totality of an organism's chemical reactions; an emergent property of life that arises from interactions between molecules within the orderly environment of the cell
begins with a specific molecule which is then altered in a series of defined steps, resulting in a certain product
'breakdown pathways'; release energy by breaking down complex molecules to simpler compounds
consume energy to build complicated molecules rom simpler ones; sometimes called biosynthetic pathways
the study of how energy flows through living organisms
the capacity to cause change; can be used to do work; ability to arrange a collection of matter
energy associated with relative motion of objects
kinetic energy associated with the random movement of atoms or molecules
energy that matter possesses because of its location or structure
a term used by biologists to refer to the potential energy available for release in a chemical reaction
the study of the energy transformations that occur in a collection of matter
the matter under study
the rest of the universe--everything outside of the system
unable to exchange either energy or matter with its surroundings
energy and matter can be transferred between the system and its surroundings
first law of thermodynamics
the energy of the universe is constant; energy can be transferred and transformed, but it cannot be created or destroyed; known as the principle of conservation of energy
a measure of disorder or randomness
second law of thermodynamics
the more randomly arranged a collection of matter is, the greater its entropy; every energy transfer or transformation increases the entropy of the universe
used to explain a process that can occur without the input of 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
proceeds with a net release of free energy; G is negative; occur spontaneously; the greater the decrease in G, the more work can be done; cellular respiration is an example
absorbs free energy from its surroundings; G is positive; non spontaneous reaction; magnitude of G is the quantity of energy required to drive the reaction
the use of an exergonic process to drive an endergonic one
contains the sugar ribose, with the nitrogenous base adenine and a chain of 3 phosphate groups bond to it
describes the recipient of the phosphate group; forms intermediate which is more reactive than the original unphosphorylated molecule
a macromolecule that acts as a catalyst
a chemical agent that speeds up a reaction without being consumed by the reaction
the energy required to contort the reactant molecules so the bonds can break; the initial investment of energy for starting a reaction; the amount of energy needed to push the reactants over an energy barrier or hill so that the "downhill" part of the reaction can begin
a pocket or groove on the surface of the protein where catalysis occurs
brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction; enzyme changes its shape slightly so that the active site fits even more snugly around the substrate
nonprotein helpers for catalytic activity, required by enzymes; may be bound tightly to the enzyme as permanent residents or may bind loosely and reversibly along with the substrate; zinc, copper, iron in ionic form=inorganic cofactors
cofactor is an organic molecule; vitamins
reduce the productivity of enzymes by blocking substrates from entering active sites
do not directly compete with the substrate to bind to the enzyme at the active site; they impede enzymatic reactions by binding to another part of the enzyme; causes the enzyme molecule to change its shape so that the active site becomes less effective in catalyzing the conversion of substrate to product
term used to describe any case in which a protein's function at one site is affected by the binding of a regulatory molecule to a separate site; may result in either inhibition or stimulation of an enzyme's activity
amplifies the response of enzymes to substrates; one substrate molecule primes an enzyme to accept additional substrate molecules more readily; substrate molecule causing induced fit in one subunit can trigger the same favorable shape change in all other subunits of the enzyme
a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway; occurs when ATP allosterically inhibits an enzyme in an ATP-generating pathway; common method of metabolic control; prevents cell from wasting chemical resources by making more isoleucine than is necessary
cellular respiration is catabolic or anabolic??
is protein synthesis from amino acids anabolic or catabolic?
open system bc they absorb energy and release heat
are organisms open systems or isolated systems and why?
some energy becomes unusable energy (unable to do work); a lot of unusable energy is converted to heat so organisms can't recycle it
why can't organisms recycle their energy since energy cannot be destroyed?
it can only be put to work when there is a temperature difference that results in heat flowing from a warmer location to a cooler one; if temperature is uniform (like in a living cell) then the only use is to make a body of matter warm
when is heat usable energy?
when there is a loss of usable energy during transfer or transformation, the universe becomes more disordered=entropy
what happens when there is a loss of usable energy?
no it means that a process can occur without an input of energy (water flowing downhill); this increases entropy
does spontaneous mean quickly?
cells are ordered--not random; they created ordered structures from less organized starting materials; they can increase their order as long as the order of their surroundings decreases
are cells/organisms considered random or not?
defined a function called the Gibbs free energy of a system--symbolized by letter G
who was J. Willard Gibbs?
the change in free energy= the change in the system's enthalpy - the temperature(the change in the system's entropy)
how is the change in free energy calculated?
we can predict whether it will be spontaneous (w/o input of energy from outside)
what is so great about knowing the value of the change in free energy?
if it has a negative change in G it is spontaneous so H must decrease or TS must increase or both; therefore every spontaneous process decreases the system's free energy
how do we know if it is spontaneous or not?
it equals the difference between the free energy of the final state and the free energy in the initial state
what else does the change in G equal?
unstable stems have a higher G and tend to change to more stable (lower G)
which is more stable, higher G or lower G?
a drop of dye is less stable (higher G) when it is spread randomly through the liquid= more likely to disperse
how does that G and stability relate to diffusion?
the free energy of the mixture of reactants and products decreases=equilibrium; when a reaction is pushed away from equilibrium there is an increase in free energy
explain the relationship between free energy and equilibrium/chemical equilibrium
no, any change from the equilibrium will have a positive G=not spontaneous; process is spontaneous and can perform work when its moving toward equilibrium
do systems ever spontaneously move away from equilibrium?
based on their free energy changes!
how are chemical reactions classified as endergonic or exergonic?
it is dead since systems at equilibrium are at a minimum of G and can do no work
what happens when a cell reaches metabolic equilibrium?
as long as our cells have a steady supply of glucose/other fuels and oxygen and are able to expel waste products to surroundings, their metabolic pathways never reach equilibrium--they can continue to do work of life
do our cells ever reach equilibrium?
are organisms open or isolated systems?
chemical work, transport work, and mechanical work
what kinds of work does a cell do?
pushing of endergonic reactions (won't occur spontaneously) ex=synthesis of polymers from monomers
pumping of substances across membranes against the direction of spontaneous movement
physical movement; ex=beating of cilia, contraction of muscle cells, movement of chromosomes during cellular respiration
ATP--acts as source of energy that powers cellular work
what is responsible for most energy coupling in cells?
bonds between the phosphate groups of ATP are broken by hydrolysis; one phosphate leaves ATP and becomes an inorganic phosphate; what is left= ADP; it is an exergonic reaction
how is ADP created?
yes--it comes from the chemical change to a state of lower free energy
is there a release of energy during the hydrolysis of ATP?
the energy it releases on losing a phosphate group is greater than the energy that most other molecules could deliver
why is ATP useful to the cell?
it is used to perform cellular work--chemical, transport, and mechanical
what do cell's use the energy released during ATP hydrolysis for?
if the change in free energy of an endergonic reaction is less than the amount of energy released by ATP hydrolysis the two reactions can be coupled so that the overall reactions are exergonic
how is the cell able to use the energy released by ATP hydrolysis to drive chemical reactions that are endergonic?
it is the formation of the phosphorylated intermediate=more reactive and less stable than the original unphosphorylated molecule
what is the key to coupling exergonic and endergonic reactions?
it comes from the exergonic breakdown of reactions in the cell
where does the free energy come from thats required to phosphorylate ADP?
this couples the cell's exergonic processes to the endergonic ones; moves at a REALLY fast pace
yes because ATP formation from ADP and inorganic phosphate are not spontaneous so free energy must be spent; the energy for the endergonic process of making ATP is provided by catabolic pathways
is free energy spent to make ATP formation occur?
the summit is when the reactants are in an unstable condition known as the transition state--they are activated and their bonds can be broken
what is the summit of the graph of the reaction?
when the molecules have absorbed enough energy to become unstable to enter the transition state; this absorption of energy increases the speed of the reactant molecules so they collide more often and more forcefully
when do the bonds of the reactants break?
yes it speeds it by allowing reactants to attain the transition state more often
does heat speed a reaction?
it lowers the activation energy barrier which enables the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures; it cant change the >G for a reaction and it can't make an endergonic reaction exergonic; they can only make reactions that would happen anyway, happen quicker=dynamic metabolism; they determine which chemical processes will go on in the cell at any particular time
how does an enzyme catalyze a reaction?
the catalytic action of the enzyme converts the substrate to the product of the reaction
what happens while the enzyme and substrate are joined?
the substrate is held in it by weak interactions, such as hydrogen or ionic bonds; the R groups of the amino acids that make up the active site catalyze the conversion of substrate to product and then the product departs from the active site and the enzyme can take in another substrate molecule into its active site
what happens at the active site?
1) the active site provides a template where the substrates can come together in the proper orientation for a reaction to occur between them 2) the active site clutches the bound substrates and may stretch the substrate molecules toward the transition-state form stressing the bonds that must be broken during the reaction 3) active site may provide a microenvironment that is more conducive to a particular type of reaction that the solution itself would be without the enzyme 4) the direct participation of the active site in the chemical reaction
what are the mechanisms that an enzyme uses to lower activation energy and speed up a reaction?
they access the active sites of the enzyme molecules more frequently but eventually there is a limit to how fast the reaction can be pushed by adding more substrate to an enzyme--substrate concentration will eventually be high enough that all enzyme molecules have their active sites engaged=saturated
what happens when there are more substrate molecules available?
it is affected by general environment factors like temperature and pH as well as chemicals that specifically influence that enzyme
what is the activity of an enzyme affected by?
favor the most active shape for the enzyme molecules; each enzyme works better under particular conditions; temperature and pH are important factors; has an optimal temp when its reaction rate is greatest--allows greatest # of molecular collisions and fastest conversion of reactants to product molecules; also has pH which it is most active
they change an enzyme's shape and the functioning of its active site by binding to a site elsewhere on the molecule by non covalent interactions
how do molecules that naturally regulate enzyme activity in a cell behave?
two or more subunits, each composed of a polypeptide chain and its own active site; the entire complex oscilates between two different shapes, one is catalytically active and the other is catalytically inactive
what are most enzymes that are allosterically regulated constructed from?
when binded to a regulatory site it stabilizes the shape that has functional active sites
binding of an inhibitor stabilizes the inactive form of the enzyme
the shape change in one subunit is transmitted to all others; a single activator or inhibitor molecule that binds to one regulatory site will affect the active sites of all subunits
what happens to the other subunits when the shape changes of one subunit in an allosteric reaction?
hemoglobin is made up of four subunits which each have an oxygen-binding site; in oxygen-deprived tissues hemoglobin will be less likely to bind oxygen and release it where it is needed; at higher oxygen levels, the protein will have an affinity for oxygen as more binding sites are filled
how is hemoglobin an example of cooperativity?
no different organelles store different enzymes; the matrix contains enzymes in solution that are involved in one stage of cellular respiration where as enzymes for another stage of cellular respiration are embedded in the inner membrane of the cristae
are enzymes stored in the same organelle?