BIO146

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Chapter 8
Chapter 8

8.1 An organism’e metabolism transforms matter and energy

metabolism - the totality of an organism’s chemical reactions; an emergent property of life that arises from orderly interactions between molecules

chemical reactions - a process that involves rearrangement of the molecular or ionic structure of a substance, as opposed to a change in physical form or a nuclear reaction.

Metabolic Pathways

metabolic pathway - a specific molecule is altered in a series of defined steps, resulting in a certain product

→ each step is catalyzed by a specific enzyme, a macromolecule that speeds up a chemical reaction

each enzyme only works with one substrate

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metabolism as a whole manages the material and energy resources of the cell

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

catabolic pathways - degradative processes, breakdown pathways

catabolic - energy releasing reaction

→ cellular respiration - breaks down glucose and other organic fuels in the presence of oxygen to carbon dioxide and water

anabolic pathways - consume energy to build complicated molecules from simpler ones; biosynthetic pathways

photosynthesis (more energy stored in products)

anabolic - energy storing reaction

→ synthesis of an amino acid from simpler molecules and synthesis of a protein from amino acids

bioenergetics - the study of how energy flows through living organisms

Forms of Energy

energy - the capacity to cause change

→ energy is the ability to rearrange a collection of matter

kinetic energy - associated with the relative motion of objects

thermal energy - kinetic energy associated with random movement o atoms or molecules

heat (thermal energy)- thermal energy in transfer from one object to another (move from high area to low area)

potential energy - enrgy that matter possesses because of its location or structure

chemical energy - a term used by biologists to refer to the potential energy available for release in chemical reaction

The Laws of Energy Transformation

thermodynamics - the study of the energy transformations that occur in a collection of matter

The First Law of Thermodynamics (the principle of conservation of energy)

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

→ by converting sunlight to chemical energy, a plant acts as an energy transformer, not an energy producer

the energy in the universe never changed

The Second Law of Thermodynamics

every enerrgy transfer or transformation increases the entropy of the universe

→ entropy - a measure of molecular disorder, or randomness; the more randomly arranged a collection of matter is, the greater its entropy

spontaneous process - the process can proceed without requiring an input of energy

Biological Order and Disorder

living systems increase the entropy of their surroundings, as predicted by thermodynamic law

8.2 The free-energy change of a reaciton tells us whether or not the reaction occurs spontaneously

Free-Energy Change, 𝛥G

Free energy - 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

𝛥G = 𝛥H - T𝛥S

** if 𝛥H increases, 𝛥G increases; if T or 𝛥S increase, 𝛥G decreases

→ change in free energy = 𝛥G

→ 𝛥H symbolizes the change in the system’s enthalpy

→ 𝛥S is the change in the system’s entropy

→ T is the absolute temperature in Kelvin

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Free Energy, Stability, and Equilibrium

𝛥G = G(final state) - G (initial state)

free energy is a measure of a system’s instability — its tendency to change to a more stable state

equilibrium — another term that describes a state of maximum stability

Free Energy and Metabolism

Exergonic and Endergonic Reactions in Metabolism

exergonic reaction — proceeds with a net release of free energy

→ 𝛥G is negative

→ chemical mixture loses free energy (G decreases)

endergonic reaction - absorbs free energy from its surroundings

→ 𝛥G is positive

→ this kind of reaction stores free energy in molecules (G increases)

** in a close system, it can reach equilibrium which means that 𝛥G = 0

** in an open system, it can never reach equilibrium which means that 𝛥G can be -/+

** 𝛥G<0: exergonic; catabolic; 𝛥G>0: endergonic; anabolic

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exergonic reaction: reactants have higher energy than the products

endergonic reaction: reactants have less energy than the products

Equilibrium and Metabolism

the fact that metabolism as a whole is never at equilibrium is one of the defining features of life

like most systems, a living cell is not in equilibrium

8.3 ATP powers cellular work by coupling exergonic reactions to endergonic reaction

a cell does three main kinds of work

chemical work - the pushing of endergonic reactions that would not occur spontaneously

→ the synthesis of polymers from monomers

transport work - the pumping of substances across membranes against the direction of spontaneous movement

mechanical work - the beating o fcilia, the contraction of muscle cells, the movement of chromosomes during cellular respiration

energy coupling - the use of an exergonic process to drive an endergonic one

ATP (adenosine triphosphate) - contains the sugar ribose, with the nitrogenous base adenine and a chain of three phosphate groups bonded to it

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

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the reaction is exergonic and release 7.3 kcal of energy per mole of ATP hydrolyzed:

ATP + H2O → ADP + Pi (energy releasing; when we are using ATP)

𝛥G = - 7.3 kcal/mol (-30.5 kJ/mol)

→ the phosphate bonds of ATP are not unusually strong bonds, as “high-energy” may imply

→ the release of energy during the hydrolysis of ATP comes from the chemical change of the system to a state of lower free energy, not from the phosphate bonds themselves

ATP is very similar to RNA

3 phosphate

has a double ring structure purine

How ATP Provides Energy That Performs Work

phosphorylated intermediate - the recipient molecule with the phosphate group covalently boned to it

hydrolysis of ATP provides the energy for chemical, transport, and mechanical work within a cell

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The Regeneration of ATP

The free energy required to phosphorylate ADP comes form exergonic breakdown reactions (catabolism) in the cell

→ if ATP could not be regenerated by the phosphorylation of ADP, humans would use up nearly their body weight in ATP each day

the regeneration of ATP from ADP and Pi is necessarily endergonic

ADP + Pi = ATP + H2O

𝛥G = +7.3 kcal/mol (+30.5 kJ/mol)

8.4 Enzymes speed up metabolic reactions by lowering energy barriers

all enzymes are proteins, biological catalyst

-ase — enzymes

How do enzymes speed up catalysts? — by lower activation energy

𝛥G never get affected by enzyme

enzyme always work with activate energy

any compound that works with enzyme are substrates

active site - the region on the enzyme where the substrate binds

allostatic — the other sites that do not bind with the substrate

enzymes can do regulation and inhibition

enzyme will never be used up

the only reason that causes losing of enzyme is aging

*The active site can lower an EA barrier by

orienting substrates correctly

straining substrate bonds

providing a favorable microenvironment

covalently bonding to the substrate

denaturation — when the general environmental factors changed the shape of the enzyme or protein

enzyme inhibitors

competitive inhibitors

when inhibitors compete with substrates for the active site

noncompetitive inhibitors

→ allosteric inhibition

when inhibitors bind with the allosteric site, which changes the shape of the active site of the enzyme

→ feedback inhibition

when there are too much product that got provided, the product that got produced can bind with the allosteric site of the enzyme, which changes the shape of the enzyme

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8.5 Regulation of enzyme activity helps control metabolism

cooperativity - another type of allosteric activation

→ form of allosteric regulation that can amplify enzyme activity

one substrate binds with the active site of the enzyme that causes another enzyme to work

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