors

molecules taht selectively interfere with the action of specific enzymes

reversible inhibition

inhibitor bound loosely by weaker bonds

Irreversible inhibition

inhibitor bound by covalent bonds (toxins and poisons are often irreversible enzyme inhibitors)

Enzyme Inhibition is necessary to…

regulate proper level of substrates being produced

competitive inhibitor

mimics the substrate competing for the active site

Noncompetitve inhibitor

binds to the enzyme away from the active site altering the conformation of the enzyme so that its active site no longer functions

ALLOSTERIC ENZYMES AND REGULATORS

a complex form of an enzyme, multi subunits (each have an active site but also regulatory site where regulator binds) unstable without regulator binding. Multiple subunits (polypeptides) each subunit has active and regulatory site. Require additional molecules (activator or inhibitor=regulator) both activator or inhibitor can bind. if activator bind it binds to the regulatory site and it locks the enzyme in its active form. Inhibitory binds to enyme it stabalizes the enzyme in inactive form. without regulators it is a flaky enzyme. regulators are reversible and noncompetitive.

Cooperativity

each subunit can bind to a substrate, binding of one subunits activates the remaining and it takes less time for them to bind bcs they cooperate. (hemoglobin- oxygen binding to hemoglobin)

What is the relationship between anabolic and catabolic pathways?

Anbolic pathways synthesize more complex organic molecules using the energy derived from catabolic pathways

What does not represent an enerygy transformation

The coupling of ATP hydrolysis to the production of a proton gradient across a membrane by a proton pump

Organisms are described as thermodynamically open systems

Organisms aquire energy from, and lose energy to, their surroundings.

Consider the growth of a farmer’s crop over a season, what correctly states a limitation imposed by the first or second law of thermodynamics

To obey the first law, crops must represent an open system

What is the relevence of the first law of thermodynamics to biology?

Energy can be freely transformed among different forms as long as the total energy is conserved

Which is the most abundant form of energy in a cell?

chemical energy

Example of the second law of thermodynamics as it applies to biological reactions

The aerobic respiration of one molecule of glucose produces six molecules each of carbon dioxide and water

What is true according the second law of thermodynamics

the decrease in entropy associated with life must be compensated for by increasing entropy in the environment in which life exists

If the entropy of a living organism is decreasing what is occuring simultaneously?

Energy input into the organism must be occuring to drive the decrease in entropy

When one molecule is broken down into 6 component molecules what is true?

delta S is positive

An exergonic reaction is a chemical reaction that…

Releases energy when proceeding in the forward direction

What is an example of an endergonic reaction?

glucose+fructose=sucrose

What determines the sign of delta G for a reaction?

the free energy of the reactants and the free energy of the products

Metabolic pathways in cells are typically far from equilibrium. What process tends to keep these pathways away from equilibrium?

Pathways can be displaced from equilibrium either by adding free energy or by removal of the products of the pathway or by other reactions

What is an example of the cellular work accomplished with the free energy derived from the hydrolysis of ATP, involved in the production of electrochemical gradients?

proton movement against a gradient of protons

In general, the hydrolysis of ATP drives cellular work by…

releasing free energy that can be coupled to other reactions

What describes some aspect of ATP hydrolysis being used to drive the active transport of an ion into the cell against the ion’s concentration gradient?

This is an example of energy coupling

Much of the suitability of ATP as an energy intermediary is related to the instability of the bonds between the phosphate groups. These bonds are unstable because _____.

The negatively charged phosphate groups viforously repel one another and the terminal phosphate group is more stable in waterthan it is in ATP

When 1 mole of ATP is hydrolyzed in a test tube without an enzyme, about twice as much heat is given off as when 1 mole of ATP is hydrolyzed in a cell. What explains these observations?

in the cell, the hydrolysis of ATP is coupled to other endergonic reactions

What best characterizes the role of ATP in cellular metabolism?

The free energy released by ATP hydrolysis may be coupled to an endergonic process via the formation of a phosphorylated intermediate.

The formation of glucose-6-phosphate from glucose is an endergonic reaction and is coupled to what reaction or pathway?

the hydrolysis of ATP

A chemical reaction is designated as exergonic rather than endergonic when _____.

the potential energy of the products is less than the potential energy of the reactants

What is changed by the presence of an enzyme in a reaction?

the activation energy

What do the sign and magnitude of the ΔG of a reaction tell us about the speed of the reaction?

Neither the sign nor the magnitude of ΔG have anything to do with the speed of a reaction.

How do enzymes lower activation energy?

by locally concentrating the reactants

Above a certain substrate concentration, the rate of an enzyme-catalyzed reaction drops as the enzymes become saturated. What would lead to a faster conversion of substrate into product under these saturated conditions?

Either increasing the enzyme concentration or slightly increasing the temperature will increase the rate of product formation.

Enzyme activity is affected by pH because _____.

high or low pH may disrupt hydrogen bonding or ionic interactions and thus change the shape of the active site

Succinylcholine is structurally almost identical to acetylcholine. If succinylcholine is added to a mixture that contains acetylcholine and the enzyme that hydrolyzes acetylcholine (but not succinylcholine), the rate of acetylcholine hydrolysis is decreased. Subsequent addition of more acetylcholine restores the original rate of acetylcholine hydrolysis. What correctly explains this observation?

Succinylcholine must be a competitive inhibitor with acetylcholine.

The process of stabilizing the structure of an enzyme in its active form by the binding of a molecule is an example of _____.

allosteric regulation

The binding of an allosteric inhibitor to an enzyme causes the rate of product formation by the enzyme to decrease. Why does this decrease occur?

The allosteric inhibitor causes a structural change in the enzyme that prevents the substrate from binding at the active site.

Under most conditions, the supply of energy by catabolic pathways is regulated by the demand for energy by anabolic pathways. Considering the role of ATP formation and hydrolysis in energy coupling of anabolic and catabolic pathways, what is most likely to be true?

High levels of ADP act as an allosteric activator of catabolic pathways

Which term most precisely describes the cellular process of breaking down large molecules into smaller ones?

Catabolism

Which of the following is (are) true for anabolic pathways?

They consume energy to build up polymers from monomers.

Which of the following is an example of potential rather than kinetic energy?

a molecule of glucose

Which of the following is true of metabolism in its entirety in all organisms?

Metabolism consists of all the energy transformation reactions in an organism.

Which of the following is true for all exergonic reactions?

The reaction proceeds with a net release of free energy.

Which of the following is most similar in structure to ATP?

an RNA nucleotide

When chemical, transport, or mechanical work is done by an organism, what happens to the heat generated?

It is lost to the environment.

Reactants capable of interacting to form products in a chemical reaction must first overcome a thermodynamic barrier known as the reaction’s

activation energy

During a laboratory experiment, you discover that an enzyme-catalyzed reaction has a G of -20 kcal/mol. If you double the amount of enzyme in the reaction, what will be the G for the new reaction?

-20 kcal/mol

The active site of an enzyme is the region that

is involved in the catalytic reaction of the enzyme.

Zinc, an essential trace element for most organisms, is present in the active site of the enzyme carboxypeptidase. The zinc most likely functions as a

cofactor necessary for enzyme activity.

When you have a severe fever, what grave consequence may occur if the fever is not controlled?

change in the tertiary structure of your enzymes

How does a noncompetitive inhibitor decrease the rate of an enzyme reaction?

by changing the shape of the enzyme’s active site

How might an amino acid change at a site distant from the active site of the enzyme alter the enzyme’s substrate specificity?

by changing the shape of the protein

The mechanism in which the end product of a metabolic pathway inhibits an earlier step in the pathway is most precisely described as

feedback inhibition.

If an enzyme in solution is saturated with substrate, the most effective way to obtain a faster yield of products is to

add more of the enzyme.

How does an enzyme increase the rate of the chemical reaction it catalyzes?

An enzyme reduces the free energy of activation (EA) of the reaction it catalyzes. (An enzyme catalyzes a reaction by lowering EA, enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures.)