AP Biology Chapter 8*** Flashcards
Metabolism is an _____ _____ of life that arises from orderly interactions between molecules
emergent property
what is a major pathway of catabolism?
cellular respiration…in which the sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water
metabolism as a whole manages the ____ and ____ ____ of the cell
- material
- energy resources
what is an example of anabolism?
the synthesis of an amino acid from simpler molecules
true or false: energy released from downhill reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways
TRUE
what is energy used for
can be used for doing work..that is, to move matter against opposing forces, such as gravity and friction
how can moving objects perform work?
by imparting motion to other matter
what is an isolated system?
is unable to exchange either energy or matter with its surroundings
what is a open system?
energy and matter can be transferred between the system and its surroundings
are organisms open or isolated systems?
open systems..they absorb energy
during every energy transfer or transformation, some energy becomes ______
unavailable to do work…more usable forms of energy are at least partly converted to heat, which is the energy associated with the random motion of atoms or molecules
when a bear eats a salmon what happens with this energy?
some energy ( a small amount) converts into the motion of the brown bear and most of it is lost as heat, which dissipates rapidly through the surroundings
a system can put heat to work only when….
there is a temp difference that results in the heat flowing from a warmer location to a cooler one…
if temp is uniform (like in a cell) then the only use for heat energy generated during a chemical reaction is to warm a body of matter, such as an organism
a logical consequence of the loss of usable energy during energy transfer or transformation is….
that each such event makes the universe more disordered
how can a process occur on its own without outside help?
it must increase the entropy of the universe
a process that cannot occur on its own is called….
nonspontaneous
true or false? cells create ordered structures from less organized starting materials
true
how can the entropy of a particular system decrease?
when the total entropy of the universe increases
—thus organisms are islands of low entropy in an increasingly random universe
what is another name for free energy?
gibbs free energy
what is the equation to find the change in free energy
G= free energy H=enthalpy T=temp in Kelvin (K= C + 273) S=change in entropy (delta)G= (delta)H - T* (delta)S
if the result of the free energy equation results in a negative G what does this mean?
What if it results in a positive G?
- means spontaneous
+ means nonspontaneous
every spontaneous process decreases the system’s ___ ____, and processes that have a positive or zero (delta)G are never _____
- free energy
2. spontaneous
we can think of free energy as….
a measure of a system’s instability-its tendency to change to a more stable state
a higher S means…
a lower S means…
- stable systems
1. unstable systems
as a reaction proceeds toward equilibrium…
the free energy decreases
any change from the equilibrium position will have a _____ G and will not be _____
- positive
2. spontaneous
because a system at equilibrium cannot spontaneously change, it can do no….
work
a process is ____ and can perform work only when it is moving towards equilibrium
spontaneous
what does the delta G for an exergonic reaction mean?
the max amount of work the reaction can perform
delta G is ____ for exergonic reactions
negative
the greater the decrease in ____, the greater the amount of ___ that can be done
- free energy
2. work
the phrase “energy stored in bonds” is shorthand for …
the potential energy that can be released when new bonds are formed after the original bonds break…as long as the products are of lower free energy than the reactants
delta G is ____ for endergonic reactions
positive…this reaction is nonspontaneous and the magnitude of G is the quantity of energy required to drive the reaction
true or false: the fact that metabolism never reaches equilibrium is a defining feature of life
true
how is the cell never at equilibrium?
constant flow of materials in and out of the cell keeps the metabolic pathways from ever reaching equilibrium
a cell does 3 main kinds of work:
- chemical work- 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- such as the beating of cilia, contraction of muscle cells, and the movement of chromosomes during cellular reproduction
what is ATP responsible for?
mediating most energy coupling in cells, and in most cases it acts as immediate source of energy that powers cellular work
-also makes RNA
what is the structure of ATP
contains the sugar ribose, with the nitrogenous base adenine and a chain of 3 phosphate groups bonded to it
how can the bonds between the groups of ATP be broken down
by hydrolysis
the phosphate bonds of ATP are sometimes referred to as high energy phosphate bonds…what does high energy mean
the reactants (ATP and water..when it comes to hydryolysis) themselves have high energy relative to the enrgy of the products (ADP and inorganic phosphate)
why is ATP useful to the cell?
the energy it releases on losing a phosphate group is somewhat greater than the energy most other molecules could deliver
when ATP is hydrolyzed the release of free energy does what
heat up its surroundings
when ATP releases energy what do proteins do with this energy?
they harness it in several ways to perform the three types of cellular work- chemical, transport, and mechanical
if the G of an endergonic reaction is less than the amount of energy released by ATP hydrolysis, then the 2 reactions can be ….
coupled so that overall, the coupled reactions are exergonic…this usually involves the transfer of a phosphate group from ATP to some other molecule, such as the reactant….the recipient of the phosphate group is called the PHOSPHORYLATED INTERMEDIATE
____ and ___ are also nearly always powered by the hydrolysis of ATP
- transport
2. mechanical work
true or false: an organism at work uses ATP continuously, but ATP is not a renewable resource that can be regenerated by the addition of phosphate to ADP
false; take out the work not
what is the ATP cycle
energy released by breakdown reactions in the cell is used to phosphorylate ADP, regenerating ATP. Chemical potential energy stored in ATP drives most cellular work
is the ATP formation from ADP and an inorganic molecule spontaneous?
no it is not spontaneous
every chemical reaction between molecules involves both ____ and _____
bond breaking and bond forming
changing one molecule into another generally involves…
contorting the starting molecule into a highly unstable state before the reaction can proceed
how do bonds reach the contorted state?
reactant molecules must absorb energy from their surroudings…when the new bonds of the product molecule form, energy is released as heat, and the molecules return to stable shapes with lower energy than the contorted state
activation energy is often supplied in the form of ….
thermal energy…this is what reactant molecules absorb from the surroundings
what does the absorption of thermal energy do?
accelerates the reactant molecules, so they collide more often and more forcefully…also agitates the atoms within the molecules, making the breakage of bonds more likely
what is the transition state?
when the molecules have absorbed enough energy for the bonds to break and the reactants are in an unstable condition
as atoms settle into their new, more stable bonding arrangements…
energy is released to the surroundings
heat speeds a reaction by….
allowing reactants to attain the transitions state more often..BUT THIS SOLUTION WOULD BE INAPPROPRIATE FOR BIOLOGICAL SYSTEMS…
how is “heat speeding up a reaction” inappropriate for cells?
high temp denatures proteins and kills cells…also heat would speed up ALL reactions, not just those needed
what do organisms use instead of heat to speed up reactions?
catalysis
an enzyme catalyzes a reaction by…
lowering the Ea (activation energy) barrier, enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temps
can an enzyme change the G for a reaction?
can it make an endergonic reaction exergonic?
No and NO
Enzymes can only ___ reactions that would eventually occur anyway….
- hasten
…but this function makes it possible for the cell to have a dynamic metabolism, routing chemicals through the cell’s metabolic pathways
while enzyme and substrate are joined, the catalytic action of the enzyme converts the substrate…
to the product of the reaction
the active site is formed by…
only a few of the enzyme’s amino acids, with the rest of the protein providing framework that determines the configuration of the active site
only ___ of the enzyme molecule actually binds to the substrate
a restricted region
do enzymes have a fit shape that doesn’t change?
no it does not. a subtle change can occur and this is only to fit more snugly around the substrate
what is the process of enzymes working with substrates?
in most enzymatic reactions, the substrate is held in the active site by weak interactions, such as hydrogen bonds and ionic bonds. R groups of a few of the amino acids that make up the active site catalyze the conversion of the substrate to product, and the product departs from the active site. the enzyme is then free to go to another substrate.
true or false: all metabolic reactions are not reversible
false; most are reversible and an enzyme can catalyze either the forward or the reverse reaction, depending on which direction has a negative G
what are the mechanisms enzymes use to lower activation energy and speed up a reaction
- in reactions involving 2 or 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 that must be broken during the reaction…because activation energy is proportional to the difficulty of breaking of the bonds, distorting the substrate helps it approach the transition state and thus reduces the amount of free energy that must be absorbed to achieve that state
- active site may also provide a microenvironment that is more conductive to a particular type of reaction than the solution itself would be without the enzyme
- the direct participation of the active site 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. next steps of the reaction restore the side chains to their original states, so that the active site is the same after the reaction as it was before
saturated
when the substrate concentration is so high that each enzyme will have their active sites occupied
what is the activity of an enzyme affected by?
the general environment factors such as temp and pH..also by chemicals that specifically influence that enzyme
UP TO A POINT, the rate of enzymatic reaction increases with ____ temperature
why?
increasing
..partly because substrates collide with active sites more frequently when the molecules move rapidly. after that certain point though 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
what is the optimal pH level for most enzymes?
pH level 6-8
the cofactors of some enzymes are….
inorganic
if the inhibitor attaches to the enzyme by ____ ____, inhibition is usually _____
- covalent bonding
2. irreversible
many enzyme inhibitors bind to the enzyme by ____ _____, in which case inhibition is _____
- weak interactions
2. reversible
how can inhibition be overcome?
by increasing the concentration of substrate so that as active sites become available, more substrate molecules than inhibitor molecules are around to gain entry to active sites
the interaction between noncompetitive inhibitors, enzymes, and substrates causes the enzyme molecule to …
change its shape in such a way that the active site becomes less effective at catalyzing the conversion of substrate to product
true or false; toxins and poisons are often irreversible competitive inhibitors
true
what do regulatory molecules do?
change an enzyme’s shape and the functioning its active site by binding to a site elsewhere on the molecule
most enzymes known to be allosterically regulated are constructed from…
two or more subunits..each composed of a polypeptide chain with its own active site…the entire complex oscillates between two different shapes, one catalytically active and the other inactive
in the simplest kind of allosteric regulation, an activating or inhibiting regulatory molecule binds to..
a regulatory site (sometimes called allosteric site)..often located where subunits join
the binding of an activator to a regulatory site….
the binding of an inhibitor to a regulatory site….
- stabilizes the shape that has functional active sites
2. the inactive form of an enzyme
a single inhibitor or activator molecule that binds to one regulatory site will…
affect the active sites of all subunits
a substrate molecule binding to one active site in the multisubunit enzyme triggers…
a shape change in all the subunits, thereby increasing catalytic activity at the other active sites
true or false: although allosteric regulation is probably quite widespread, relatively few of the many known metabolic enzymes have been shown to be regulated in this way.
true
why are allosteric regulatory molecules hard to characterize?
they tend to bind the enzyme at low affinity and are therefore hard to isolate
when ATP allosterically inhibits an enzyme in an ATP generating pathway.. the result is….
feedback inhibition a common mode of metabolic control.. when a metabolic pathway is closed off
Talk about the R groups
the interaction of r groups determines the structure and function of the proteins, they are coded for by DNA which makes RNA which assembles the proteins
enzymes are specific because of the shape, which is determined by
the sequence of amino acids.
The primary structure of the amino acids ultimately determines the tertiary structure of the proteins
quick note
delta G and delta H always have to same sign (+ or -)
What does it mean if G is positive, negative, or zero
G has to be negative for a spontaneous process, G at zero or positive is never spontaneous
what does G, T, S, and H mean in the equation…
delta G= delta H - (T* delta S)
G- Free energy
T- temp
S- Entropy
H- enthalpy
cellular respiration is exergonic or endergonic
exergonic
what does cellular respiration do?
breaks down glucose to H2O and CO2 and ATP
how do enzymes lower activation energy
- they put stress on the bonds on the substrate so theyre easier to break
- The active site has a different environment than the cytoplasm. Different pH for example will help break the bonds.
- puts stress on the bonds through environmental factors within the active site, that weaken it and makes it easier to break
True or false: when some noncompetitive inhibitors attach to the site, they can permanently alter the shape of the enzyme so it no longer works
true
for the equation delta G= delta H - (T* delta S)…what does it mean if the free energy (G) of the products is less than the reactants’ free energy? exergonic or endergonic?
exergonic
for the equation delta G= delta H - (T* delta S)…what does it mean if delta G is negative?
it means the reaction doesn’t need a lot of or any energy at all to react…or spontaneous
for the equation delta G= delta H - (T* delta S)…what does it mean if the free energy (G) of the products is greater than the reactants’ free energy? exergonic or endergonic?
endergonic
for the equation delta G= delta H - (T* delta S)…what does it mean if delta G is positive?
endergonic…it means the reaction needs energy to react
does ATP use coupling?
yes!
what is phosphorylation?
adding a phosphate group to a molecule to make it unstable
what are characteristics of enzymes?
- made of amino acids
- lock and key
- active site and allosteric site (made by tertiary structure)
- regulated by factors in environment…denatured
- not used up
- induced fit
- lowers activation energy
example of anabolic?
photosynthesis and making polypeptides
is negative feedback the same as feedback inhibition?
yes
coenzymes are (vitamin/minerals) cofactors are (vitamins/minerals)
- vitamin
- mineral
