Insta-Review
Unit 3
Courtesy of @APBioPenguins
3.1: Enzyme Structure
3.1: Enzyme Structure
ENE-1.D.1
The structure of enzymes includes the active site that specifically interacts with substrate molecules.
ENE-1.D.2
For an enzyme-mediated chemical reaction to occur, the shape and charge of the substrate must be compatible with the active site of the enzyme.
Which macromolecules are enzymes?
Which macromolecules are enzymes?
Why can morphine provide the same response as endorphins?
Why can morphine provide the same response as endorphins?
Morphine and endorphins have a similar molecular shape. Due to this, it binds to the same active site to result in the same response.
Why does the substrate binding activate the enzyme?
Why does the substrate binding activate the enzyme?
What does osmotic pressure mean?
What does osmotic pressure mean?
Pressure from the solute
The more solute, the higher the osmotic pressure.
The less solute, the lower the osmotic pressure.
What is Gibbs free energy and do enzymes affect the Gibbs free energy of a reaction?
What is Gibbs free energy and do enzymes affect the Gibbs free energy of a reaction?
Gibbs free energy is the energy available to do work. If a reaction releases stored energy, it is available for work. (Water falls from a waterfall releases potential energy as it falls and the water turns a turbine).
Enzymes DO NOT AFFECT the Gibbs free energy of a reaction. The reaction must be able to take place with or without the enzyme. The enzyme only makes it faster because the enzyme decreases the activation energy.
What is Gibbs free energy and do enzymes affect the Gibbs free energy of a reaction?
See the Gibbs free energy is the same between the catalyzed and uncatalyzed reaction.
What are plastids?
What are plastids?
Family of organelles… for example: ChloroPLAST
3.2: Enzyme Catalysis
3.2 Enzyme Catalysis
ENE-1.E.1
The structure and function of enzymes contribute to the regulation of biological processes—
a. Enzymes are biological catalysts that
facilitate chemical reactions in cells by
lowering the activation energy.
What is activation energy?
What is activation energy?
The energy required to start the reaction. It is the energy that must be added to get the reactants into their transition state.
How does an enzyme affect activation energy?
How does an enzyme affect activation energy?
Due to lower activation energy, how is the reaction rate affected?
Due to lower activation energy, how is the reaction rate affected?
Due to lower activation energy, how is the reaction rate affected?
Since less activation energy is required, it allows the reaction to occur more frequently. This means that there is an increase in the reaction rate.
3.3 Environmental Impacts of Enzyme Function
ENE-1.F.1
Change to the molecular structure of a
component in an enzymatic system may result in a change of the function or efficiency of the system—
a. Denaturation of an enzyme occurs when the protein structure is disrupted, eliminating the ability to catalyze reactions.
b. Environmental temperatures and pH outside the optimal range for a given enzyme will cause changes to its structure, altering the efficiency with which it catalyzes reactions.
3.3 Environmental Impacts of Enzyme Function
ENE-1.F.2
In some cases, enzyme denaturation is
reversible, allowing the enzyme to regain activity.
ENE-1.G.1
Environmental pH can alter the efficiency of enzyme activity, including through disruption of hydrogen bonds that provide enzyme structure.
ENE-1.G.2
The relative concentrations of substrates
and products determine how efficiently an
enzymatic reaction proceeds.
3.3 Environmental Impacts of Enzyme Function
ENE-1.G.3
Higher environmental temperatures increase the speed of movement of molecules in a solution, increasing the frequency of collisions between enzymes and substrates and therefore increasing the rate of reaction.
ENE-1.G.4
Competitive inhibitor molecules can bind
reversibly or irreversibly to the active site of the enzyme. Noncompetitive inhibitors can bind allosteric sites, changing the activity of the enzyme.
What happens to an enzyme if the temperature increases too high?
What happens to an enzyme if the temperature increases too high?
What happens to an enzyme if the temperature decreases too low?
What happens to an enzyme if the temperature decreases too low?
If the enzyme is denatured…
If the enzyme is denatured…
Recall:
Enzymes increase the reaction rate, but do not affect the Gibbs free energy. This means that the reaction will take place with or without the enzyme present.
If the enzyme is absent/denatures the reaction will still take place, just slower.
Enzymes get consumed by reaction and must be re-added
Enzymes get consumed by reaction and must be re-added
Describe what happens when the enzyme is denatured
Describe what happens when the enzyme is denatured
The secondary structure and up are disrupted.
The bonds between the R groups (tertiary / quaternary) and hydrogen bond between the backbone (secondary) will break, but the peptide bonds (primary) will stay intact.
If the pH increases, why does the enzyme denature?
If the pH increases, why does the enzyme denature?
What is reaction rate?
What is reaction rate?
rate = change in x over time
Reaction rate is the amount of product formed over time. If there is an increase in reaction rate, then there is an increase in product formed over time.
Inhibitor that binds to the active site
Inhibitor that binds to the active site
How does a noncompetitive inhibitor block binding of substrate?
How does a noncompetitive inhibitor block binding of substrate?
As you can see, the competitive inhibitor binds to the same site as the substrate/ligand to block it from binding.
As you can see, the noncompetitive inhibitor causes a conformational change which blocks the substrate/ligand from binding.
Any increase in heat will denature enzyme
Any increase in heat will denature enzyme
What happens with a small increase in temperature?
What happens with a small increase in temperature?
As the temperature increases, the particles will move faster. This increases the kinetic energy of substrate which increases the interactions with the enzyme. As the enzyme has more interactions, it will cause an increase in reaction rate. Also, the increased temperature can provide energy for activation of the reaction.
As pH increases, what happens to the hydrogen ion concentration?
As pH increases, what happens to the hydrogen ion concentration?
During cellular respiration, protons are pumped from the matrix to the intermembrane space. What happens to the pH of the matrix?
During cellular respiration, protons are pumped from the matrix to the intermembrane space. What happens to the pH of the matrix?
How do you overcome a competitive inhibitor?
How do you overcome a competitive inhibitor?
What happens to the reaction rate as the reaction proceeds? Why?
What happens to the reaction rate as the reaction proceeds? Why?
Reaction rate will decrease.
As the reaction proceeds, there is less reactants to bind to the enzyme for the reaction and more products that act as a competitive inhibitor.
3.4 Cellular Energy
ENE-1.H.1
All living systems require constant input of energy.
ENE-1.H.2
Life requires a highly ordered system and does not violate the second law of thermodynamics—
a. Energy input must exceed energy
loss to maintain order and to power
cellular processes.
b. Cellular processes that release energy may be coupled with cellular processes that require energy.
c. Loss of order or energy flow results in death.
3.4 Cellular Energy
ENE-1.H.3
Energy-related pathways in biological systems are sequential to allow for a more controlled and efficient transfer of energy. A product of a reaction in a metabolic pathway is generally the reactant for the subsequent step in the pathway
Which describes an endergonic reaction?
Which describes an endergonic reaction?
Which describes an exergonic reaction?
Which describes an exergonic reaction?
What is energy coupling?
What is energy coupling?
Energy coupling is pairing an exergonic reaction with an endergonic reaction. The exergonic reaction releases the energy that is used to fuel the endergonic reaction.
Example:
Hydrolysis of ATP (exergonic) & move Na against concentration gradient (endergonic)
What is the first law of thermodynamics?
What is the first law of thermodynamics?
Energy cannot be created or destroyed but can be transformed or transferred.
All of the energy on Earth comes from the solar radiation that was released that was released by reactions on sun from its creation. That energy was transformed from stored potential chemical energy to solar energy to heat energy, chemical energy, etc.
Then all of the energy leaves Earth in the form of heat.
What does the second law of thermodynamics state about disorder?
Loss of energy results in…
Loss of energy results in…
What is the function of B in the metabolic pathway?��A 🡪 B 🡪 C
What is the function of B in the metabolic pathway?��A 🡪 B 🡪 C
B is an intermediate. It is the product of the A 🡪 reaction AND the reactant for the B 🡪 C reaction
A 🡪 B 🡪 C 🡪 D��Enzyme B is inhibited. What happens to the concentration of C?
enzyme B
A 🡪 B 🡪 C 🡪 D��Enzyme B is inhibited. What happens to the concentration of C?
enzyme B
3.5 Photosynthesis
ENE-1.I.1
Organisms capture and store energy for use in biological processes—
a. Photosynthesis captures energy from the sun and produces sugars.
i. Photosynthesis first evolved in prokaryotic organisms.
ii. Scientific evidence supports the
claim that prokaryotic (cyanobacterial)
photosynthesis was responsible for the
production of an oxygenated atmosphere.
iii. Prokaryotic photosynthetic pathways
were the foundation of eukaryotic
photosynthesis.
3.5 Photosynthesis
ENE-1.I.2
The light-dependent reactions of photosynthesis in eukaryotes involve a series of coordinated reaction pathways that capture energy present in light to yield ATP and NADPH, which power the production of organic molecules.
ENE-1.J.1
During photosynthesis, chlorophylls absorb
energy from light, boosting electrons to a
higher energy level in photosystems I and II.
3.5 Photosynthesis
ENE-1.J.2
Photosystems I and II are embedded in the
internal membranes of chloroplasts and are connected by the transfer of higher energy electrons through an electron transport chain (ETC).
ENE-1.J.3
When electrons are transferred between
molecules in a sequence of reactions as they pass through the ETC, an electrochemical gradient of protons (hydrogen ions) is established across the internal membrane.
3.5 Photosynthesis
ENE-1.J.4
The formation of the proton gradient is linked to the synthesis of ATP from ADP and inorganic phosphate via ATP synthase.
ENE-1.J.5
The energy captured in the light reactions
and transferred to ATP and NADPH powers
the production of carbohydrates from carbon dioxide in the Calvin cycle, which occurs in the stroma of the chloroplast.
Where did photosynthesis originate?
Where did photosynthesis originate?
Earth included oxygen when it was first formed
Earth included oxygen when it was first formed
What evidence do scientists have to determine when O2 came?
What evidence do scientists have to determine when O2 came?
Iron oxide (rust) layers in the rock layers of fossils
Where was oxygen initially formed?
Where was oxygen initially formed?
Based on endosymbiotic theory, where did chloroplasts come from?
Based on endosymbiotic theory, where did chloroplasts come from?
Engulfed photosynthetic prokaryotes
Which step of photosynthesis stores solar energy as ATP?
Which step of photosynthesis stores solar energy as ATP?
Which step of photosynthesis stores high energy electrons as NADPH?
Which step of photosynthesis stores high energy electrons as NADPH?
Which step of photosynthesis synthesizes G3P?
Which step of photosynthesis synthesizes G3P?
Which step of photosynthesis takes place in stroma?
Which step of photosynthesis takes place in stroma?
Which step of photosynthesis takes place in the thylakoid?
Which step of photosynthesis takes place in the thylakoid?
In a plant cell, where is ATP synthesized?
In a plant cell, where is ATP synthesized?
In the electron transport chain…
Chloroplast has an ETC in the light reactions of the thylakoid.
Mitochondria has an ETC in oxidative phosphorylation on the cristae.
Don’t get tripped up on this type of question. ATP synthesized by mitochondria is for cellular energy vs. ATP synthesized by chloroplast is for synthesis of G3P.
Where do the light reactions take place?
Where do the light reactions take place?
Where does photolysis take place?
Where does photolysis take place?
What is photolysis?
What is photolysis?
The process of using light energy to split a water molecule.
The water molecule is split into oxygen and hydrogen and electrons. These electrons replace the ones that were taken from the reaction center complex.
Describe the flow of electrons through the light reactions.
Describe the flow of electrons through the light reactions.
Electrons are taken from the reaction center complex in Photosystem II, travel down an electron transport chain to Photosystem I, then down another electron transport chain to be stored in NADPH.
Which direction are hydrogen ions pumped for the electron transport chain in photosynthesis?
Which direction are hydrogen ions pumped for the electron transport chain in photosynthesis?
What is synthesized in the light reactions for use in the Calvin Cycle?
What is synthesized in the light reactions for use in the Calvin Cycle?
ATP & NADPH
Where does Calvin Cycle take place?
Where does Calvin Cycle take place?
What are the three steps of the Calvin Cycle?
What are the three steps of the Calvin Cycle?
Carbon fixation
Reduction
Rearrangement
What enzyme used is for carbon fixation?
What enzyme used is for carbon fixation?
How many carbon dioxides are used in the Calvin Cycle?
How many carbon dioxides are used in the Calvin Cycle?
What is the product of the Calvin Cycle?
What is the product of the Calvin Cycle?
How many ATPs and NADPHs are needed for the Calvin Cycle? Where do the extra come from?
How many ATPs and NADPHs are needed for the Calvin Cycle? Where do the extra come from?
9 ATP and 6 NADPH
(6 ATP and 6 NADPH in reduction & 3 ATP in rearrangement)
The extra ATP comes from cyclic electron flow.
What is cyclic electron flow?
What is cyclic electron flow?
Electrons flow from the Photosystem II to Photosystem I through the ETC to facilitate ATP synthesis, then when the electron gains energy in Photosystem I it goes down the ETC between Photosystem II and Photosystem I. It cycles using only the ETC and Photosystem I only.
3.6 Cellular Respiration
ENE-1.K.1
Fermentation and cellular respiration use
energy from biological macromolecules to
produce ATP. Respiration and fermentation are characteristic of all forms of life.
ENE-1.K.2
Cellular respiration in eukaryotes involves
a series of coordinated enzyme-catalyzed
reactions that capture energy from biological macromolecules.
3.6 Cellular Respiration
ENE-1.K.3
The electron transport chain transfers energy from electrons in a series of coupled reactions that establish an electrochemical gradient across membranes—
a. Electron transport chain reactions occur in chloroplasts, mitochondria, and prokaryotic plasma membranes.
b. In cellular respiration, electrons delivered
by NADH and FADH2 are passed to a series of electron acceptors as they move toward the terminal electron acceptor, oxygen. In photosynthesis, the terminal electron acceptor is NADP+. Aerobic prokaryotes use oxygen as a terminal electron acceptor, while anaerobic prokaryotes use other molecules.
3.6 Cellular Respiration
ENE-1.K.3
The electron transport chain transfers energy from electrons in a series of coupled reactions that establish an electrochemical gradient across membranes—
c. The transfer of electrons is accompanied by the formation of a proton gradient across the inner mitochondrial membrane or the internal membrane of chloroplasts, with the membrane(s) separating a region of high proton concentration from a region of low proton concentration. In prokaryotes, the passage of electrons is accompanied by the movement of protons across the plasma membrane.
3.6 Cellular Respiration
ENE-1.K.3
The electron transport chain transfers energy from electrons in a series of coupled reactions that establish an electrochemical gradient across membranes—
d. The flow of protons back through membrane-bound ATP synthase by chemiosmosis drives the formation of ATP from ADP and inorganic phosphate. This is known as oxidative phosphorylation in cellular respiration, and photophosphorylation in photosynthesis.
e. In cellular respiration, decoupling oxidative phosphorylation from electron transport generates heat. This heat can be used by endothermic organisms to regulate body temperature.
3.6 Cellular Respiration
ENE-1.L.1
Glycolysis is a biochemical pathway that
releases energy in glucose to form ATP from ADP and inorganic phosphate, NADH from NAD+, and pyruvate.
ENE-1.L.2
Pyruvate is transported from the cytosol to the mitochondrion, where further oxidation occurs.
3.6 Cellular Respiration
ENE-1.L.3
In the Krebs cycle, carbon dioxide is released from organic intermediates, ATP is synthesized from ADP and inorganic phosphate, and electrons are transferred to the coenzymes NADH and FADH2.
ENE-1.L.4
Electrons extracted in glycolysis and Krebs
cycle reactions are transferred by NADH and FADH2 to the electron transport chain in the inner mitochondrial membrane.
3.6 Cellular Respiration
ENE-1.L.5
When electrons are transferred between
molecules in a sequence of reactions as they pass through the ETC, an electrochemical gradient of protons (hydrogen ions) across the inner mitochondrial membrane is established.
ENE-1.L.6
Fermentation allows glycolysis to proceed in the absence of oxygen and produces organic molecules, including alcohol and lactic acid, as waste products.
ENE-1.L.7
The conversion of ATP to ADP releases energy, which is used to power many metabolic processes.
Which step is anaerobic?
Which step is anaerobic?
Where does glycolysis take place?
Where does glycolysis take place?
How does that prove glycolysis was the first evolved metabolic step?
How does that prove glycolysis was the first evolved metabolic step?
All organisms undergo glycolysis.
Glycolysis takes place in the cytosol and does not require membrane bound organelles. Evolved before the membrane bound organisms since the process does not need it.
Glycolysis does not require oxygen. Pre-historic earth did not have oxygen and so it evolved before oxygen was found in the atmosphere.
Fermentation synthesizes ATP…
Fermentation synthesizes ATP…
What is the function of fermentation?
What is the function of fermentation?
To regenerate the NAD+ that is needed for cellular respiration steps.
NAD+ takes an electron (and a hydrogen) to become reduced. This NADH is the electron shuttle around the steps of Cellular Respiration. If all the NADH is reduced there is no available NAD+ and the processes will halt. Fermentation allows the NADH to offload the electrons (and become oxidized)
Where does Krebs Cycle take place?
Where does Krebs Cycle take place?
Where does the electron transport chain of cellular respiration occur?
Where does the electron transport chain of cellular respiration occur?
ATP is synthesized in the electron transport chain…
ATP is synthesized in the electron transport chain…
If the ETC doesn’t make ATP, what is the function of the electron transport chain?
If the ETC doesn’t make ATP, what is the function of the electron transport chain?
ETC generates the proton gradient that is used in chemiosmosis to synthesize ATP from ADP.
Proton gradient is the concentration gradient of the protons on one side of the membrane resulting in a potential energy that is used to add the terminal phosphate to the ADP molecule.
Which side has the high proton concentration?
Which side has the high proton concentration?
What is the first step of cellular respiration?
What is the first step of cellular respiration?
What is the starting material for glycolysis?
What is the starting material for glycolysis?
Glucose
(NAD+ & ADP)
What are the products of glycolysis?
What are the products of glycolysis?
2 pyruvate
2 ATP
2 NADH
Why is the step of glycolysis important?
Why is the step of glycolysis important?
Provide NADH with high energy electrons to shuttle to the ETC in the mitochondria
Break down glucose into pyruvate for the next step
Substrate level phosphorylation of ATP
What is the second step of cellular respiration?
What is the second step of cellular respiration?
What step occurs between glycolysis and the Krebs cycle?
What step occurs between glycolysis and the Krebs cycle?
Pyruvate oxidation
Where the pyruvate is oxidized (loses electron to NADH) and loses a CO2 then adds a coenzyme to make Acetyl CoA
How many of the 2 carbons from acetyl CoA remain after Krebs Cycle?
How many of the 2 carbons from acetyl CoA remain after Krebs Cycle?
What is the function of the Krebs Cycle?
What is the function of the Krebs Cycle?
To complete the breakdown of “glucose” by releasing the remaining carbons as CO2
Provide more high energy electrons to ETC with NADH and FADH2
Substrate level phosphorylation for ATP
What two parts make up oxidative phosphorylation?
What two parts make up oxidative phosphorylation?
Electron Transport Chain
Chemiosmosis
During ETC, protons are pumped across the cristae. How does the pH in the mitochondria compare?
During ETC, protons are pumped across the cristae. How does the pH in the mitochondria compare?
The pH of the matrix is higher than the pH of the intermembrane space.
The protons are pumped OUT of the matrix INTO the intermembrane space. As the concentration increases in the IM space, pH the decreases.
Which enzyme in the cristae adds the P to ADP?
Which enzyme in the cristae adds the P to ADP?
Which enzyme in the cristae adds the P to ADP?
3.7 Fitness
SYI-3.A.1
Variation at the molecular level provides
organisms with the ability to respond to a
variety of environmental stimuli.
SYI-3.A.2
Variation in the number and types of molecules within cells provides organisms a greater ability to survive and/or reproduce in different environments.
Which pigment would be more favorable in green light?
Which pigment would be more favorable in green light?
Justify your claim that Pigment A (Graph I) is more favorable in green light.
Justify your claim that Pigment A (Graph I) is more favorable in green light.
Pigment A absorbs more light for photosynthesis than Pigment B at green wavelengths.
If you forget to brush your teeth, which bacteria is favorable in your mouth (for them not you)?
If you forget to brush your teeth, which bacteria is favorable in your mouth (for them not you)?
Justify the S. mutans is more favorable in a non-brushed mouth.
Justify the S. mutans is more favorable in a non-brushed mouth.
If you don’t brush your teeth, there is less oxygen (you don’t aerate your teeth). The S. mutans is favorable in an anaerobic environment.