Metabolism. Metabolism refers to the cell's capacity to acquire energy and use it to build, store, break apart, and eliminate substances in controlled.

Metabolism

Metabolism refers to the cell's capacity to acquire energy and use it to build, store, break apart, and eliminate substances in controlled ways.

Energy and the Underlying Organization of LifeA. Defining Energy

1. Potential energy is the capacity to make things happen, to do work.; it can also be called chemical energy, measured in kilocalories.2. Kinetic energy is the energy of motion; it includes heat energy.

B. What Can Cells Do With Energy?1. Energy from the sun or from organic substances becomes coupled to thousands of energy-requiring processes in cells.2. Cells use the energy to perform chemical,

mechanical, and electrochemical work.

C. How Much Energy Is Available?1. First law of thermodynamics states that the total amount of energy in the universe is constant; it cannot be created nor destroyed; it can only change form.2. Energy cannot be produced by a cell; it can only be borrowed from someplace else.3. Energy can be of high quality, that is, highly

concentrated and usable; or it can be of low quality, such as heat that is released into the universe.

D. The One-Way Flow of Energy1. Second law of thermodynamics states that the spontaneous direction of energy flow is from high- to low-quality forms.2. Each conversion produces energy (usually heat) that is unavailable for work.3. As systems lose energy they become more

disorganized; the measure of this disorder is called entropy.

4. The world of life (plant and animal) maintains a high degree of organization only because it is being re-supplied with energy from the sun.

Energy Inputs, Outputs, and Cellular Work

A. Cells and Energy Hills1. Endergonic (“energy in”) reactions require energy input resulting in products with more energy than the reactants had; for example: photosynthesis.2. Exergonic (“energy out”) reactions release energy such that the products have less energy than the

reactants had; for example: cellular respiration.

B. ATP Couples Energy Inputs With Outputs1. ATP is composed of adenine, ribose, and three phosphate groups.

a. Energy input links phosphate to ADP to produce ATP (phosphorylation).b. ATP can in turn donate a phosphate group to another molecule, which then becomes primed and energized for specific reactions.

2. ATP's role is like currency in an economy: earning ATP during exergonic reactions and spending it

duringendergonic ones.3. ADP can be recycled to ATP very rapidly in the ATP/ADP cycle.

C. Phosphorylation – transferring of a phosphate group from one molecule to another (this is how ATP is made)

-2 types of phosphorylation result in ATP formation1. substrate level phosphorylation (the phosphate is simply removes from one chemical and placed onto another)

2. Oxidative phosphorylation – Electron Transfers Drive ATP Formation

***OIL – RIG or LEO - GERredox reactions release energy, which is used to form ATP

B. Electron transfer chains are similar to staircases where electrons flow down the steps from the top (most energy) to the bottom (least energy), releasing a small amount at each step.

C. The energy is harnessed to move hydrogen ions, which in turn establish pH and electric gradients necessary for ATP production.

Cells Juggle Substances as Well as EnergyA. Participants in Metabolic Reactions

1. Reactants are substances that enter reactions.2. Intermediates are the compounds formed between the start and the end of a pathway.3. Products are the substances present at the conclusion of a pathway.4. Energy carriers are mainly ATP.5. Enzymes are proteins that catalyze (speed up) reactions.6. Cofactors are small molecules and metal ions

that help enzymes by carrying atoms or electrons.

7. Transport proteins are membrane-bound proteins that participate in adjusting concentration gradients that will influence the direction of m etabolic reactions.

B. What Are Metabolic Pathways?1. Metabolic pathways form series of reactions that regulate the concentration of substances within cells by enzyme-mediated linear and circular sequences.2. In biosynthetic (anabolic) pathways, small

molecules are assembled into large molecules; for example, simple sugars are assembled into complex carbohydrates.

3. In degradative (catabolic) pathways, large molecules such as carbohydrates, lipids, and proteins are broken down to form products of lower energy. Released energy can be used for cellular work.

D. No Vanishing Atoms at the End of the Run1. The law of conservation of mass states that the total mass of all substances entering a reaction equals the total mass of all the products. This is why you must always "balance" a chemical equation by having an equal number of atoms of each element on both sides of the arrow.

Enzymes Help With Energy HillsA. Enzymes are catalytic molecules that alter the rate of a chemical reaction without being used in them.

1. there names usually reflect their function and end in “ase”

B. Enzymes have four features:1. Enzymes speed up reactions.2. Enzymes can be reused.3. Enzymes, at least some of them, can recognize both reactants and products in order to catalyze a reaction in both directions.4. Enzymes are very selective about the substrates to which they will bind and thereby bring about change

C. Enzymes increase the rate of a reaction by lowering the activation energy (the amount of energy needed to get a reaction going).

D. they don’t “force” reactions, they just speed up reactions that already occur

E. enzymes are specific

1. most catalyze only a few closely related chemical reactions; many only 1

How Do Enzymes Lower Energy Hills?

A. The Active Site

1. Enzymes increase the rate of reactions by creating a microenvironment that is energetically more

favorable for the reaction.2. Each enzyme molecule has an active site where the substrate binds to the enzyme during a reaction

B. Transition at the Top of the Hill1. Activation energy brings the reactive chemical groups into alignment so that chemical bonds can be broken, created, and rearranged.2. The substrate is brought to its transition state, the point when a reaction can occur.3. enzyme + substrate enzyme-substrate complex (intermediate) enzyme + product

C. How Enzymes Work1. Binding energy helps bring about the transition state by four mechanisms:

a. Helping substrates get together;b. Orienting substrates in positions favoring reaction;c. Shutting out water;d. Inducing changes in enzyme shape (induced-fit model).

-induce strain in the substrate

D. About Those Cofactors-Some enzymes have 2 parts; a protein called the apoenzyme and an additional cofactor 1. Cofactors are nonprotein groups that bind to many enzymes and make them more reactive. Without the cofactors, the enzyme doesn’t function properly

a. coenzymes – organic, nonpolypeptide compounds that serve as cofactors

-they are not permanently bonded to the enzyme-they also act as carrier molecules that transfer electrons or part of a substrate between molecules

b. prosthetic groups – permanently bonded to the enzyme2. Inorganic metal ions such as Fe++ also serve as cofactors when assisting membrane cytochrome proteins in their electron transfers in chloroplasts and mitochondria.

E. Why Are Enzymes So Big?1. A large molecule affords structural stability.2. The extensive folding of the polypeptide chains puts amino acids and functional groups in locations and orientations that favor interaction with water and substrate.

Enzymes Don't Work in a VacuumA. How Is Enzyme Activity Controlled?

1. Some controls regulate the number of enzyme molecules available by speeding up/slowing down their synthesis.

a. remember, genes direct the synthesis of each type of enzyme and genes can be switched on and off; therefore controlling the amount of enzyme present in the cell

2. we refer to the series of chemical reactions in which the product of one reaction is the substrate of the next as a metabolic pathway

3. inhibitors – substances that bind to an enzyme and slow down the reaction

a. some inhibitors occur naturally, some are artificialb. reversible vs irreversible

-reversible inhibitors can leave the enzyme and the enzyme will return to normal function-irreversible inhibitors never allow the enzyme to return to normal function

c. competitive vs noncompetitive-competitive inhibitors bond to the enzymes in their active site so the substrate cannot; they are in direct competition with the substrate for the active site

-noncompetitive inhibitors bond to the enzyme somewhere other than the active site; but, their bonding causes a conformational change in the enzyme which changes the active site so that it no longer accepts the substrate

4. feedback inhibition – type of enzyme regulation in which the formation of a product inhibits an earlier reaction5. Allosteric enzymes have (in addition to active sites) regulatory sites where control substances can bind to alter enzyme activity; if this control substance is the end product in the enzyme’s metabolic pathway, feedback inhibition can occur.

a. allosteric regulators bind to a site on the enzyme that is not the active siteb. negative regulators – act as inhibitors; when they are in place the enzyme is not activec. positive regulators – act as activators; when they are in place the enzyme can function

B. Do Temperature and pH Affect Enzymes?1. Because enzymes operate best within defined

temperature ranges, high temperatures decrease reaction rate by disrupting the bonds that maintain three-dimensional shape (denaturation occurs); cold temperatures decrease the movement of particles and therefore the reaction. Some archaebacteria can survive extreme temperatures.

2. Most enzymes function best at a pH near 7 (pepsin in the stomach is an exception); higher or lower values disrupt enzyme shape and halt function.

C. Substrate Concentration can affect reaction rate1. adding more substrate will increase the reaction rate to a certain point, after which the enzymes are working at a maximum rate and all of the active sites are filled; therefore, adding more substrate will no increase the rate