Ap Bio Unit 3: Cellular Energetics
I’m cooked (this is from AJ’s study guide)
Enzymes
Within almost all biochemical reactions, the rate at which the reactions take place are majorly affected by the presence of an enzyme.
Enzyme: a biological catalyst that speeds up the rate of biochemical reactions
Most cells have a specific concentration of enzymes within them
Most enzymes end in the letters “-ase” (like that of ATPase)
Almost every chemical reaction involves an enzyme and without enzymes, most of those chemical reactions wouldn’t even happen in the first place
In case you don’t remember, a catalyst is not chemically changed after a reaction occurs
This means that enzymes (or catalysts in general) can be used over and over again to help speed up the rate of the reaction
We call any reactions (from an individual step of an entire reaction mechanism to the overall reaction mechanism itself) enzyme-mediated reactions
A reaction mechanism just refers to the combination of all of the smaller steps in a chemical reaction (which you might’ve learned in a Chemistry course)
Note that most enzymes are proteins; which is a super important detail due to the complexity of protein structure
Remember, the tertiary structure of an individual protein determines what types of substances can interact with it; and this is true for enzymes as well
An enzyme will interact with other molecules in a biochemical reaction at the enzyme’s active site: a physical location on the enzyme where the reactants go to
We call the reactants that interact with the enzyme the substrates
When the substrate comes into contact with the active site of an enzyme, it forms an enzyme-substrate complex
The shape and charge of the substrate should be compatible to the active site of the enzyme
Because enzymes are proteins, they also have to follow the idea of “lock-and-key” for protein interactions
Enzymes can help speed up the rate of the synthesis or decomposition molecules
Those new molecules are typically used in another step of the chemical reaction
Just like all chemical reactions, biochemical reactions require some initial starting energy for the reaction to take place.
Activation energy (Ea): the amount of energy needed for a chemical reaction to take place
The moment in the reaction that has the highest amount of (free) energy is known as the transition state of the reaction
Before the transition state is reached, the reaction needs to have sufficient energy to occur, and after the transition state occurs the rest of the reaction will proceed
Even though all reactions need activation energy, the overall chemical reaction can either have a net gain (absorption) of energy or a net loss (release) of energy
Most chemical reactions that release energy overall need less activation energy compared to reactions that gain energy overall
Enzymes, just like all catalysts, lower the activation energy of a (bio)chemical reaction
Having a lower activation energy means that more of the individual particles in a chemical reaction have sufficient energy to proceed with the reaction
The amount of energy needed for a reaction to proceed is equal to the activation energy
Environmental Impacts on Enzyme Function
The individual behavior of enzymes, and proteins in general, can change due to the changes in the environment; changing their complex structure.
Remember, the denaturation of proteins means that a particular protein, like an enzyme, is unable to serve its original purpose
Some changes in the environment that could lead to denaturation include changes in temperature and pH
Denaturation is usually irreversible, but not always
For enzymes (or proteins in general), there are certain conditions that are considered to be optimal for the efficiency of enzyme activity.
The optimal conditions for an enzyme allows for the enzyme-mediated reactions to occur at the fastest rate possible
When an optimal condition is changed to a different value, the rate of the enzyme-mediate reaction will decrease
The optimal conditions for an enzyme are a specific value, but being within a close enough interval to the optimal conditions won’t change the rate of the reaction too much
Changing temperature will change the rate of the reaction, and each individual enzyme has its own specific optimal temperature.
As you start from absolute zero and increase the temperature, the rate of the reaction increases because it allows for more movement and collisions and the molecular level; which includes the frequency of the enzyme-substrate complex forming through random collisions
The rate of the reaction starts to decrease once you increase the temperature past the optimal temperature of the particular enzyme-mediated reaction, and the enzyme starts to denaturate
Note that going from a higher temperature to a lower temperature will not denaturate an enzyme (but it likely won’t be able to “fix” an already denatured one)
There is also an optimal pH for the environment of the enzyme to work under optimal conditions.
pH is a measure of the concentration of Hydrogen ions (H+) within a solution, where pH=-log(H+)
Smaller pH values have a higher concentration of Hydrogen ions
Decreasing pH by 1 means that there are 10 times more Hydrogen ions
The optimal pH level is the pH level that allows the enzyme-mediated reactions to occur at the fastest rate possible
Increasing or decreasing pH (from the optimal pH) will not only decrease the rate of the reaction, but also cause denaturation at the extreme ends of the pH scale
Changing the concentration of the reactants / substates, the products, and the enzymes of an enzyme-mediated reaction can also increase the rate of the reaction.
Generally, increasing the concentration of the substrates will increase the rate of the reaction because more products can be formed due to the random collisions being more frequent
However, when there is too much substrate; the rate of the reaction will no longer increase
This is because the rate at which enzymes can form enzyme-substrate complexes with the reactants can only increase up to a point where there won’t be enough enzymes to change the reactants simultaneously
Having too much product molecules within the system where a reaction takes place will eventually slow down the rate of reaction
This is because those products take up space, making it harder for random collisions to occur between the enzymes and the substrates
Being able to dispose of the products out of the system would ensure this wouldn’t cause the rate of reaction to slow down
Increasing the concentration of enzymes also increases the chances for random collisions to occur between the substrates and the enzyme, increasing the rate of the reaction because of it
However, if there isn’t enough substrate for all of the enzymes to be used, adding more enzymes wouldn’t increase the rate of the reaction because all of the reactants got used up
When there is an excess amount of substrate, increasing the concentration of the enzymes allows more of the substrates to form enzyme-substrate complexes which increases the rate of the reaction
Certain molecules can bind to parts of an enzyme causing the enzyme to no longer bind to the substrate and speed up the rate of the reaction. Some of these types of molecules don’t need to come into direct contact with the active site of an enzyme.
Inhibitor: a molecule that, when attached to an enzyme, makes the active site of the enzyme inaccessible to its specific substrate
The presence of inhibitors, in general, lowers the overall rate of the reaction
However, if the concentration of inhibitors are insignificant to the concentration of the substrate and enzymes, there will be very little effect on the rate of the reaction because the inhibitors can’t make all of the enzymes’ active sites inaccessible
Competitive inhibitors are directly bound to the active site of the enzyme, taking up the physical space that the substrate would have taken
The competitive inhibitor has to have a similar shape and size to that of the substrate it is blocking access to the enzyme
We say that it “competes” with the substrate of the enzyme for the active site of the enzyme
Noncompetitive inhibitors are not bound to the active site of the enzyme, but are instead bound to their specific region on the enzyme known as the allosteric site
Once a noncompetitive inhibitor is bound to the allosteric site, the active site of the enzyme changes shape and the enzyme loses function (decreasing the rate of the reaction)
The effects of some inhibitors can be undone, while others are irreversible
If an inhibitor is reversible, the removal of the inhibitor allows the enzyme to regain its function
Activator molecules are also able to give back the enzyme’s function by reopening up the active site of the enzyme
If an inhibitor is part of the overall chemical pathway (where it is a product that decreases the rate of a previous step in the pathway), the inhibitor is known as a feedback inhibitor
Feedback inhibitors (indirectly) control the rate of the reaction in which they themselves are produced because they are part of the chemical pathway
Cellular Energy
In all living organisms, some input of energy is required for them to survive. Usually, that energy comes in the form of sunlight.
Autotrophs are able to produce energy on their own by taking in the molecules from the environment
Most autotrophs capture energy from the sun (to be used in photosynthesis), but there are some other autotrophs that are able to take in energy from other physical or chemical sources
Any energy that is not used up or wasted by the autotroph (during its life through heat or excrement) will usually be consumed by a heterotroph
Note that all energy transfer, in and outside of the biological world, has to follow the laws of thermodynamics.
The first law of thermodynamics states that energy cannot be created, not destroyed (so all energy has to come from something)
The second law of thermodynamics states that all energy transfer has to increase the amount of disorder in the universe (known as entropy)
A substance that can take up more possible states, like liquids and gases that are able to move around more freely at the molecular level than that of solids, have a higher entropy because they have more disorder
For anything to live, there must be a constant flow of energy
The flow of energy specific to the energy transfer of living organisms is known as bioenergetics
No living organism will be at equilibrium (because they would die if they were), and there should be a constant flow of materials in and out of a cell / organism for it to survive
There has to be a large enough input of energy for an organism to survive (which is the amount of energy is used during its cellular functions)
Multiple chemical reactions that happen in direct succession of one another forms a chemical pathway. We can use chemical pathways to allow for individual chemical reactions that would not have originally occurred to happen anyways.
Chemical pathway: a collection of chemical reactions, where the product of a previous chemical reaction serves as the reactants of the next one
All of the chemical pathways in an organism is referred to the metabolism of the organism
Faster metabolism means that the rate of the reactions in the organism happen quicker than that of a slower metabolism
Free energy: energy within a system that is readily available to do work
Systems prefer to have less free energy compared to having more free energy
We tend to denote free energy with the letter G (for Gibbs free energy), and the change in Gibbs free energy as G=GF-GI; where GF and GI is the Gibbs free energy of the system in the final and initial states (after and before the reaction)
A chemical reaction is favorable / spontaneous if the free energy of the products is less than that of the reactants
Favorable reactions have a G<0
Reactions are more favorable at higher temperatures as well as when the change in heat energy of the system is negative, and the change in entropy of the system is positive
Catabolic reactions / pathways are reactions / pathways that involve the breaking of a larger molecule into smaller ones which release energy and is considered to be favorable
For example, ATP turning into ADP and a phosphate group releases energy
ATP isn’t extremely abundant in most organisms because it is relatively unstable and will break down when not immediately used (so it is only made on demand)
Chemical reactions that increase in free energy going from the reactants to the products are known as unfavorable / nonspontaneous reactions
Unfavorable reactions have a G>0
Reactions are less favorable at lower temperatures as well as when the change in heat energy of the system is positive, and the change in the entropy of the system is negative
Anabolic reactions / pathways are reactions / pathways that involve the formation of a larger molecule from smaller ones, taking in energy to form new bonds, and is considered to be unfavorable
For example, ADP and a phosphate group joining together to form ATP absorbs energy
Unfavorable reactions will not occur on their own because a system would never want to gain energy
However, we can join a favorable reaction with an unfavorable reaction in a chemical pathway so that the unfavorable reaction occurs and then the favorable reaction will decrease the amount of free energy that was greater than what was gained through the unfavorable reaction
Chaining an unfavorable reaction to a favorable one like this is known as energy coupling
The existence of chemical pathways allows for the individual chemical reactions to be controlled (more specifically, the rates in which they occur) and be energy efficient
Photosynthesis
As mentioned in previously, living organisms need to use some form of energy to survive. The most common way organisms produce their own energy is through photosynthesis.
Photosynthesis: the chemical pathway where sugar molecules (Glucose) are synthesized using Carbon Dioxide, Water, and light energy
Photosynthesis originally evolved within prokaryotic organisms, and is also the most likely explanation for the abundance of Oxygen in the atmosphere
Light in both the form of a wave and a particle (a photon) contain energy, but it’s usually in the state of a photon when the energy of light is being used
Other organisms might undergo chemosynthesis: the production of glucose molecules without sunlight
Photosynthesis (equation): 6CO2+12H2OC6H12O6+6O2+6H2O
You might see this equation written in a way where the water molecules on the reactant side is 6 instead of 12 and an absence of product water molecules, but the given chemical equation is more “true” to the actual process of photosynthesis
You might also see “light energy” written above the reaction arrow to denote that light energy is involved in the reaction (or you might also see it as a reactant)
Photosynthesis involves some reactions that are dependent on light energy, while some of the reactions are independent of the light energy to proceed
Within photosynthesis, the light-dependent reactions occur before the light-independent reactions.
The light-dependent reactions need light energy to proceed
The light-dependent reactions use up Water molecules and light energy of the overall pathway of photosynthesis
All light-dependent reactions happen in the chloroplast, more specifically: the thylakoids (which are stacked on top of each other in the form of grana)
They get the light energy through pigments: types of molecules that absorb light energy
A common type of pigment is chlorophyll, found in plants which give it that green color
Plants, and other organisms, have accessory pigments: pigments that are not the main pigment that help in the collection of light energy
Chlorophyll absorbs mostly red and blue wavelengths of light and reflects green wavelengths of light (which is why we see it as green)
Special types of integral proteins known as photosystems (PS) contain the chlorophyll in the chloroplast
There are 2 photosystems; labelled as photosystem I and photosystem II
PSI uses the electrons from the light-energy from the sun, while PSII feeds electrons into PSI from the breakage of water molecules (where 12H2O24H++24e-+6O2)
The protons (H+) are used to create an electrochemical gradient around the chloroplast
The movement of protons in the electrochemical gradient is known as the electron transport chain (ETC)
ETC occurs in chloroplasts, mitochondria, and the plasma membranes of prokaryotic organisms
Pigments also allow for the transformation of light energy to chemical energy
Chlorophyll captures light energy from the sun and turns it into the form of high-energy electrons; these highly energized electrons help reduce NADP+ into NADPH
This chemical energy is temporarily stored in the form of NADPH; a type of carrier molecule (which carries the proton, H+ from one reaction to another)
Most ETC’s exist because of the presence of carrier molecules
Light-dependent reactions help in the formation of ATP
ATP synthase is the enzyme that helps forms ATP as the protons in the ETC pass through it in a process known as photophosphorylation (which is just the formation of ATP in photosynthesis)
Both ATP and NADPH are later used in another reaction in the overall pathway of photosynthesis
After the light-dependent reactions, the ATP and NADPH are used within the light-independent reactions: the Calvin cycle.
The light-independent reactions form the overall chemical pathway known as the Calvin cycle and are not directly dependent on light energy to occur
Occurs in the stroma of the chloroplast
Note that the Calvin cycle is part of photosynthesis, even if it is also a chemical pathway
Within the Calvin cycle, Carbon atoms (from absorbed Carbon Dioxides in the environment) are fixated (joined / bounded to) the organic molecules to form carbohydrates
The Calvin cycle uses ATP, NADPH, and CO2 to produce carbohydrates: primarily, Glucose
NADPH and ATP will be turned into NADP+ and ADP (with an inorganic phosphate group) respectively, which are primarily recycled back for the light-dependent reactions of photosynthesis
Cellular Respiration
For all organisms, both prokaryotes and eukaryotes, the synthesis of ATP is through a chemical pathway known as cellular respiration.
Cellular respiration are present in all living organisms
The presence of Oxygen determines which type of cellular respiration is undergone in an organism
Cellular respiration: the chemical pathway that allows for the release of chemical energy from organic molecules, like that of glucose
Most glucose molecules are made in the process known as photosynthesis, as discussed in “Cellular Energy”
Cellular respiration stores that chemical energy in a final product known as ATP
As I’m sure you’ve seen by now, ATP is pretty important: being used in pretty much every single chemical reaction within a living organism as its source of metabolic energy
Aerobic cellular respiration: cellular respiration that involves Oxygen
Anaerobic cellular respiration: cellular respiration that does not involve Oxygen
The net gain or loss of a Carbon atom in any molecule is related to the donation of a Carbon atom from Carbon Dioxide or the formation of a Carbon Dioxide molecule
In both aerobic and anaerobic cellular respiration, the process begins with glycolysis: the process in which glucose (usually from photosynthesis) is broken down into pyruvate
Glycolysis occurs in the cytoplasm
Glycolysis uses NAD+ as a carrier molecule to be reduced in the form of NADH+H+ to temporarily store chemical energy
You might also see NADH+H+ written as just NADH2 (with or without that subscript 2)
Pyruvate (a molecule with 3 Carbon atoms (along with some other stuff that isn’t too important)) is then used in both aerobic and anaerobic cellular respiration
Two pyruvate molecules are formed during glycolysis
Pyruvate is then transported from the cytosol into the mitochondria for aerobic cellular respiration, but stays in the cytosol for anaerobic cellular respiration
Within aerobic cellular respiration, additional chemical reactions form other chemical pathways such as the oxidation of pyruvate, the Krebs cycle, and oxidative phosphorylation, all of which occur in the mitochondria of the cell.
Pyruvate oxidation uses that pyruvate to form a compound known as acetyl CoA, which undergoes the Krebs cycle
Pyruvate enters the outer mitochondrial membrane and passes into the matrix of the mitochondria
NAD+ and NADH+H+ are both used in the oxidation of pyruvate as the carrier molecules
The Krebs cycle turns that acetyl CoA into citrate (which is why you might also see the Krebs cycle be called the Critic Acid cycle) within th matrix of the mitochondria
That CoA is recycled as acetyl CoA turns into citrate
Coenzyme A (CoA) is used to transfer the electrons to allow for another occurrence of the oxidation of pyruvate in the inner mitochondrial membrane
The Krebs cycle uses both NAD+ and FAD (where FAD turns into FADH2) as the carrier molecules
The Citric Acid is used and recycled within the Krebs cycle itself and won’t be used within the oxidation of pyruvate
A bit of ATP is made within the Krebs cycle, but it isn’t too significant to the overall production of ATP
Some Carbon Dioxide is also made in the Krebs cycle
Finally, the process known as oxidative phosphorylation uses those additional carrier molecules (the NADH+H+ and the FADH2 molecules) in the production of a lot of ATP
NADH+H+ and FADH2 both lose 2 protons (and 2 electrons) as they pass through integral membrane proteins in their oxidation reactions
The now free-floating protons contribute to the ETC to pass through the ATP synthase and form more ATP by binding ADP and a Phosphate group together
The protons move through the ATP synthase because there is a higher concentration of Hydrogen ions outside of the cristae of the mitochondria and a lower concentration inside of the cristae, so they have to pass through the ATP synthase (because the rest of the cristae (other than the integral membrane proteins that separated them) does not allow the transfer of protons)
We refer to the movement of H+ down this gradient, leading to the production of ATP, as chemiosmosis
The electrons are also part of the ETC, where the energy of the electrons, along with the proteins that allow for the ETC to take place in general, help couple together more reactions
Both the movement of electrons and protons contribute to the ETC, but only protons contribute to the electrochemical gradient
The ETC is used to transfer energy from electrons to the proton’s concentration gradient
Oxygen is used as a molecule to accept the electrons and become reduced while the electron carrier molecules are being oxidized
Decoupling the process of oxidative phosphorylation generates heat
This is because the proton’s concentration gradients store heat, and decoupling the overall pathway means that the gradient isn’t used to produce ATP
This allows endothermic organisms to intentionally regulate the temperature of the body
Not all environments include Oxygen, and not all cells are able to aerobically respirate. Instead, anaerobic cellular respiration has to take place for those organisms / cells to survive.
Fermentation: the process of turning pyruvate into lactic acid and ethanol while producing ATP without any Oxygen
One of the pyruvates turns into lactate (which usually ends up in the form of lactic acid), while the other turns into ethanol
Instead of Oxygen, the pyruvate molecules accept the electrons to turn into lactate and ethanol so that the electron carrier molecules can be recycled
The ATP production from fermentation comes from the formation lactic acid, where the electron carrier molecules are recycled and are able to undergo glycolysis again
No new ATP is made in fermentation, it’s just that it allows for glycolysis to repeat itself and make more ATP that way
Note that even aerobically cellular respirating organisms can undergo anaerobic cellular respiration, it’s just a lot less efficient than that of aerobic cellular respiration
Some organisms don’t make enough ATP under just anaerobic cellular respiration, so even though they can do it; they would die doing so
Obligate anaerobes are forced to undergo anaerobic cellular respiration (where Oxygen would kill them)
Facultative anaerobes are not forced to undergo anaerobic cellular respiration and can do either anaerobic or aerobic cellular respiration
Aerobic cellular respiration is preferred because it produced much more ATP overall