Chapter 8: An Introduction to Metabolism

Merged flashcards from Chapter 8 of Pearson's Campbell Biology, Twelfth Edition.

First Law of Thermodynamics

Law that states that energy can be transferred or transformed, but not created or destroyed

• Demonstrated through energy use by living things

Second Law of Thermodynamics

Law that states that energy transfer or transformation increases universal entropy

• Demonstrated through the conversion of energy to heat by living things through inefficienies in conversion

Metabolism

The totality of an organism’s chemical reactions

• Arises from orderly interactions between molecules

Metabolic pathway

Pathway where a specific molecule is altered in a series of steps to produce a product, catalyzed by enzymes

Enzyme

A macromolecule that speeds up a specific reaction

Catabolic pathway

Metabolic pathway that releases energy by breaking down complex molecules into simpler compounds

• Seen through cellular respiration breaking down glucose with O₂

• Allows for energy use by anabolic pathways

• Described as “downhill”

Anabolic pathway

Metabolic pathway that consumes energy by building up complex molecules from simpler ones

• Seen through the synthesis of protein from amino acids

• Uses energy from catabolic pathways

• Described as “uphill”

Energy

The capacity to cause change or do work, existing in various forms

• Living cells must transform energy from one form to another to do the work of life

Kinetic energy

Energy associated with motion

• Moving objects impart motion to other matter

Thermal energy

The kinetic energy associated with random movement of atoms or molecules

• One object to another is called heat

• Light is another type, done through photosynthesis

Potential energy

Energy that matter possesses because of its location or structure

• Possessed due to the arrangement of electrons in bonds between atoms

Chemical energy

Potential energy available for releaes in a chemical reaction

• Glucose has more of this as it is released during catabolism

Thermodynamics

The study of energy transformations in a collection of matter

Isolated system

A system that is unable to exchange energy or matter with its surroundings, as in a vacuum-sealed drink bottle

Open system

A system that is able to transfer energy and matter between the system and its surroundings, as in organisms that absorb energy and release heat and waste

Spontaneous processes

Processes that increase the entropy of the universe without energy input, happening at varying rates

• Balances out anabolic reactions that build up molecules through the breakdown of molecules in catabolic reactions for heat and small molecules

Nonspontaneous processes

Processes that decrease entropy and require an input of energy

• Seen through anabolic reactions amongst amino acids to proteins

• Balanced by the catabolic breakdown of organized form of matter

Free energy (G)

The portion of a system’s energy that can do work when temperature and pressure are uniform throughout the system, as in a living cell

Delta G

The change in free energy, related to changes in temperature, total energy, and entropy

• Represents the difference between the free energy of the final state and free energy of the initial state

• Lower levels signify more stability after spontaneous expenditure

Spotaneous processes

Processes that use energy and increase total entropy

• Causes a negative change in free energy (negative delta G)

• Creates more stability in a system to work towards equilibrium

Nonspontaneous processes

Processes that build up or maintain total levels of energy or entropy

• Causes a zero or positive change in free energy (positive delta G)

• Used by the cell to perform work

Unstable systems

Systems with higher levels of free energy (G)

• Seen with a diver on a platform being less stable than in the water

Stable systems

Systems with lower levels of free energy

• Seen with a diver in the water after jumping off a platform, thus using energy

Equilibrium

The point at which forward and reverse reactions occur at the same rate, creating maximum stability

• Systems must nonspontaneously work to move away from equilibrium

• Eventually reached by closed or isolated systems, but never reached in an open living cell with flowing materials enabling work

Exergonic reaction

A reaction that creates a net release of free energy to the surroundings, causing energy to be expended outward

• Products store less free energy than reactants, creating a negative delta G and thus signifying a spontaneous reaction towards equilibrium

  • This releases potential energy

• G determines how much work a reaction can perform

Endergonic reaction

A reaction that absorbs free energy from the surroundings, causing energy to be drawn inward

• Products store more free energy than the reactants, creating a positive delta G and thus signifying a nonspontaneous reaction away from equilibrium

• Higher delta G amounts require more initial energy input

Catabolic pathway

A chain of reactions as seen in cellular respiration’s individual products becoming reactants for the next steps

• Steady glucose and waste progression ensure that equilibrium is never reached

Chemical work

Work that pushes endergonic reactions

Transport work

Work that pumps substances across membranes against the direction of spontaneous movement

Mechanical work

Work such as beating cilia or contracting muscle cells

Energy coupling

The use of an exergonic process to drive an endergonic one to manage energy resources in a cell

• Mediated by ATP in most cells

Adenosine triphosphate (ATP)

Particle composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups

• Functions in energy coupling and as one of the nucleoside triphosphates used to make RNA

• Energy is released when the terminal phosphate bond is broken by hydrolysis (adding water molecules)

Hydrolysis

The addition of a water molecule to break a bond in another molecule

• Used to release energy in ATP by breaking the terminal bond through its chemical change to a state of lower free energy in the products

  • This is an exergonic change to drive later endergonic reactions as well as transport and mechanical work in the cell

Repulsion

A word that describes molecules pushing away from each other in a bond

• Phosphate groups do this in ATP, creating lots of potential energy as in a compressed spring

Phosphorylation

The transfer of a phosphate group from ATP to another molecule typically used to power endergonic reactions

• Seen in ADP gaining a group after exergonic, catabolic reactions

Adenosine diphosphate (ADP)

One of the products after ATP hydrolysis that helps regenerate ATP through the addition of a phosphate molecule

ATP cycle

The shuttling of inorganic phosphate and energy between ATP and ADP that couples energy-yielding processes to energy-consuming ones

Spontaneous reaction

A reaction that does not need added energy but can be slow enough to be imperceptible

• Hydrolyzing sucrose to glucose and fructose with water can take years without a catalyst

Catalyst

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

Enzyme

A macromolecule (typically protein) that acts as a catalyst to speed up a specific reaction

• These lower the activation energy barrier enough for the reaction to occur at moderate temperatures while being reusable

• Names typically end in -ase for a specific reaction and substrate

Chemical bonds

These break and form in a chemical reaction

• Breakage requires excessive contortion before absorbing energy from its surroundings

Activation energy (E_A)

The initial energy needed to break the bonds of the reactants, often seen as heat from the surroundings

• Instability occurs when enough energy is absorbed to start the reaction

• Provides a barrier that determines the rate of spontaneous reactions

• Only changes speed and not overall effect of the reaction

Exergonic reaction

A reaction that releases more energy than was initially invested through the formation of new bonds

• These new bonds increase stability

Catalysis

The process by which a catalyst selectively speeds up a reaction without itself being consumed

• Avoids the excessive use of heat to speed up reactions which can cause denaturation

Substrate

The reactant that an enzyme acts on through catalytic activity for a conversion to products

• Typically held in the enzyme’s active site by weak bonds, such as hydrogen bonds

• Can be reoriented, stretched, or placed in a microenvironment to favor the reaction

• Rates of reaction can be increased with higher concentrations until complete enzyme saturation

Active site

The region on the enzyme that binds to the substrate, fitting the specific shape of the substrate

Induced fit

The slight change in shape of the enzyme like a handshake that results from chemical interactions on the substrate and active site

• This ultimately enhances catalysis of the reaction

Optimal conditions

Conditions that are most conducive to an enzyme’s function, mainly defined within a range of temperature, pH, and chemicals that influence the enzyme

Optimal temperature

The temperature at which an enzyme catalyzes its reaction at the maximum possible rate, increasing with increasing temperature until it is met and begins to drop and denature

• Typically defined by the environment in which it functions — human enzymes adapt to human body temperature, or around 37 degrees C

Optimal pH

The pH at which an enzyme is typically active, usually dependent on the environment at which it functions

• Pepsin in the stomach has an optimal pH of 2

Cofactors

Nonprotein helpers that bind to the enzyme permanently or reversibly with the substrate

• Inorganic includes metal atoms such as zinc, iron, and copper in ionic form

• Organics are called coenzymes, found in vitamins or made from their raw materials

Coenzymes

Organic cofactors that include vitamins or their raw materials as helpers to enzymes

Enzyme inhibitor

A chemical that inibits the action of specific enzymes

• Inhibition with covalent bonds to the enzyme are usually irreversible

• Weak interactions can be reversible and are used in most cases

Competitive inhibitors

Inhibitors that closely resemble the substrate of an enzyme and can bind to the enzyme’s active site, thus reducing enzyme productivity due to blockage

Noncompetitive inhibitors

Inhibitors that bind to another part of the enzyme away from the active site

• These cause the enzyme to change shape and makes the active site less effecive at catalyzation

Genes

The encoding method for enzymes; mutations in these can lead to a positive or negative change in the enzyme’s amino acid composition and thus new activity or substrate specificity