Biothermodynamics Flashcards
Thermodynamics tells us about the transfer of ___ that can occur between __ ___.
energy, living organisms
Energy associated with anything in motion; e.g. a flagella whipping back and forth
kinetic energy
Found in objects that are not moving
potential energy
Potential energy is like ___ energy. It allows the organism to make use of energy from processes like __ __ for use later. In biology potential energy is stored within the __ ___ of molecules such as ___ and ___ stored in the muscles that fuels the body activities
stored, food intake, chemical bonds, glucose, glycogen
____ reactions are spontaneous, and there is a net ___ of free energy to the surroundings. This means the products are more ____ than the reactants. This means there is a ______ gibbs free energy
exergonic, release, stable, negative
____ reactions are non spontaneous, and free energy is ___in from the surroundings. This means that the products are at a ___ energy than the reactants. This means there is a ____ gibbs free energy.
endergonic, absorbed, higher,positive
Non spontaneous can be driven by linking them with ____ __ _____ reactions. For example, during the ___ of ___
energetically favorable spontaneous, breakdown, ATP
ATP is a combination of an ____ base, ____ sugar, and ___ phosphate groups. ATP powers _____ chemical reactions through ____ and ____ energy from exergonic reactions. The bonds between the ___ groups store significant amounts of energy and release it when ____. This is because each phosphate group is ____ charged and close together, making the region ___. By breaking the bonds and releasing the molecules, a more ___ molecule results, and energy is ___. This makes its hydrolysis highly ____ because of how exergonic its breakdown is.
adenosine, ribose, 3, endergonic, harnessing, storing, phosphate, hydrolyzed, negatively, unstable, stable, release, favorable
When ATP is hydrolyzed for energy, it becomes _____. ADP then must undergo ___ to reform ATP. This process is _____.
ADP, phosphorylation, endergonic
ATP can capture and ___ energy from the exergonic reactions of ___ ____. That stored energy can then fuel _____ reactions.
store, oxidative phosphorylation, endergonic
Cell ____ is all an organism’s chemical reaction. It makes the inaccessible __ ___ coming from food into available energy. It is categorized into ___ and ___ pathways, and provides the reactions necessary to produce the ____ every cell needs.
metabolism, stored molecules, catabolic, anabolic, energy
pathways that breakdown complex molecules into simpler ones; tends to be energy releasing, and drives anabolic pathways
catabolic pathway
pathways that use simple substrates to build a complex substrates; energy is consumed
anabolic pathway
States that energy cannot be created or destroyed, only transferred and transformed
first law of thermodynamics
States that the entropy of a closed system increases over time
second law of thermodynamics
In general, as organisms grow and develop, they become more _____. However, they do so by making the ____ more disordered
ordered, disordered
States that as a system approaches absolute zero temperature, entropy reaches a minimum
third law of thermodynamics
Molecules that speed up reactions by lowering the activation energy without being consumed
catalysts
Many reactions in the human body would take __ to be complete. Catalysts are the reason the reactions __ __ and keep up with our bodies. For a molecule to be changed to a product, it must overcome the __ ___, the energy required to break the starting molecule and reach an intermediate form. The ___ the activation energy the more quickly the reaction occurs
years, speed up, activation, lower
Catalysts can stabilize the ____ ___, or provide an __ __ for the reaction. These both lower the activation energy
transition state, alternate pathway
a biological macromolecule that serves as a catalyst to increase the rate of reactions; mostly proteins
enzymes
The reactant or starting molecule that an enzyme acts on
substrate
the location on an enzyme where a substrate binds
active site
formed when enzymes and substrate are bound together by weak interactions
enzyme-substrate complex
Enzymes are _____ to a substrate or a group of related substrates due to their ___, specifically the shape at their __ ____
specific, structures, active sites
and old and outdated model of enzyme binding that says that the active site is exactly made to fit the substrate
lock and key model
The new theory that says the structure of the enzyme molds to the substrate while maintaining specificity
induced fit model
In the induced model, the molding of the enzyme provides a ____ fit of the substrate to the enzyme. This brings the __ __ of the substrate closer together and creates a more ___ environment for the reaction to occur
tighter, chemical groups, favorable
Nonprotein molecules or ions required for an enzyme to function properly; can be permanently or reversibly bound during catalysis
cofactors
Organic cofactors or ____, are composed of ___ and ___ groups. They can further be divided into ______ which bind reversibly to enzymes and __ groups which bind ___ to enzymes. Inorganic cofactors are composed of metal ions such as ____, or ____.
coenzymes, vitamins heme, cosubstrates, prosthetic, covalently, Fe, Mg
First a substrate will bind to an ___ __ of an enzyme. it is held in place via ____ ______ bonds. While the substrate is bound to the active site, the enzymes catalyzes its conversion into a ___ molecule. Enzymes can convert many substrates into many products. Then the product molecule is ______ from the active site and a new substrate will bind
active site, temporary, noncovalent, product, released
Enzymes are not ___ as part of a reaction, thus small amounts of enzymes can dramatically increase reaction rates through __. Enzymes also do not change the __ of a reaction or its ___ __ ___. They only accelerate what would already take place. Almost all enzymes are ___ meaning they are subject to being denatured and losing their function in ___ ___.
consumed, reuse, equilibrium, gibbs free energy, proteins, extreme conditions
____ also known as proenzymes, are the __ ___ to enzymes. Once they are ___ they are turned into an active form that is able to function. For example, the enzyme ______ is usually inactive, but when the pH of the stomach becomes ____, such as when we are preparing to digest food, it is cleaved into the active form called _____, as its __ ___ is removed. It is then able to catalyze the digestion of proteins.
zymogens, inactive precursors, cleaved, pepsinogen, low, pepsin, blocking sequence
RNA molecules that function as enzymes.
ribozymes
Different ___ have different ideal pH’s for the enzymes associated with their function. For example, stomach enzymes like ___ function best at a __ pH. While intestinal enzymes like __ and ____ work best at a higher pH. The further you deviate from the ideal pH of the enzyme, the ___ the rate of the reaction as those enzymes start to ____
organs, pepsin, low, urease, trypsin, lower, denature
As you increase ____ you generally see an increase in reaction rate. This is because the enzyme and substrate molecules have more __ __ and are bouncing around more quickly. This makes it easier for them to ____ with each other and to catalyze the reaction. If the temperature is raised too high, the enzyme will ____,
temperature, kinetic energy, collide, denature
Enzymes in their ___ conditions can ___ into their __ ___, which results in a loss of function
non-optimal, denature, primary structure
is critical to making sure only the reactions we need are occurring.
enzyme regulation
At the genetic level, ___ that produce enzymes can either be __ or ___ depending on the needs of the cell.
genes, disabled activated
At the physical level, enzymes can be stored in _____ to physically ____ it from reactions where we don’t need it. It can be _____ when the cell requires their activity
vesicles, isolate, released
At the enzyme level, enzymes can be ___ from inactive to active forms. They can also be activated or disabled via ___ ____ (for example through _____). They can also be modified by having another molecule bind to them, altering their __ of activity.
cleaved, chemical modification, phosphorylation, level
A form of regulation in which the end product inhibits the process that formed it as it accumulates
negative feedback/feedback inhibition
A negative feedback system provides ___ ___ to stop too much product from being formed. This is the primary way the body maintains ____
automatic regulation, homeostasis
When a product of an enzyme triggers even more of its own production
Positive feedback
A positive feedback loop creates a loop that increases in ____. For example, in labor, the head of the fetus pushes against the ___, stimulating the brain to release ___. This molecule causes the ___ to contract, pushing the fetus further against the cervix, which stimulates the brain to release even more oxytocin
magnitude, cervix, oxytocin, uterus
The maximum rate of a reaction
Vmax
Half of the maximum rate of the reaction
1/2 Vmax
The concentration of the substrate at 1/2Vmax
michaelis constant
Vmax increases as the amount of ___ increases. However, too much substrate and no __ __, means substrate molecules will have to wait for enzymes to free up from their ____. This means the increase in reaction rate will taper off.
substrate, free enzymes, saturation
Km is inversely proportional to the __ ___ of the enzyme to the substrate. If km is low, it means the enzyme binds to the substrate very ___. That means in order to reach 1/2Vmax, we do not need a lot of ___. When Km is high, it means that enzyme and substrate do not bind very easily, and in order to reach the 1/2Vmax, we need a higher ___ concentration. Km can only be changed with the use of __ ____. This is because Km is an ____ property
binding affinity, easily, substrate, substrate, certain inhibitors, intrinsic
__ ___ is when a substance binds to the active site of the enzyme, preventing the substrate is bound. this is ____. They do not change ____, because by increasing the concentration of substrate, the presence of the competitive inhibitors can be ____, and the maximum rate of the reaction can be increased. However they increase the ___ by interfering with the binding of the substrate. They tend to be similar in ___ to the substrate
competitive inhibition, reversible, Vmax, overcome, Km, structure
in _____ _____ the substance inhibits the action of an enzymes by binding to it at a location other than the active site. This lowers _____, because increasing the amount of substrate does not change the enzyme effectiveness. It also has no impact on ____, because it doesn’t effect the ability of the substrate to bind to the enzyme
non-competitive inhibition, Vmax, Km
___ ____ occurs when a substance binds to the enzyme and induces the enzyme’s inactive form. __ ___ occurs when the substance binds and induces the enzyme’s active form. This happens at a site other than the __ ___. Allosteric inhibition can be ____, where binding results in an __ __ in the active site, or directly blocks the substrate binding, and it can also be______.
allosteric inhibition, allosteric activation, active site, competitive, induced changed, noncompetitive
In ___ ___, one substrate attachment makes other substrates attach more easily to other active sites. The more substrate is present, the more _____ the enzyme can bind it.
positive cooperativity, effectively
In __ ___, after the first substrate attaches, the enzyme alters to make additional attachment difficult
negative cooperativity
Non enzyme proteins that bind to molecules can also show cooperativity, for example with ____ and ___.
hemoglobin, oxygen
