BIO 121, Chapter 8: An introduction to Metabolism (Exam 3)

spontaneous change

- more free energy (higher G) - less stable - greater work capacity In a spontaneous change: "The free energy of the system decreases; the system becomes more stable; the released free energy can be harnessed to do work" - less free energy (lower G) - more stable - less work capacity

how enzyme lowers activation energy

- when there are two of more reactants, the active site provides a template on which the substrates can come together in the proper orientation for a reaction to occur between them. - as the active site of an enzyme clutches the bound substrates, the enzyme may stretch the substrate molecules toward their transition state form stressing and bending critical chemical bonds to be broken during the reaction. Because Activation energy is proportional to the difficulty of breaking the bonds, distorting the substrate helps it approach the transition state and reduces the amount of free energy that must be absorbed to achieve that state. - The active site may also provide a microenvironment that is more conducive to a particular type of reaction than the solution itself would be without the enzyme. For example, if the active site has amino acids with acidic R groups, the active site may be a pocket of low pH in an otherwise neutral cell. In such cases, an acidic amino acid may facilitate H+ transfer to the substrate as a key step in catalyzing the reaction. - Amino acids in the active site directly participate in the chemical reaction. Sometimes this process even involves brief covalent bonding between the substrate and the side chain of an amino acid of the enzyme. Subsequent steps of the reaction restore the side chains to their original states so that the active site is the same after the reaction it was before. **subsequent: coming after something in time; following. The active site can lower an Ea barrier by: - orienting substrates correctly - straining substrate bonds - providing a favorable microenvironment - covalently bonding to the substrate

Cellular work

A cell does three main kinds of work: - 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 membranes against the direction of spontaneous movement. - mechanical work: beating of cilia, the contraction of muscle cells, and the movement of chromosomes during cellular reproduction. ATP powers cellular work by coupling exergonic reactions to endergonic reactions.

enzyme

A macromolecule serving as a catalyst, a chemical agent that changes the rate of a reaction without being consumed by the reaction.

endergonic reaction

A non-spontaneous chemical reaction in which free energy is absorbed from the surroundings.

enzyme's specificity altered by mutation

A permanent change in a gene is known as a mutation. In the case of an enzyme, If the changed amino acids are in the active site or some other crucial region, the altered enzyme might have a novel activity or might bind to a different substrate. Under environmental conditions where the new function benefits the organism, natural selection would tend to favor the mutated form of the gene, causing it to persist in the population.

How ATP Drives Transport and Mechanical Work

ATP hydrolysis causes changes in the shapes and binding affinities of proteins. This can occur either a) directly, by phosphorylation, as shown for a membrane protein carrying out active transport of a solute, or b) indirectly, via noncovalent binding of ATP and its hydrolytic products, as is the case for motor proteins that move vesicles (and other organelles) along the cytoskeletal "tracks" in the cell. a) Transport work: ATP phosphorylates transport proteins, causing a shape change that allows transport of solutes. b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed, causing a shape change that walks the motor protein forward. ***hydrolyze: break down (a compound) by chemical reaction with water.

How pathways save energy

Catabolic and anabolic pathways are the "downhill" and "uphill" avenues of the metabolic landscape. Energy released from downhill reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways.

Phosphorylated Intermediate (How ATP drives chemical work)

Conversion reaction coupled with ATP hydrolysis: In the cell, glutamine synthesis occurs in two steps, coupled by a phosphorylated intermediate. 1. ATP phosphorylates glutamic acid, making it less stable, with more free energy (higher energy). 2. Ammonia displaces the phosphate group, forming glutamine. *phosphorylation: to introduce a phosphate group into (a molecule or compound). *displaces: to take over the place, position, or role of (someone or something).

first law of thermodynamics

Energy can be transferred and transformed, but it cannot be created or destroyed. Also known as the principle of conservation of energy. The electric company does not make energy, but merely converts it to a form that is convenient for us to use. By converting sunlight to chemical energy, a plant acts as an energy transformer, not an energy producer.

ATP cycle

Energy released by breakdown reactions (catabolism) in the cell is used to phosphorylate ADP, regenerating ATP. Chemical potential energy stored in ATP drives most cellular work. **catabolism: the breakdown of complex molecules in living organisms to form simpler ones, together with the release of energy; destructive metabolism. *phosphorylation: to introduce a phosphate group into (a molecule or compound).

second law of thermodynamics

Every energy transfer or transformation increases the entropy of the universe. as the bear runs, disorder is increased around its body by the release of heat and small molecules that are the by-products of metabolism. A brown bear can run at speeds up to 35 miles per hour- as fast as a racehorse. *molecules moving fast are disordered. * entropy: the measure of a molecular disorder, or randomness. The more randomly arranged a collection of matter is, the greater its entropy.

anabolic pathways

Metabolic pathways that consume energy to build complicated molecules from simpler ones. these are sometimes called biosynthetic pathways.

catabolic pathways

Metabolic pathways that release energy by breaking down complex molecules into simpler compounds.

competitive inhibitors

Reduce the productivity of enzymes by blocking substrates from entering active sites. A competitive inhibitor mimics the substrate, competing for the active site

Hydrolysis of ATP

The reaction of ATP and water yields ADP and inorganic phosphate (Pi) and releases energy. 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.

thermodynamics

The study of energy transformations that occur in a collection of matter.

Biological Order and Disorder

The universe can be ordered on the organismal level but still disordered overall. As open systems, organisms can increase their order as long as the order of their surroundings decreases. Living systems increase the entropy of their surroundings as predicted by thermodynamic law. It is true that cells create ordered structures from less organized starting materials. For example, simpler molecules are ordered into the more complex structure of an amino acid, and amino acids are ordered into polypeptide chains. At the organismal level as well, complex and beautifully ordered structures result from biological processes that use simpler starting materials.

energy coupling

The use of an exergonic process to drive an endergonic one. exergonic: losing energy endergonic: gaining or using energy A key feature in the way cells manage their energy resources to do work. ATP is responsible for medicating most energy coupling in cells, and in most cases it acts as the immediate source of energy that powers cellular work.

Negative Free Energy (Gibbs)

When a process occurs spontaneously in a system, we can be sure that Delta G is negative. Another way to think of Delta G is to realize that is represents the difference between the free energy of the final state and the free energy of the initial state: ΔG= G final state- G initial state Thus, ΔG can be negative only when the process involves a loss of free energy during the change from initial state to final state. Because it has less free energy, the system in its final state is less likely to change and is therefore more stable than it was previously.

activator

activates enzyme

activator and inhibitor regulating enzyme

allosteric regulation: 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. Through this interaction of sub-units of an allosteric enzyme fit together in such a way that a shape change in one sub-unit is transmitted to all others.

How the enzyme works

an enzyme catalyzes a reaction by lowering the activation energy (Ea) barrier, enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures.

cooperativity

another type of allosteric regulation.. It amplifies the response of enzymes to substrates. 4 enzymes that are the same.. If a substrate is binding to one of the enzymes, the other three most likely will bind to the substrate. Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation. *** active conformation: A macromolecule is usually flexible and dynamic. It can change its shape in response to changes in its environment or other factors; each possible shape is called a conformation, and a transition between them is called a conformational change.

allosteric regulation

any case in which a protein's function at one site is affected by the binding of a regulatory molecule to a separate site. It may result in either inhibition or stimulation of an enzyme's activity. something that is binding to the enzyme that causes it to either turn on or off. It is non-competitive but it can be reversed.

noncompetitive inhibitors

bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective, or preventing enzymatic reaction.

Inhibitor

deactivates enzyme

activation energy

energy that is needed to get a reaction started amount of energy needed to push the reactants to the top of an energy barrier, or uphill, so that the "downhill" part of the reaction can begin. Energy profile of an exergonic reaction: - The reactants AB and CD must absorb enough energy from the surroundings to reach the unstable transition state, where bonds can break. - After bonds have broken, new bonds form, releasing energy to the surroundings.

how to overcome competitive inhibition

increase substrate concentration so that the active sites become available, more substrate molecules than inhibitor molecules are around to gain entry to the sites.

Free energy (Gibbs)

is the portion of a system's energy that can perform work when temperature and pressure are uniform throughout that system, as in a living cell. Let's consider how we determine the free-energy change that occurs when a system changes- for example, during a chemical reaction. The change in free energy, ΔG, can be calculated for a chemical reaction by applying the following equation: ΔG = ΔH- T Δ S This equation uses only properties of the system (the reaction) itself: Δ H symbolizes the change in the system's enthalpy (in biological system's, equivalent to total energy); S Δ is the change in the system's entropy; and T is the absolute temperature in Kelvin (K) units (K= °C + 273). ΔG = ΔH − TΔS ∆G= free energy ∆H= enthalpy (total energy) T= temperature (in Kelvin) ∆S= entropy Using chemical methods, we can measure ΔG (change in free energy) for any reaction. (The value will depend on conditions such as pH, temperature, and concentrations of reactants and products.) Once we know the value of ΔG for a process, we can use it to predict whether the process will be spontaneous (that is, whether it is energetically favorable and will occur without an input of energy). ENTHALPY (total energy): When a substance changes at constant pressure, enthalpy tells how much heat and work was added or removed from the substance. Enthalpy is similar to energy, but not the same. When a substance grows or shrinks, energy is used up or released. ENTROPY: the measure of a molecular disorder, or randomness. The more randomly arranged a collection of matter is, the greater its entropy.

Thermal energy

kinetic energy associated with the random movement of atoms or molecules. Energy in its most random form. It results in an object or a system having a temperature that can be measured. this energy in transfer from one object to another is called heat. Energy pushed into motion by heat.

ATP (adenosine triphosphate)

main energy source that cells use for most of their work An adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed. This energy is used to drive endergonic reactions in cells.

lower energy

more stable system examples: - diver floating in water - dye spread randomly through the liquid - simpler molecules of glucose

cofactors

non-protein helpers for catalytic activity, often for chemical processes like electron transfers that cannot easily be carried out by the amino acids in proteins. Any nonprotein molecule or ion that is required for the proper functioning of an enzyme. Cofactors can be permanently bound to the active site or may bind loosely with the substrate during catalysis. The cofactors of some enzymes are inorganic.

coenzymes

organic cofactors an organic molecule serving as a cofactor. Most vitamins function as coenzymes in metabolic reactions.

chemical energy

potential energy available for release in a chemical reaction. Recall that catabolic pathways release energy by breaking down complex molecules. Biologists say that these complex molecules, such as glucose, are high in chemical energy. During a catabolic reaction, some bonds are broken and others are formed, releasing energy and resulting in lower-energy breakdown products. This transformation also occurs in the engine of a car when the hydrocarbons of gasoline react explosively with oxygen, releasing the energy that pushes the pistons and producing exhaust. Although less explosive, a similar reaction of food molecules with oxygen provides chemical energy in biological systems, producing carbon dioxide and water as waste products. Biochemical pathways, carried out in the context of cellular structures, enable cells to release chemical energy from food molecules and use the energy to power life processes.

exergonic reaction

refers to a reaction where energy is released. Because the reactants lose energy (G decreases), Gibbs free energy (ΔG) is negative under constant temperature and pressure. These reactions usually do not require energy to proceed, and therefore occur spontaneously.

Factors that affect enzyme activity

temperature and pH, or chemicals that specifically influence that enzyme. temperature: - the rate of an enzymatic reaction increases with increasing temperature, partly because substrates collide with active sites more frequently when the molecules move rapidly. Above that temperature, however, the speed of the enzymatic reaction drops sharply. The thermal agitation of the enzyme molecule disrupts the hydrogen bonds, ionic bonds, and other weak interactions that stabilize the active shape of the enzyme, and the protein molecule eventually denatures. Each enzyme has an optimal temperature at which its reaction rate is greatest. Most human enzymes have optimal temperature of about 35-40 degrees Celsius. pH: The optimal pH values for most enzymes fall in the range of pH 6-8, but there are exceptions, for example, pepsin, a digestive enzyme in the human stomach, works best at a very low pH. Such an acidic environment denatures most enzymes, but pepsin is adapted to maintain its functional three dimensional structure in the acidic environment of the stomach. In contrast, trypsin, a digestive enzyme residing in the more alkaline environment of the human intestine would be denatured in the stomach.

Energy

the capacity to cause change. in everyday life, this is important because some forms can be used to do work- that is, to move matter against opposing forces, such as gravity and friction. Rearranges a collection of matter. It exists in various forms, and the work of life depends on the ability of cells to transform it from one form to another.

Kinetic energy

the energy an object has due to its motion moving objects can perform work by imparting motion to other matter: A pool player uses the motion of the cue stick to push the cue ball, which in turn moves the other balls; water gushing through a dam turns turbines; and the contraction of leg muscles pushes bicycle pedals.

entropy

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

Bioenergetics

the study of how energy flows through living organisms

Induced fit of enzyme

the tightening of the binding after initial contact brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction. enzyme- substrate match process in which the substrate enters the active area of the enzyme and the enzyme shapes around it (like play-doh) **catalyze: cause or accelerate (a reaction) by acting as a catalyst.

Metabolism

the totality of an organism's chemical reactions. It is an emergent property of life that arises from orderly interactions between molecules. This as a whole manages the material and energy resources of a cell.

Heat

thermal energy in transfer from one object to another

higher energy

unstable system examples: - diver in a platform, more likely to fall - a drop of concentrated dye, more likely to disperse - a glucose molecule, more likely to break down Unless something prevents it, each of these systems will move toward greater stability, the diver falls, the solution is uniformly colored, and the glucose molecule is broken down into small molecules.

Energy flow in an open system

work is constant because the system never reaches equilibrium. This system NEVER reaches equilibrium. ex: An open hydroelectric system. Water flowing through a turbine keeps driving the generator because intake and outflow of water keep the system from reaching equilibrium.

Energy flow in an closed system

work is done until the system reaches equilibrium. Once it reaches equilibrium, it is done. ex: Water flowing downhill turns a turbine that drives a generator providing electricity to a light bulb, but only until the system reaches equilibrium.

positive free energy (Gibbs)

ΔG can be positive only when the process involves the absorption of energy during the change from initial state to final state.