BISC 1111 Group Activity 4

Membrane potential

• the voltage across a membrane

• voltage is created by differences in the distribution of positive and negative ions across a membrane

• the inside of the cell is negative in charge relative to the outside, favoring passive transport of cations into and anions out of the cell

Electrochemical gradient

• two combines forces that drive the diffusion of ions across a membrane

• a chemical force (the ion’s concnetration gradient)

• an electrical force (the effect of the membrane potential on the ion’s movement) 

• an ion diffuses down its electrochemical gradient

Electrogenic pumps

• a transport protein that generates voltage across a membrane, storing energy that can be used for cellular work

• the main electrogenic pump differs between plants and animals

• animals use sodium-potassium pumps

• Plants, fungi, and bacteria use proton pumps, which actively transports hydrogen ions out of the cell

Cotransporter

• coupled the movement of H+ back down its concentration gradient to the active transport of sucrose into the cell

• this is how plants load sucrose into their veins for transport around the plant body

Receptor-mediated endocytosis

• vesicle formation is triggered by solute binding to receptors

• receptor proteins bound to specific solutes from the extracellular fluid are clustered in coated pits that form coated vesicles

• emptied receptors are recycled to the plasma membrane by the same vesicle

LDL (low density lipoprotein)

• delivers lipid molecules to cells from the liver

• involved in atherosclerosis, a process in which it is oxidized within the walls of arteries forming plaques

HDL (high density lipoprotein)

• unlike the larger lipoprotein particles, which deliver fat molecules to cells, HDL particles remove fat molecules from cells & blood stream and deliver them to the liver

Chylomicrons

• transport lipids absorbed from the intestine to adipose, cardiac, and skeletal muscle tissue, where their triglyceride components are hydrolyzed by the activity of the lipoprotein lipase, allowing the release free fatty acids to be absorbed by the tissues

• when a large portion of the triglyceride core has been hydrolyzed, chylomicron remnants are formed and are taken up by the liver, thereby transferring dietary fat to the liver

metabolism

the totality of an organism’s chemical reactions

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

Anabolic pathways

• consumer energy to build complex molecules from simpler ones (“uphill”)

  • ex. the synthesis of protein from amino acids is an anabolic pathway

Catabolic pathway

• release energy by breaking down complex molecules into simpler compounds (“downhill”)

  • ex. cellular respiration, the breakdown of glucose in the presence of O2

energy

the capacity to cause change, can be used to do work—move matter against opposing forces, such as gravity and friction

kinetic energy

energy associated with motion

thermal energy

the kinetic energy associated with random movement of atoms or molecules

Potential energy

energy that matter possesses because of its location or structure

Chemical energy

potential energy available for release in a chemical reaction

Energy transformations

• chemical energy from food is used to perform the work of climbing up to a diving platform

• the kinetic energy of muscle movements 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

The first law of thermodynamics

• the energy of the universe is constant

  • this means that energy can be transferred and transformed, but it cannot be created or destroyed

  • the first law is also called the principle of conservation of energy

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 of the universe

Entropy

• a measure of molecular disorder, or randomness

  • may decrease in a particular system, such as an organism, as long as the total entropy of the system and surroundings increases

Spontaneous processes

occur without energy input; they can happen quickly or slowly

• increase the entropy of the universe

• spontaneous means that a reaction is energetically favorable, not that it will occur rapidly

Nonspontaneous processes

decrease entropy; they require an input of energy

Biological order

• cells create ordered structures from less organized starting materials

• the increase in order within living systems is balanced by the catabolic breakdown of organized forms of matter, releasing heat and small molecules

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 cel

• change in free energy during a reaction is related to temperature and changed in enthalpy and entropy

ΔG

• can be used to determine whether a process is spontaneous or not

• negative for all spontaneous processes

  • spontaneous decreases free energy—can be harnessed by the cell to perform work

  • system loses free energy and becomes more stable

• positive for nonspontaneous processes

  • nonspontaneous increases free energy

• represents the different between free energy of the final state and free energy of the initial state

Equilibrium

• the point at which forward and reverse reactions occur at the same rate, describes a state of maximum stability

• systems never spontaneously move away from this

• process is spontaneous and can perform work only when it is moving towards this

Exergonic reaction (“energy outward”)

• proceeds with a net release of free energy to the surroundings

• products store less free energy than the reactants

• ΔG is negative

  • because of this, these reactions occur spontaneously

• breaking bonds requires energy, not releases—potential energy is released when bonds are formed after the original bonds break

Endergonic reaction (“energy inward”)

• absorbs free energy from the surroundings

• products store more free energy than the reactants

• ΔG is positive

  • reactions are nonspontaneous

• ex. photosynthesis—this reaction is powered by converting light energy to chemical energy

Closed systems

• reactions, such as an isolated hydroelectric system, eventually reach equilibrium and can then do no work

Open systems (living things)

• chemical reactions of metabolism are reversible, but never reach equilibrium in a living cell

• more apt analogy.

  • a catabolic pathway in a cell releases free energy in a series of reactions

    • ex. cellular respiration, reactions are “pulled” in one direction because the products of each reaction are the reactants in the next step

    • steady inflow of glucose and release of waste products ensures that equilibrium is never reached

Transport work

pumping substances across membranes against the direction of spontaneous movement

• nearly always powered by ATP hydrolysis

Mechanical work

beating cilia or contracting muscle cells

• nearly always powered by ATP hydrolysis

Chemical work

pushing endergonic reactions

ATP powers cellular work

• cells manage energy resources to do work through energy coupling, the use of an exergonic process to drive an endergonic one

• most energy coupling in cells is mediated by ATP

ATP (adenosine triphosphate)

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

• in addition to energy coupling, ATP functions as one of the nucleoside triphosphates used to make RNA

ATP hydrolysis

• energy is released from ATP when the terminal phosphate bond is broken by hydrolysis, the addition of a water molecule

• the energy does not come directly from the phosphate bonds, but from the chemical change to a state of lower free energy in the products

• causes a change in protein shape and binding ability

Phosphorylation

• transfer of a phosphate group form ATP to another molecule, is typically used to power endergonic reactions

Phosphorylated intermediate

• recipient molecule of phosphorylation

• is more reactive (less stable, with more free energy) than the original molecule

ATP regeneration

• ATP is regenerated by addition of a phosphate group to adenosine diphosphate (ADP)

• free energy needed to phosphorylate ADP comes from exergonic breakdown reactions (catabolism)

• the shuttling of inorganic phosphate and energy is called the ATP cycle; it couples energy-yielding processes to energy-consuming ones

Catalyst

chemical agent that speeds up a reaction without being consued by the reaction

Enzyme

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

Activation energy (EA)

the initial energy needed to break the bonds of the reactants

• heat in the form of thermal energy absorbed from the surroundings often supplies this

• molecules become unstable when enough energy is absorbed to break bonds; this is the transition state

• as atoms settle into new, more stable bonds, energy is released to the surroundings

• in an exergonic reaction, the formation of new bonds releases more energy than was invested in breaking the old bonds

Activation energy barrier

• provides a barrier that determines the rate of spontaneous reactions

• for some reactions, EA is low enough that thermal energy a room temperature is sufficient enough to overcome the activation barrier

• most reactions have high EA, and need additional energy (usually heat) to reach the transition state

Free energy diagrams

How enzymes speed up reactions

• adding heat not useful because it denatures proteins

• heat speeds up all reactions—not just ones needed

• instead organisms carry out catalysis

Catalysis

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

• enzyme catalyzes a reaction by lowering the EA barrier enough for the reaction to occur at moderate temperatures

• an enzymes cannot change ΔG; it only speeds up a reaction that would eventually occur anyways

Substrate

the reactant that an enzyme acts on

Enzyme-substrate complex

forms from the enzyme binding to its substrate

• each enzyme catalyzes a specific reaction and can recognize its specific substrate among even closely related compounds

Active site

the region on the enzyme, often a pocket or groove, that binds to the substrate

• when the substrate enters the active site, the enzyme changes shape slightly, tightening around the substrate like a handshake

induced fit

results from interactions between chemical groups on the substrate and the active sit

Catalysis in the enzyme’s active site 

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

• rate of enzyme-catalyzed reaction can be sped up by increasing substrate concentration

Saturated enzyme

• when all enzyme molecules have their active sited engaged

  • if the enzyme is saturated, the reaction rate can only be sped up by adding more enzyme

Effects of temperature on enzymes

• each enzyme has an optimal temperature at which it catalyzes its reaction at the maximum possible rate

• up to this point, the reaction rate increases with increasing temperature; beyond this point the rate of reaction begins to drop

Effects of pH on enzymes

• each enzyme has an optimal pH that is dependent on the environment in which it is typically active

  • ex. the optimal pH for pepsin—a human stomach enzyme—is 2, whereas the optimal pH for trypsin—an intestinal enzyme—is 8

Cofactors

• are nonprotein helpers that bind to the enzyme permanently, or reversibly with the substrate

  • inorganic cofactors include metal atoms such as zinc, iron, and copper ionic form

Coenzymes

organic cofactors

Competitive inhibition

• competitive inhibitors closely resemble 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

Noncompetitive inhibition

• noncompetitive inhibitors 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

• noncompetitive inhibitors bind to the enzyme regardless of whether the substrate is attached yet; the inhibitor can EITHER bind to the enzyme or the enzyme-substrate complex

Regulation of enzymes helps control metabolism

• chemical chaos would result 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

Allosteric regulation of enzymes

• occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site

• most of these enzymes are made from polypeptide subunits, each with its own active site

• the complex oscillates between two shapes, one catalytically active and the other inactive

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

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

Localization of enzymes

• compartmentalization of the cell helps to bring order to metabolic pathways

• in some cases, the enzymes for several steps in a metabolic pathway form a multienzyme complex

• some enzymes have fixed locations an act as structural components of particular membranes