Chapter 8 Flashcards
What termite larval species produces green glowing spots?
Pyrophorus nyctophanus
How do the laws of thermodynamics relate to biological processes?
Energy use by living things demonstrates the first law of thermodynamics.
The conversion of energy to thermal energy released as heat by living things demonstrates the second law of thermodynamics.
What is the first law of thermodynamics?
Energy can be transferred and transformed, but not created or destroyed. (Law of conservation of energy)
What is the second law of thermodynamics?
Every energy transfer or transformation increases the entropy (disorder) of the universe.
What is metabolism?
The totality of an organism’s chemical reactions. An emergent property of life that arises from orderly interactions between molecules.
What is a metabolic pathway?
A specific molecule is altered in a series of steps to produce a product. Each step is catalyzed by a specific enzyme, a macromolecule that speeds up a specific reaction.
What are catabolic pathways?
They release energy by breaking down complex molecules into simpler compounds.
What does cellular respiration do?
Breakdown glucose in the presence of O2, an example of pathway catabolism.
What are anabolic pathways?
They consume energy to build complex molecules into simpler ones. Ex. the synthesis of protein from amino acids is an anabolic pathway.
What are catabolic and anabolic pathways described as?
Catabolic are “downhill” reactions, and anabolic are “uphill” reactions.
What is bioenergetics?
The study of how energy flows through living organisms.
What is energy?
The capacity to cause change, can be used to do work; move matter against opposing forces, such as gravity and friction.
How do cells use energy?
Transform energy from one form to another to do the work of life. Energy exists in various forms.
What is kinetic energy?
Energy associated with motion.
How do moving objects work?
Perform work by imparting motion to other matter. Ex. water gushing through a dam turns turbines.
What is thermal energy?
The kinetic energy associated with random movement of atoms or molecules.
What is heat?
Thermal energy in transfer from one object to another.
What is light?
A type of energy that can be harnessed to do work, such as photosynthesis.
What is potential energy?
Energy that matter possesses because of its location or structure.
EX. water behind a dam possesses energy because of its altitude above sea level.
Do molecules possess potential energy?
Yes; due to the arrangement of electrons in bonds between their atoms.
What is chemical energy?
Potential energy available for release in a chemical reaction.
What complex molecules are high in chemical energy?
Glucose, because energy is released as they are broken down to simpler products.
Can energy be converted from one form to another?
Yes; chemical energy from food is used to perform the work of climbing up to a diving platform.
Ex. the kinetic energy of muscle movement is transformed into potential energy as the diver climbs higher above the water. The potential energy is then transformed to kinetic energy as the diver falls back down to the water.
What is thermodynamics?
The study of energy transformations in a collection of matter.
What is an isolated system?
Unable to exchange energy or matter with its surroundings. Ex. liquid in a thermos bottle
What is an open system?
Energy and matter can be transferred between the system and its surroundings.
What can be considered open systems?
Organisms; they absorb energy from light or food and release heat and metabolic wastes, such as CO2, to the surroundings.
What is the first law of thermodynamics called?
The principle of conservation of energy.
What is the second law of thermodynamics?
During every energy transfer or transformation, some energy is converted to thermal energy and lost as heat, becoming unavailable to do work.
Every energy transfer or transformation increases the entropy (disorder) of the universe.
What is entropy?
A measure of molecular disorder, or randomness.
How do living organisms increase the entropy of their surroundings?
Through metabolism; the breakdown of food releases heat and small molecules, such as CO2.
What are spontaneous processes?
Processes that increase the entropy of the universe that happen spontaneously; occur without energy input and can happen quickly or slowly.
What are nonspontaneous processes?
Processes that decrease entropy and require an input of energy.
What do cells create?
Ordered structures from less organized starting materials. Ex. simple molecules are ordered into amino acids, which are assembled into ordered polypeptides.
How is the increase in order within living systems balanced?
By catabolic breakdown of organized forms of matter, releasing heat and small molecules. At larger scales, energy flows into ecosystems as light and exits as heat.
Does the evolution of complex organisms from simpler ancestors violate the second law?
No; entropy may decrease in a particular system like an organism, as long as the total entropy of the system and its surroundings increases.
How do biologists determine whether chemical reactions require an input of energy or not?
Follow the energy and entropy changes during chemical reactions.
What is Gibbs energy?
Gibbs free energy, G, can be simplified and referred to as free energy.
What is free energy?
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.
What is change in free energy during a reaction related to?
Temperature and changes in enthalpy and entropy.
ΔG° = ΔH° - TΔS°
ΔG° = change in free energy
ΔH° = Change in enthalpy (total energy)
T = Temperature in Kelvin
ΔS° = Change in entropy
What can the change in G be used to determine?
Whether it is spontaneous or not. It is negative for all spontaneous processes, and zero or positive for nonspontaneous processes.
What decreases a system’s free energy?
Every spontaneous process; but can be harnessed by the cell to perform work.
What does the Change in G represent?
The difference between free energy of the final state and free energy of the initial state.
If a reaction has negative change in G, the system loses free energy and becomes more stable.
What can free energy be thought of?
A measure of a system’s stability; unstable systems (higher G) tend to become more stable (lower G).
Ex. diver on a platform is less stable than when floating in water.
What is equilibrium?
The point at which forward and reverse reactions occur at the same rate, describes a state of maximum stability.
Do systems move away from equilibrium?
Not spontaneously. A process is spontaneous and can perform work only when it is moving toward equilibrium.
What can the process of free energy be applied to?
The chemistry of life’s processes.
How can chemical reactions be classified?
Based on their free energy changes.
What are the classifications of reactions?
Exergonic reactions (energy outward) proceeds with a net release of free energy to the surroundings.
Endergonic reactions (energy inward) absorbs free energy from the surroundings.
What happens in exergonic reactions?
The products store less free energy than the reactants. Because the change in G is negative, exergonic reactions occur spontaneously. It will not always occur rapidly, it might take a bit of time.
What does the magnitude of the change of G determine?
The maximum amount of work an exergonic reaction can perform. Ex. for each mole of glucose broken down during cellular respiration, 686 kcal of energy is available for work.
Does breaking bonds during a reaction require energy?
Yes; it releases energy but requires energy to react. If the products are of lower free energy than the reactants, potential energy is released when new bonds are formed after the original bonds break.
What happens in endergonic reactions?
The products store more free energy than the reactants. Because the change in G is positive, endergonic reactions are nonspontaneous.
What does the magnitude of the change in G mean in endergonic reactions?
Determines the quantity of energy required to drive an endergonic reaction.
Ex. to produce glucose and O2 from CO2 and H2O requires input of 686 kcal/mol; the products of photosynthesis store 686 kcal more free energy per mole than the reactants.
Do reactions in a closed system reach equilibrium?
Yes; but they will not be able to do work anymore. Ex. isolated hydroelectric system
Are the chemical reactions of metabolism reversible?
Yes, but never reach equilibrium in a living cell, which is a defining feature of life. Cells allow materials to flow in and out, and the flow of materials prevents metabolic equilibrium, enabling cells to continue doing work.
What does a catabolic pathway do in a cell?
Releases free energy in a series of reactions. Ex. in cellular respiration, reactions are “pulled” in one direction because the products of each reaction are the reactants in the next step.
What kinds of work does a cell do?
Three main kinds: Chemical work, transport work, and mechanical work.
What is chemical work?
Pushing endergonic reactions.
What is transport work?
Pumping substances across membranes against the direction of spontaneous movement.
What is mechanical work?
Beating cilia or contracting muscle cells.
What is energy coupling?
Cells manage energy resources to do work through energy coupling, which is the use of an exergonic process to drive an endergonic one.
What mediates energy coupling in cells?
ATP
What is ATP?
Adenosine triphosphate; composed of ribose (sugar), adenine (a nitrogenous base), and three phosphate groups.
What can ATP do?
Can function as one of the nucleoside triphosphates used to make RNA.
How does ATP correlate to making energy?
Energy is released from ATP when the terminal phosphate bond is broken by hydrolysis, or the addition of a water molecule.
The energy does not come directly from the group, but from the chemical change to a state of lower free energy in the products.
Why is ATP used?
It releases more energy with the loss of a phosphate than most other molecules could deliver. Repulsion between the negative charges of the three phosphate groups creates a lot of potential energy. The triphosphate tail is the chemical equivalent of a compressed spring.
What does ATP power?
Cellular work (mechanical, transport, and chemical) through the ATP hydrolysis.
It is also used to drive endergonic reactions.
What is phosphorylation?
Transfer of a phosphate group from ATP to another molecule, and is typically used to power endergonic reactions.
What is the recipient molecule of phosphorylation?
A phosphorylated intermediate, which is more reactive (less stable, with more free energy) than the original molecule.
What can ATP hydrolysis do to proteins?
Change in protein shape and binding ability.
How is ATP regenerated?
Adding a phosphate group to the adenosine diphosphate (ADP)
Where does the free energy needed to phosphorylate ADP come from?
Exergonic breakdown reactions (catabolism).
What is the ATP cycle?
The shuttling of inorganic phosphate and energy, it couples energy yielding processes to energy consuming ones.
What spontaneous reactions can sit for years?
Sucrose in sterile water, without appreciable hydrolysis.
What is a catalyst?
A chemical agent that speeds up a reaction without being consumed by the reaction.
What is an enzyme?
A macromolecule (typically a protein) that acts as a catalyst to speed up a specific reaction.
What does every chemical reaction involve?
Bond breaking and bond forming.
What must a molecule do before starting a reaction?
Contorted into a highly unstable state before bonds can break to start the reaction. To reach this state, the molecule must absorb energy from its surroundings.
What is activation energy?
The initial energy needed to break the bonds of the reactants. Heat in the form of thermal energy absorbed from the surroundings often supplies activation energy.
When do molecules become unstable?
When enough energy is absorbed to break bonds, it is the transition state.
What barrier does the activation energy produce?
Determines the rate of spontaneous reactions.
Most reactions have high activation energy and need additional energy (usually heat) to reach the transition state.
What is catalysis?
The process by which a catalyst selectively speeds up a reaction without itself being consumed.
How does an enzyme catalyze a reaction?
By lowering the activation energy barrier enough for the reaction to occur at moderate temperatures.
What is a substrate?
The reactant that an enzyme acts on.
What is an enzyme substrate complex?
The enzyme binds to its substrate.
What do most enzyme names end in?
-ase
Ex. the enzyme sucrase catalyzes the hydrolysis of sucrose into glucose and fructose.
What is special about enzymes?
Each enzyme catalyzes a specific reaction and can recognize its specific substrate among even closely related compounds.
What is an active site?
The region on the enzyme (often a pocket or groove) that binds to the substrate.
What is responsible for enzyme specificity?
The complementary fit between the shape of the active site and the shape of the substrate.
What happens when the substrate enters the active site?
The enzyme changes shape slightly, tightening around the substrate like a handshake. (induced fit)
What is induced fit?
Results from interactions between chemical groups on the substrate and the active site. It brings the chemical groups of the active site into positions that enhance catalysis of the reaction.
How is the substrate held in the enzyme’s active site?
By weak bonds such as hydrogen bonds.
What are the variety of mechanisms to lower activation energy?
Substrates can be oriented to facilitate reaction
Substrates can be stretched to make the bonds easier to break
The active site may provide a microenvironment that favors the reaction
Amino acids in the active site may participate in the reaction
How can an enzyme catalyzed reaction be sped up?
By increasing substrate concentration.
When is an enzyme saturated?
When all enzyme molecules have their active sites engaged.
What happens if an enzyme is saturated?
The reaction rate can only be sped up by adding more enzyme.
How can enzyme activity be affected?
By general environmental factors such as temperature and pH. It can also be affected by chemicals that specifically influence the enzyme.
What do enzymes need to catalyze at the maximum possible rate?
Optimal temperature. If the temperature increases too far beyond the optimal range, the enzyme begins to denature.
What is the optimal temperature of an enzyme dependent on?
The environment in which it typically functions. Ex. the optimal temperature for human enzymes is about 30-40 Celsius, whereas the optimal temperature for thermophilic bacteria is about 75 Celsius.
What is an enzyme’s optimal pH range?
Dependent on the environment it is typically active. Ex. pepsin (human stomach enzyme) is 2, and trypsin (intestinal enzyme) is 8.
What are cofactors?
Nonprotein helpers that bind to the enzyme permanently, or reversibly with the substrate.
Inorganic cofactors include metal atoms such as zinc, iron, and copper in ionic form.
What are coenzymes?
Organic cofactors.
Most vitamins either act as coenzymes or provide the raw materials needed to make them.
What happens if an inhibitor forms covalent bonds with the enzyme?
The inhibition is usually irreversible. Many inhibitors bind to the enzyme by weak interactions, resulting in reversible inhibition.
What are competitive inhibitors?
Closely resembles the substrate, and can bind to the enzyme’s active site. Enzyme productivity is reduced because the inhibitor blocks the substrate from entering the active site.
Increasing substrate concentration can overcome this type of inhibition.
What are noncompetitive inhibitors?
They bind to another part of the enzyme, away from the active site. Binding of the inhibitor causes the enzyme to change shape, making the active site less effective at catalyzing the reaction.
What are often irreversible enzyme inhibitors?
Toxins and poisons.
Ex. sarin gas binds covalently to the active site of acetylcholinesterase, an enzyme important in the nervous system (war crime)
Other examples include pesticides and antibiotics
What are enzymes made of?
They are proteins encoded by genes. Changes in genes (mutations) lead to changes in the amino acid composition of the enzyme. Altered amino acids, particularly at the active site, can result in novel enzyme activity or altered substrate specificity.
When would natural selection favor a mutated allele (mutation)?
If the mutation results in a new enzyme function that is beneficial to the orgnaism.
When would chemical chaos occur?
If a cell’s metabolic pathways were operating simultaneously. Cells can regulate metabolic pathways by switching on or off the genes that encode specific enzymes, or by regulating the activity of existing enzymes.
What is allosteric regulation?
Occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site. This type of regulation may either inhibit or stimulate enzyme activity.
What are allosterically regulated enzymes made from?
Polypeptide subunits, each with its own active site. The complex oscillates between two shapes, one catalytically active and the other inactive.
What happens when an activating or inhibiting molecules bind to a regulatory site?
The binding of an activator stabilizes the shape that has functional active sites, whereas the binding of an inhibitor stabilizes the inactive form of the enzyme.
What is cooperativity?
Substrate binding to one active site triggers a shape change in the enzyme that stabilizes the active form for all other sites.
This mechanism amplifies the response by priming the enzyme to act on additional substrate molecules more readily.
What is feedback inhibition?
The end product of a metabolic pathway shuts down the pathway. Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed.
