BISC ch.8

What accounts for this molecular recognition between a substrate and enzyme?

most enzymes are proteins, and proteins are macromolecules with unique three-dimensional configurations. The specificity of an enzyme results from its shape, which is a consequence of its amino acid sequence.

A process is spontaneous and can perform work only when it is _________________________.

moving toward equilibrium

A process that, on its own, leads to a decrease in entropy is said to be

non spontaneous

_____________________ do not directly compete with the substrate to bind to the enzyme at the active site. Instead, they impede enzymatic reactions by binding to another part of the enzyme.

noncompetitive inhibitors

endergonic reactions are spontaneous or not spontaneous?

nonspontaneous

positive or zero ∆G means that the system is

not spontaneous

Organisms are examples of what type of system?

open systems

Unstable systems (higher G) tend to change in such a way that they become more stable (lower G) or even less stable?

more stabl example: a glucose molecule is less stable (more likely to break down) than the simpler molecules into which it can be split

thermal energy

kinetic energy associated with the random movement of atoms or molecules

what are catabolic pathways?

metabolic pathways that release energy by breaking down complex molecules to simpler compounds

true or false: all spontaneous processes occur quickly

False; Some spontaneous processes, such as an explosion, may be virtually instantaneous, while others, such as the rusting of an old car over time, are much slower.

what letter denotes Gibbs free energy?

G

define what happens in an isolated hydroelectric system.

Water flowing downhill turns a turbine that drives a generator providing electricity to a lightbulb, but only until the system reaches equilibrium.

define what happens in an open hydroelectric system.

Water flowing through a turbine keeps driving the generator because intake and outflow of water keep the system from reaching equilibrium.

a chemical agent that speeds up a reaction without being consumed by the reaction is called what ?

a catalyst

cofactors may be bound tightly to the enzyme as _______________ or ________________

(1) permanent residents or (2) they may bind loosely and reversibly along with the substrate

ATP hydrolysis causes changes in the shapes and binding affinities of proteins. This can occur in two ways- directly and indirectly. what are they?

(a) directly, by phosphorylation, as shown for a membrane protein carrying out active transport of a solute (b) indirectly, via noncovalent binding of ATP and its hydrolytic products, as is the case for motor proteins that move vesicles (and other organelles) along cytoskeletal "tracks" in the cell

Most enzyme names end in

-ase

cellular respiration, in which the sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water, is a type of anabolic or catabolic pathways?

. catabolic pathway

a single enzyme molecule typically acts on about _________________ substrate molecules per second, and some enzymes are even faster

1,000 substrate molecules

what are the 2 types of Metabolic pathways ?

1. Anabolic pathways (take small and make big) 2. Catabolic pathway (take big and make small)

what are the 2 major complex cellular molecules that are rich in free energy and have the potential to decompose spontaneously

1. Proteins 2. DNA the laws of thermodynamics favor their breakdown. These molecules only persist because at temperatures typical for cells, few molecules can make it over the hump of activation energy

A cell does three main kinds of work:

1. chemical 2. transport 3. mechanical

Heat can increase the rate of a reaction by allowing reactants to attain the transition state more often, but this would not work well in biological systems. What are the 2 reasons why?

1. high temperature denatures proteins and kills cells. 2. heat would speed up all reactions, not just those that are needed.

What makes up an ATP?

1. sugar ribose 2. nitrogenous base adenine 3. a chain of three phosphate groups (the triphosphate group) bonded to the nitrogenous base adenine

what are the 2 equations for ∆G

1. ∆G = ∆H - T∆S 2. ∆G = Gfinal state - Ginitial state

Most human enzymes have optimal temperatures of about _________

35-40°C (close to human body temperature).

the typical enzyme works best in environments that have a pH of

6-8

The thermophilic bacteria that live in hot springs contain enzymes with optimal temperatures of _________________

70°C or higher

When the terminal phosphate bond is broken by addition of a water molecule, a molecule of inorganic phosphate leaves the ATP, and the ATP turns into

ADP

____ is responsible for mediating most energy coupling in cells, and in most cases it acts as the immediate source of energy that powers cellular work.

ATP

what is one of the nucleoside triphosphates used to make RNA

ATP

___________________________ describes any case in which a protein's function at one site is affected by the binding of a regulatory molecule to a separate site.

Allosteric regulation

a system that is unable to exchange either energy or matter with its surroundings is called .

An isolated system

liquid in a thermos bottle is an example of what type of system?

An isolated system

synthesis of an amino acid from simpler molecules and the synthesis of a protein from amino acids is an example of anabolic or catabolic pathways?

Anabolic pathways

why does the enzyme undergo a shape change when the substrate attaches to its active site?

As the substrate enters the active site, the enzyme changes shape slightly due to interactions between the substrate's chemical groups and chemical groups on the side chains of the amino acids that form the active site. This shape change makes the active site fit even more snugly around the substrate

why is it that a cell that has reached metabolic equilibrium is dead

Because systems at equilibrium are at a minimum of G and can do no work; so the fact that metabolism as a whole is never at equilibrium is one of the defining features of life.

is ∆G for an exergonic reaction positive or negative and is it increasing or decreasing?

Because the chemical mixture loses free energy (G decreases), ∆G is negative for an exergonic reaction.

is ∆G for an endergonic reactions positive or negative and is it increasing or decreasing?

Because this kind of reaction stores free energy in molecules (G increases), ∆G is positive.

define what happens in a multistep open hydroelectric system.

Cellular respiration is analogous to this system: Glucose is broken down in a series of exergonic reactions that power the work of the cell. The product of each reaction is used as the reactant for the next, so no reaction reaches equilibrium; like an open system there is a constant flow in and out.

the potential energy available for release in a chemical reaction is called?

Chemical energy

kinetic energy

Energy can be associated with the relative motion of objects

allosteric regulation may result in 2 things what are they?

It may result in either inhibition or stimulation of an enzyme's activity

when a process is non spontaneous it means

It will happen only if energy is supplied.

what are Anabolic pathways

Metabolic pathways that consume energy to build complicated molecules from simpler ones.

what exactly does the Activation energy do?

The absorption of thermal energy accelerates the reactant molecules, so they collide more often and more forcefully. It also agitates the atoms within the molecules, making the breakage of bonds more likely. When the molecules have absorbed enough energy for the bonds to break, the reactants are in an unstable condition known as the transition state.

what is the phosphorylated intermediate

The recipient molecule with the phosphate group covalently bonded to it

how do noncompetitive inhibitors work?

There interaction causes the enzyme molecule to change its shape in such a way that the active site becomes much less effective at catalyzing the conversion of substrate to product.

when the reactants are in the transition state they are...

They are activated, and their bonds can be broken

what decreases the chances of the competitive inhibitor?

This kind of inhibition can be overcome by increasing the concentration of substrate so that as active sites become available, more substrate molecules than inhibitor molecules are around to gain entry to the sites.

Only a restricted region of the enzyme molecule actually binds to the substrate. This region is called the __________

active site

the hydrolysis of ATP provides energy to what?

all cellular work so it is exergonic

why does this hydrolysis of ATP into ADP release so much energy?

all three phosphate groups are negatively charged. These like charges are crowded together, and their mutual repulsion contributes to the instability of this region of the ATP molecule. The triphosphate tail of ATP is the chemical equivalent of a compressed spring.

regulatory site is sometimes called an _____________________

allosteric site

a system in which energy and matter can be transferred between the system and its surroundings is called

an open system

biosynthetic pathways is also known as?

anabolic pathways

A metabolic pathway

begins with a specific molecule (can have more than one starting molecule or product), which is then altered in a series of defined steps, resulting in a certain product. Each step of the pathway is catalyzed by a specific enzyme:

Sometimes an inhibitor attaches to the enzyme by ______________________, in which case the inhibition is usually irreversible

by covalent bonds

a process by which a catalyst (for example, an enzyme) selectively speeds up a reaction without itself being consumed is called

catalysis

instead of using heat to increase the rate of a reaction by allowing reactants to attain the transition state more often, biological systems use:

catalysis

An enzyme is a macromolecule that acts as a _____________

catalyst

If the cofactor is an organic molecule, it is referred to, more specifically, as a

coenzyme

vitamins are considered cofactors or enzymes?

coenzyme

Many enzymes require nonprotein helpers for catalytic activity, often for chemical processes like electron trans- fers that cannot easily be carried out by the amino acids in proteins. These are called

cofactors

Some reversible inhibitors resemble the normal substrate molecule and compete for admission into the active site ... what are these called?

competitive inhibitors

reduce the productivity of enzymes by blocking substrates from entering active sites.

competitive inhibitors

t or f: The subunits of an allosteric enzyme fit together in such a way that a shape change in one subunit is not transmitted to all others.

false: The subunits of an allosteric enzyme fit together in such a way that a shape change in one subunit is transmitted to all others. Through this interaction of subunits, a single activator or inhibitor molecule that binds to

"energy inward"

endergonic ; An endergonic reaction is one that absorbs free energy from its surroundings

when a process is spontaneous it is energetically_________________

energetically favorable

Scientists use a quantity called _____________ as a measure of molecular disorder, or randomness.

entropy

the only way to increase the rate of product formation is to add more substrate, enzyme, or both?

enzyme

Enzyme +Substrate(s) L------> enzyme+ substrate comples--->

enzyme + product (s)

The enzyme binds to its substrate (or substrates, when there are two or more reactants), forming an

enzyme-substrate complex

how do enzymes, unlike heat, avoid from speeding up all reactions, not just those that are needed.

enzymes are very specific for the reactions they catalyze, so they determine which chemical processes will be going on in the cell at any given time.

a term that describes a state of maximum stability is

equilibrium

"surroundings" is used to denote

everything outside the system

"energy outward"

exergoni; net release of free energy

when ATP is converted into ADP it is known as exergonic or endergonic?

exergonic A T P + H 2 O -------> A D P + P i ∆G = -7.3 kcal/mol (-30.5 kJ/mol)

exergonic reactions are those that occur spontaneously or not spontaneously?

exergonic reactions are those that occur spontaneously

Toxins and poisons are often reversible or irreversible enzyme inhibitors

irreversible

Thermal energy

kinetic energy associated with the random movement of atoms or molecules

True or false: Amino acids in the active site do not participate in the chemical reaction.

false; Amino acids in the active site directly participate in the chemical reaction. Sometimes this process even involves brief covalent bonding between the substrate and the side chain of an amino acid of the enzyme.

true or false: An enzyme catalyzes a reaction by making the EA barrier higher

false; An enzyme catalyzes a reaction by lowering the EA barrier

true or false: As a reaction proceeds toward equilibrium, the free energy of the mixture of reactants and products increases.

false; As a reaction proceeds toward equilibrium, the free energy of the mixture of reactants and products decreases.

true or false: For a system at equilibrium, G is at its hightest possible value in that system.

false; For a system at equilibrium, G is at its lowest possible value in that system.

true or false: a system at equilibrium can spontaneously change, it can do work.

false; a system at equilibrium cannot spontaneously change, it can do no work.

true or false: an enzyme can change the ∆G for a reaction

false; an enzyme cannot change the ∆G for a reaction

true or false: an enzyme can make an endergonic reaction exergonic

false; an enzyme cannot make an endergonic reaction exergonic

true or false: every spontaneous process increases the system's free energy

false; every spontaneous process decreases the system's free energy

true or false: the regeneration of ATP is necessarily exergonic

false; the regeneration of ATP is necessarily endergonic

true or false: ∆G can be negative only when the process involves a gain of free energy during the change from initial state to final state.

false; ∆G can be negative only when the process involves a loss of free energy during the change from initial state to final state.

which law of thermodynamics state: energy of the universe is constant; Energy can be transferred and transformed, but it cannot be created or destroyed

first law of thermodynamics

when sucrose is broken down via hydrolysis the H+ from the H20 attaches to the fructose or glucose?

fructose

The binding of an activator to a regulatory site stabilizes the shape that has ______________ active sites, whereas the binding of an inhibitor stabilizes the _____________ form of the enzyme

functional ; inactive

when sucrose is broken down via hydrolysis the OH- from the H20 attaches to the fructose or glucose?

glucose

The more randomly arranged a collection of matter is, the __________________ (worse/greater) its entropy.

greater

what is transport work?

he pumping of substances across mem- branes against the direction of spontaneous movement

when thermal energy is in transfer from one object to another it is called

heat

Activation energy is often supplied by ________________ in the form of ___________________ that the reactant molecules absorb from the surroundings.

heat ; thermal energy

In most enzymatic reactions, the substrate is held in the active site by so-called weak interactions, such as _____________________ & ________________________

hydrogen bonds and ionic bonds

The bonds between the phosphate groups of ATP can be broken by

hydrolysis

this process is known for bringing chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction.

induced fit

The tightening of the binding of an enzyme and its substrate after initial contact is called

induced fit.

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.

The key to coupling exergonic and endergonic reactions is the formation of this

phosphorylated intermediate

Energy that is not kinetic is called__________ it is energy that matter possesses because of its location or structure.

potential energy

compared to the unphosphorylated molecule the phosphorylated intermediate is

reactive (less stable, with more free energy)

These regulatory molecules change an enzyme's shape and the functioning of its active site by binding to a site elsewhere on the molecule, via noncovalent interactions.and this is known as __________________

regulatory enzymes

does the breaking of bonds release energy or requires energy?

requires energy

which law of thermodynamics state: Every energy transfer or transformation increases the entropy of the universe

second law of thermodynamics:

negative ∆G means that the system is

spontaneous

If a given process, by itself, leads to an increase in entropy, that process can proceed without requiring an input of energy. Such a process is called a

spontaneous process

The reactant an enzyme acts on is referred to as the enzyme's

substrate

Sucrase + Sucrose+H20 ------> Sucrase + Sucrose + H20 complex ------->

sucrase+Glucose + Fructose

what two things can affect how an enzyme works?

temperature and pH

a pocket or groove on the surface of the enzyme where catalysis occurs

the active site

metabolism

the chemical processes that occur within a living organism in order to maintain life. The totality of an organism's chemical reactions.

what is mechanical work?

the contraction of muscle cells, and the movement of chromosomes during cellular reproduction

on the activation graph the uphill portion of the graph represents ...

the free energy content of the reactant molecules is increasing

The initial investment of energy for starting a reaction— the energy required to contort the reactant molecules so the bonds can break is known as the ____________ ; the amount of energy needed to push the reactants to the top of an energy barrier, or uphill, so that the "downhill" part of the reaction can begin

the free energy of activation, or activation energy

"system" is used to denote

the matter under study

the first law of thermodynamics is also known as

the principle of conservation of energy

why is it that a system can never reach equilibrium in a multistep open hydroelectric system?

the product of a reaction does not accumulate but instead becomes a reactant in the next step

what is chemical work?

the pushing of endergonic reactions that would not occur spontaneously, such as the synthesis of polymers from monomers

the magnitude of ∆G is

the quantity of energy required to drive the reaction.

what is bioenergetics?

the study of how energy flows through living organisms

phosphorylation is

the transfer of a phosphate group from ATP to some other molecule, such as the reactant.

on the activation graph the peak represents ...

the transition state

define energy coupling

the use of an exergonic process to drive an endergonic one

The study of the energy transformations that occur in a collection of matter is called

thermodynamics

True or false: energy flows into most ecosystems in the form of light and exits in the form of heat

true

true or false: An enzyme is not a stiff structure locked into a given shape. In fact, enzymes (and other proteins) seem to "dance" between subtly different shapes in a dynamic equilibrium, with slight differences in free energy for each "pose."

true

true or false: Any change from the equilibrium position will have a positive ∆G and will not be spontaneous.

true

true or false: Free energy increases when a reaction is somehow pushed away from equilibrium

true

true or false: Most enzymes known to be allosterically regulated are constructed from two or more subunits, each composed of a polypeptide chain with its own active site. The entire complex oscillates between two different shapes, one catalytically active and the other inactive

true

true or false: The reactants must absorb enough energy to reach the top of the activation energy barrier before the reaction can occur.

true

true or false: a non spontaneous process also leads to an increase in the entropy of the universe as a whole

true

true or false: when a system has less free energy, the system in its final state is less likely to change and is therefore more stable than it was previously.

true

true or false:Energy released by breakdown reactions (catabolism) in the cell is used to phosphorylate ADP, regenerating ATP

true

true or false:cofactors, may be bound tightly to the enzyme as permanent residents, or they may bind loosely and reversibly along with the substrate.

true

true or false:unstable systems are rich in free energy, G. They have a tendency to change spontaneously to a more stable state

true

true or false: the rate of an enzymatic reaction increases with increasing temperature. Above a certain temperature, however, the speed of the enzymatic reaction drops sharply. Explain why it is so.

true: (As temp inc. so does enzymatic rxn) partly because substrates collide with active sites more frequently when the molecules move rapidly. (certain temp. cause the enzyme to stop working)The thermal agitation of the enzyme molecule disrupts the hydrogen bonds, ionic bonds, and other weak interactions that stabilize the active shape of the enzyme, and the protein molecule eventually denatures.

true or false: during every energy transfer or transformation, some energy becomes unavailable to do work

true; this is because Every energy transfer or transformation increases the disorder (entropy) of the universe

trypsin, a digestive enzyme residing in the human intestine works best at very low or very high pH

very high

pepsin, a digestive enzyme in the human stomach, works best at a very low or very high pH

very low

Many enzyme inhibitors bind to the enzyme by ______________ , and when this occurs the inhibition is reversible.

weak interactions

an activating or inhibiting regulatory molecule binds to a regulatory site (sometimes called an allosteric site), often located ???

where subunits join.

what can we use to predict whether the process will be spontaneous (that is, whether it is energetically favorable and will occur without an input of energy) or not?

∆G

what is the ∆G for regenerating ATP

∆G = +7.3 kcal/mol in standard conditions and even more for conditions that are not standard

what is the ∆G for converting glucose and O2 molecules into carbon dioxide and water?

∆G = -686 kcal/mol C6H12O6 + 6O2 ----->6CO2 + 6H2O

what is the ∆G for converting ATP to ADP?

∆G = -7.3 kcal/mol

The change in free energy, ∆G, can be calculated for a chemical reaction by applying the following equation:

∆G = ∆H - T∆S ∆H symbolizes the change in the system's enthalpy ∆S is the change in the system's entropy T is the temperature in Kelvin (K) (K = °C + 273)