Chapter 8

True or false: Catabolic and anabolic pathways are the "downhill" and "uphill" avenues of the metabolic landscape.

catabolic pathways are the "downhill" and anabolic pathways are the "uphill". True!

Kinetic Energy

energy can be associated with relative motion of objects

endergonic

energy inward

Exergonic

energy outward

Coenzyme

if the cofactor is an ORGANIC molecule, it is referred to as a coenzyme

When a the G is less than zero is means..

it is exergonic and therefore occurs spontaneously

Allosteric Regulation

the term used to describe 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 may result in inhibition or stimulation of an enzyme's activity

Metabolism

the totality of an organism's chemical reactions . Metabolism is an emerging property of life that arises from orderly interactions between molecules.

True or False: If the temp is uniform, then the heat generated by chemical reactions will warm a body of matter, making a room full of people feel extremely stuffy!

true!

True or false: a cell that has reached metabolic equilibrium is dead

true! - the overall sequence of reactions is kept going by the huge free-energy difference between glucose and oxygen at the top of the energy "hill" and carbon dioxide and water at the "downhill" end

True or false: When the molecules have absorbed enough energy for the bonds to break, the reactants are in an unstable condition known as the transition state

true! Once the molecules have absorbed enough energy, they are in the transition state

True or false: the overall decrease in activation energy is repaid with dividends, as the formation of new bonds releases more energy than the investment of break old bonds

true! The decreases in activation energy is repaid with interest because the amount of energy created by breaking old bonds is only a fraction of the energy released by forming new ones

True or false: an enzyme uses a variety of mechanisms that lower activation energy and speed up a reaction

true! there are 4 different ways

true or false: a catabolic pathway in cell releases free energy in a series of reactions

true: a catabolic pathway in a cell releases free energy in a series of reactions

How can calculating the G be useful?

we can see if it is energetically favorable and will occur without an input of energy

When does free energy increase?

when a process is somehow pushed away from equilibrium

How can the change is free energy, or G, be calculated?

ΔG change in free energy=ΔH change in enthalpy−TΔS(temperature) change in entropy

Another way to think of (triangle)G is that it represent the free energy of a final state and free energy of the initial state. Thus, G can negative only when the process involves a loss of free energy during the change from final to initial state - think of free energy as a measure of the systems instability (its tendency to change to a more stable state) - unstable systems (higher G) - stable systems (lower G)

(triangle)G= G final state- G initial state (the system in its final state has less energy and therefore more likely to be stable)

ATP (adenosine triphosphate)

- ATP contains sugar ribose with the nitrogenous base adenine and a chain of three phosphate groups bonded to it - ATP is one of the nucleotide triphosphate used to make RNA - the bonds between the phosphates groups of ATP can be broken by hydrolysis - when the terminal bond is broken down by the addition of water, a molecule of inorganic phosphate leaves ATP making it ADP - This reaction is exergonic - because ATP hydrolysis releases energy, the phosphate groups of ATP are sometimes referred to as high energy bonds - however this term is misleading (pg. 149) - ATP releases a bunch of energy bc their phosphate groups are negatively charged (these like charges are crowded together and their mutual repulsion contributes to the instability of the region)

The Regeneration of ATP

- ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP - the free energy required to phosphrylate ADP comes from exergonic breakdown reactions (catabolism) - catabolic (exergonic) pathways, especially in cellular respiration, provides the energy for the endergonic process of making ATP

ATP powers cellular work by coupling exergonic interactions to outward interactions

- Chemical Work: the pushing of endergonic reactions that would not occur spontaneously, such as the synthesis of polymers from monomers - Transport Work: the pumping of substances across the membrane against the direction of spontaneous movement - Mechanical Works: such as the beating of cilia, the contraction of muscle cells, and the movement of chromsomes for cellular reproduction

Willard Gibbs

- defined a very useful function called the Gibbs free energy of a system (without considering its surroundings) Symbolize as the letter G

Enzyme Facts

- most enzymes end in "ase" - most enzymes are proteins - the specificity of an enzyme results from its shape which is a consequence of the amino acid sequence

Allosteric Activation and Inhibition

- most enzymes known to be allosterically regulated are constructed from two or more subunits, each composed of a polypeptide chain with its own activation site - the entire complex oscillates between 2 different shapes, one catalytically active and the other inactive

Cofactors

- most enzymes require nonprotein helpers for catalytic activity - the adjuncts, called cofactors, may be bound tightly to the enzyme as permanent residents, or they may binds loosely and reversibly along with the substrate - the cofactors of SOME enzymes are inorganic, such as metal, iron, and copper

How the Hydrolysis of ATP Performs work

- shivering uses ATP hydrolysis during muscle contraction to warm the body. In most cases, the generation of heat alone would be an inefficient use of valuable energy resource - instead, a cell's proteins harness the energy released by ATP hydrolysis to perform the three types of cellular work: chemical, transport, and mechanical - With HELP of specific enzymes, the cell is able to use the energy released by ATP hydrolysis to drive chemical reactions, that by themselves, are endergonic. - HOWEVER, if the (triangle) G or an endergonic reaction is less than the amount of energy released by the ATP hydrolysis, then the two reactions can be coupled so that, overall, the coupled reactions are exergonic

Effect of Local Conditions on Enzyme Activity

- the activity of an enzyme, or how efficiently an enzyme functions, is affected by general environmental factors (such as temperature and PH) - it can also be impacted by chemicals that specifically influence that enzyme - like proteins, enzymes have optimal conditions - up to a point, the rate of an enzymatic reaction increases with increasing temperature, too high can denature the enzyme. most human enzymes are 30-40 C - optimal pH for enzymes are 6-8 but there are exceptions.. like pepsin, a digestive enzyme in the human stomach, has a pH of 2

Activator and 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 - the products of ATP hydrolysis (ADP plus P) balance the flow of traffic between anabolic and catabolic pathways - If ATP lags behind its use, ADP accumulates and activates enzymes that speed up catabolism, producing more ATP. - If supply of the ATP molecules exceeds demands, then catabolism slows down as ATP molecules accumulate and bind to the same enzymes, inhibiting the. pp. 158

ATP Cycle

1. ATP synthesis from ADP plus Pi requires energy - energy from Catabolism (exergonic, energy releasing process) synthesizes ATP from ADP plus Pi 2. ATP hydrolysis to ADP plus Pi yields energy - ATP then gives energy for cellular work (endergonic, energy consuming process) which then creates the ATP - The ATP Cycle: Energy released by breakdown reactions (catabolism) is used to phosphorylate ADP, regenerating ATP.

Enzyme

A macromolecule that acts as a catalyst

Entropy

A measure of disorder, or randomness. The more randomly arranged a collection of matter is, the greater its entropy

Mechanical Work:

ATP bonds noncovalently to motor proteins and then is hydrolyzed

Transport Work

ATP phosphorylates transport proteins

T

Absolute temperature in Kelvin or K Units

Potential Energy

An object not moving may still possess energy. Energy that is not kinetic is called potential energy.

What happens when the product exists the active site?

As soon as the product exists the active site, another substrate molecule enters. At this substrate concentration, the enzyme is said to be saturated and the rate of the reaction is determined by the speed at which the active site converts substrate to product.

Enzyme Inhibitors

Certain chemicals specifically inhibits the actions of specific enzymes. - sometimes the inhibitor attaches to the enzyme by covalent bonds, in which case the inhibition is usually irreversible - other times, enzyme inhibitors bind to the enzyme by weak interactions, and when this occurs the inhibition is reversible

Chemical Energy

Chemical Energy is a termed used by biologists to refer to the potential energy available for release in a chemical reaction. (ex. glucose is high in potential energy because catabolic pathways will break it down and release energy)

Endergonic Reaction

Endergonic is one that absorbs free energy from its surroundings - Gi s greater than zero - energy required, non-spontaneous - because this type of reaction essential stores free energy in molecules, G is positive - if a chemical process is exergonic (downhill), releasing in one direction, then the reverse reaction must be endergonic (uphill), using energy

Energy Coupling

Energy coupling is the use of a exergonic process to drive an endergonic one - ATP is responsible for managing most energy coupling in cells

How ATP drive chemical work:

Energy coupling using ATP hydrolysis

Enthalpy

Enthalpy refers to total energy in biological systems

What is it called when a system reaches its maximum stability?

Equilibrium

Second Law of Thermodynamics

Every energy transfer or transformation increases the entropy of the universe

Free energy

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

Spontaneous Process

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

If a process has a negative G, then what does that say about the process?

If the process has a negative G, then the process in spontaneous

Cooperativity

In another kind of allosteric activation, a substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all subunits, thereby increasing catalytic activity at other active sites. Called Cooperativity, this mechanism amplifies the response of enzymes to substrates: one substrate molecule primes an enzyme to act on additional substrate molecules more readily. - this is considered allosteric regulation because binding of the substrate to one active site affect catalysis in another active site

Anabolic Pathways

In contrast, anabolic pathways consume energy to build complex molecules from simpler ones; they are sometimes called biosynthetic pathways. (ex. synthesis of amino acids from simpler molecules and the synthesis of proteins from amino acids)

Noncompetitive Inhibitors

In contrast, noncompetitive inhibitors do not directly compete with the substrate to bind the enzyme at the active site. Instead, they impede enzymatic reactions by binding to another part of the enzyme. - this interaction causes the enzyme molecule to change its shape in such a way that the active site becomes less effective at catalyzing the conversion of substrate to product. - reversible - non covalent - a form of regulating

Feedback Inhibition

In feedback inhibition, a metabolic pathway is halted by the inhibitory binding its end product to an enzyme that acts early on in its pathway

Phosphorylation

In order to couple an endergonic reaction into an overall exergonic reaction, you usually will have to involve phosphorylation - Phosphorylation is the transfer of a phosphate group from ATP to some other molecule, such as a reactant - the recipient molecule with the phosphate group covalently bonded to it is then called the phosphorylated intermediate

Phosphorylated Intermediate

In order to couple an endergonic reaction into an overall exergonic reaction, you usually will have to involve phosphorylation - Phosphorylation is the transfer of a phosphate group from ATP to some other molecule, such as a reactant - the recipient molecule with the phosphate group covalently bonded to it is then called the phosphorylated intermediate - this is the KEY to coupling exergonic and endergonic interactions

The cell has the ability to tightly regulate metabolic pathways by controlling when and where its various enzymes are active. How does it regulate this?

It regulates this by switching on and off the genes that encode specific enzymes or by regulating the activity of enzymes once they are made

Thermal Energy

Kinetic energy associated with random movement of atoms or molecules

Active site

Only a restricted region of the enzyme molecule actually binds to the substrate. - this region is called the active site and it is typically a pocket or groove on the surface of the enzyme where the catalysis occurs - as the substrate enters the active site, the enzyme changes shape due to its interactions between the substrate's chemical groups and chemical groups on the side chains pf the amino acids that form the site

Competitive Inhibitors

Some reversible inhibitors resemble the normal substrate molecule and compete for admission into the active site. These mimics, called competitive inhibitors, reduce the productivity of enzymes by blocking substrates from entering the active sites.

Spontaneous

Spontaneous simply means energetically favorable

S

Symbolize a change in the system's entropy

H

Symbolizes a systems change in a system's enthalpy (total energy)

True or False: ATP Hydrolysis leads to a protein's change in shape and often its ability to bind another Molecule

TRUE! ATP hydrolysis does cause protein's to change their shape - a cycle occurs in which ATP is bound noncovalently to the motor protein - next, ATP is hydrolyzed releasing adp and Pi - Another ATP molecule can then bind the cytoskeleton, resulting in movement of protein along the cytoskeleton track

First Law of Thermodynamics (principle of conservation energy)

The energy of the universe is constant: Energy can be transferred and transformed but it cannot be created or destroyed. The first law is known as the principle of conservation energy.

Enzyme-Substrate Complex

The enzyme binds to its substrate (or substrates, when there are two or more reactants) forming an enzyme-substrate complex. - while an enzyme and substrate are joined, the catalytic action of the enzyme converts the substrate to the product (or products) of the reaction.

Substrate

The reactant that an enzyme works on is referred to as the enzyme's substrate

Thermodynamics

The study of the energy transformations that occur in a collection of matter is called thermodynamics - they refer to the rest of the universe, everything outside of the system, as surroundings - an isolated system, such as that approximated by liquid in a thermos bottle, is unable to exchange their energy or matter with its surroundings outsides the thermos. -In an open system, energy and matter can be transferred between the systems and its surroundings. Organisms are open systems.

Heat

Thermal Energy in transfer from one object to another is called heat

Induced fit

This shape change makes the active sit fit even more snugly around the substrate. This process is like a clasping handshake, with binding between an enzyme and substrate becoming tighter after the initial contact. This is called the induced fit, which brings chemical groups of the active site into positions that enhance their ability to catalyze a chemical reaction - it is held in the active site by weak interaction such as hydrogen and ionic bonds

True or false: Biochemical energy, carried out in the context of cellular structures, enables cell to release chemical energy from food molecules and use the energy to power to life processes.

True!

True or False: A process is spontaneous and can perform work only when it is moving toward equilibrium

True! A process is spontaneous and can perform work only when it is moving toward equilibrium

True or false: activation energy can be thought of as the amount of energy needed to push the reactants to the top of an energy barrier

True! Activation energy can be thought of as the amount of energy required to push the reactant to the top of the energy barrier - activation energy is often supplied by heat in the form of thermal energy that the reactant must absorb from its surroundings

True of false: every spontaneous process decreases the systems free energy and and processes that have a positive or ZERO G are never spontaneous

True! Every spontaneous processes decreases the systems free energy and processes that have a positive or ZERO G are never spontaneous

True of false: In order the G to be negative H must also be OR have TS must be positive OR both

True! In order for G to be negative H must also be because the system gives up enthalpy and H decreases OR have TS be positive meaning the system gives up order and S increases OR both: when H and S are tallied, G has a negative value for all spontaneous processes

True or False: A system can put energy to work only when there is a temperature difference that results in thermal energy flowing as heat from a warmer location to a cooler one.

True! Only when there is temperature difference can thermal energy flow

True or false: the more substrate molecules that are available, the more frequently they access the active sites of the enzyme molecules

True! The more substrate molecules that are available, the more frequently they access the active sites of the enzyme molecule

True or false: an enzyme catalyzes a reaction by lowering the Ea barrier

True! an enzyme catalyzes a reaction by lowering the Ea barrier

Catabolic Pathways

When metabolic pathways release energy by breaking down complex molecules to simpler compounds. The degradative processes are called breakdown pathways. Which is a major pathway of catabolism is cellular respiration, in which the sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water. Energy that was stored in the organic molecules becomes available to do work of the cell, such as ciliary beating or membrane transport.

Does the activation energy provide a barrier that determines the rate of reaction?

Yes, the activation energy provides a barrier that determines the rate of reaction - if Ea is too high, reaction cannot really be pursued, however, enzymes can lower the barrier!

Catalyst

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

Metabolic Pathway

a metabolic pathway begins with a specific molecule, which is then altered in a series of defined steps, resulting in a certain product.

exergonic reaction

proceeds with a net release of free energy (G is negative) - G is less than zero - energy released, spontaneous - because a lot of energy is released the total energy goes down to a more stable state - for cellular respiration: the products are, in a sense, the spent exhaust of a process that tapped the free energy stored in bonds (potential energy that can be released when news bonds are formed after original bonds break) of the sugar molecules

Most metabolic reactions are

reversible! - depending on which direction has a negative G, an enzyme can either catalyze or reverse a reaction

Energy

the capacity to cause change

Activation Energy

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 free energy of activation or activation energy abbreviated Ea

Bioenergetics

the study of how energy flows through living organisms