BackExam 3 Core Concepts in General Biology: Metabolism, Cellular Respiration, and Photosynthesis
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Chapter 8: Metabolism and Energy Transformations
Overview of Metabolism
Metabolism encompasses all chemical reactions that occur within living organisms to maintain life; the totality of an organism’s chemical reactions.
These reactions are organized into metabolic pathways, which can be classified as either anabolic (building up) or catabolic (breaking down).
Metabolic Pathways: begins with a specific molecule and ends with a product
Catabolism: The breakdown of complex molecules into simpler ones, releasing energy.
Anabolism: The synthesis of complex molecules from simpler ones, requiring energy input.
Example: Cellular respiration is a catabolic pathway; photosynthesis is an anabolic pathway.
Types of Systems
An isolated (closed) system, doesn’t exchange energy with the environment outside of its system.
E.g. such as that approximated by liquid in a thermos, is isolated from its surroundings.
In an open system, energy and matter can be transferred (exchanged) between the system and its surroundings.
All living things and organisms are open systems.
Thermodynamics in Biology
Thermodynamics: the study of energy transformations. The first law states that energy cannot be created or destroyed, only transformed.
First Law of Thermodynamics (law of conservation of energy): The energy of the universe is constant; the amount of energy doesn't change. Energy can be transferred and transformed, but it cannot be created or destroyed.
Entropy (S): A measure of disorder; biological processes tend to increase entropy.
During energy transformations (like when cells convert glucose to ATP), some energy is always lost as heat, increasing the disorder of the surroundings.
Second Law of Thermodynamics: every energy transfer or transformation increases the entropy of the universe.
This means that no energy transformation is 100% efficient—some energy will always become more disordered (higher entropy).
Energy: the capacity to cause change or the ability to do work.
Free Energy Change (): Determines whether a reaction is spontaneous.
Free Energy (G): is energy that can do work
Equation:
The change in free energy (ΔG) during a process is related to the change in enthalpy, or change in total energy (ΔH), change in entropy (ΔS), and temperature in Kelvin (T).
If ΔG is negative, free energy is released.
If ΔG is positive, free energy is consumed.
Exergonic: proceeds with a net release of free energy and is spontaneous.
Exergonic reactions release energy (); increase entropy
You subtract the products from the reactants which gives a negative number.
catabolism
Endergonic: reactions consume free energy energy (+ΔG)
Endergonic reactions require energy (); entropy decreases.
you subtract the products from the reactants which gives a positive number
anabolism
ATP: The Energy Currency
Adenosine triphosphate (ATP) is the primary energy carrier in cells, used to power various cellular processes; the cell's rechargeable battery
ATP Structure: Composed of adenine, ribose, and 3-phosphate groups.
ATP Hydrolysis: Releases energy by converting ATP to ADP and inorganic phosphate.
o When the bond between one of the phosphate groups of ATP’s tail is broken, it releases one of the phosphate groups and energy.
ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP).
Equation:
Enzymes and Regulation
Enzymes are biological catalysts that speed up chemical reactions by lowering activation energy.
How they work:
They work by lowering the activation energy () needed for a reaction to start. This makes reactions happen faster!
Enzymes have a special region called the active site where the substrate (reactant) binds.
The enzyme and substrate fit together (like a "lock and key" or "induced fit"), helping the reaction occur more easily.
After the reaction, the enzyme releases the product and is ready to catalyze another reaction.
Key points:
Enzymes do not change the overall free energy () of the reaction.
They only make reactions faster by lowering the activation energy barrier
Activation Energy (free energy of activation) (EA): The energy required to start a chemical reaction.
often supplied in the form of heat that reactant molecules absorb from their surroundings.
Enzymes EA Barrier: Enzymes catalyze reactions by lowering the EA barrier.
Enzymes speed up chemical reactions by lowering the activation energy needed for that chemical reaction to happen.
Enzymes do not affect the change in free energy (ΔG)
Catalysis in the Enzyme’s Active Site: The active site can lower an EA (activation energy) barrier by:
Orienting substrates correctly
Straining substrate bonds
Providing a favorable microenvironment
Covalently bonding to the substrate
The way that an active site lowers the activation energy depends on that specific enzyme; different enzymes work in different ways.
Enzyme Activity: Influenced by temperature, pH, and substrate concentration.
Cofactors: nonprotein enzyme helpers
inorganic or organic (coenzyme)
Active Site: The region on the enzyme where substrates bind.
Inhibitors: Competitive inhibitors bind to the active site; noncompetitive inhibitors bind elsewhere, altering enzyme function by changing its shape.
our bodies don't make them; we're exposed to them.
Allosteric enzyme: an enzyme that changes shape all on its own.
It changes shape between an on state and off state
On state: the active site is exposed, so it can turn substrates into products.
Off state: the active site is not exposed, so it can’t turn substrates into products.
Allosteric Inhibitor: inhibits the enzyme by holding it in the off state.
Allosteric Activator: activates the enzyme by holding it in the on state.
Feedback Inhibition: End product of a pathway inhibits an earlier step, regulating metabolic flow; the end product shuts down the pathway..
prevents the cell from wasting time and energy.
The end product feeds back and is an allosteric inhibitor for the 1st enzyme (it turns it off).
The thing that is being made turns off the thing that is making it.
Energy Coupling
Cells couple exergonic and endergonic reactions to efficiently manage energy resources.
Energy Coupling: The use of energy released from exergonic reactions to drive endergonic reactions.
Example: ATP hydrolysis powers active transport across membranes.
Chapter 9: Cellular Respiration and Fermentation
Redox Reactions and Electron Carriers
Cellular respiration involves a series of redox reactions, where electrons are transferred from one molecule to another.
Redox reactions: chemical reactions that transfer electrons between reactants
Oxidation: Loss of electrons; the less free energy it stores
Reduction: Gain of electrons; the more free energy it stores
Reducing agent: the electron donor
Oxidizing agent: the electron receptor
Some redox reactions don’t transfer electrons but change the electron sharing in covalent bonds
OIL RIG — Oxidation Is Loss, Reduction Is Gain (of electrons)
Electrons have a negative electrical charge, so if you add electrons, the number gets smaller
Cellular "Batteries"
Dead | Charged |
|---|---|
ADP | ATP |
GDP | GTP |
Electron Carrier Batteries
Dead (oxidized) | Charged (reduced) |
|---|---|
NAD+ | NADH |
FAD | FADH2 |
NAD+: An electron carrier that becomes NADH when reduced.
NADH then carries these high-energy electrons to the electron transport chain, where they are used to make ATP.
Stages of Cellular Respiration (Total: 32 ATP)
Aerobic cellular respiration occurs in three main stages: glycolysis, pyruvate oxidation (minor), the citric acid cycle, and oxidative phosphorylation.
1) Glycolysis: Occurs in the cytoplasm; breaks glucose (6-carbon) into 2 pyruvate (3-carbon), producing ATP and NADH.
Has 2 major phases: energy investment and energy payoff
Energy Investment (1-5): you start with one molecule of glucose and spend 2 ATP
Energy Payoff (6-10): yield NADH and ATP.
10 enzyme-catalyzed reactions
requires no CO2 or O2
Products of Glycolysis: 2 NET ATP (you spend 2 to make 4 which results in a NET of 2), 2 NADH, 2 pyruvate per glucose.
1.5) Pyruvate Oxidation: Occurs in mitochondrial matrix; transforms the pyruvate into Acetyl CoA.
this step is carried out by a multienzyme that catalyzes 3 reactions.
During Pyruvate Oxidation, you’ll break off 1 of the carbons from the other 2 carbons. This broken off carbon has 2 oxygens attached to it (or 2 carbon dioxides). This is the 1st time that CO2 has been released (as waste that we breathe out) in this reaction. Since you took a 3-carbon molecule and broke it apart into a 2-carbon molecule and a carbon (CO2), it is catabolic. Meaning that the reaction is exergonic, it’s going to release energy. That released energy is going to be captured through energy coupling and it’s going to be used to charge 2 NADH (the electron carrier batteries). Then using the 2 leftover carbon molecules, they will be combined with coenzyme A (CoA), to form 2 Acetyl CoA.
Products of Pyruvate Oxidation: 2 NADH, 2 Acetyl CoA, and 2 CO2 (waste)
2) Citric Acid Cycle: Occurs in mitochondrial matrix; completes glucose breakdown, generating NADH and FADH2.
Acetyl CoA ( 2-carbon) joins the cycle by combining with oxaloacetate (4-carbon), forming citrate (6-carbon).
The next 7 steps decompose the citrate back to oxaloacetate, making the process a cycle.
Since we’re breaking citrate down into oxaloacetate, it releases energy (exergonic) that charges up the batteries NADH, FADH2, and ATP using GTP
8 reactions
Products of the Citric Acid Cycle: 6 NADH, 2 FADH2, 2 ATP, 4 CO2 (waste)
3) Oxidative Phosphorylation: Uses electron transport chain and chemiosmosis to produce most ATP.
In the electron transport chain, NADH gives their electrons away to the dead battery NAD+ and FADH2 to FAD.
Electrons pass through the chain, release an energy, and that energy is used in the end to make ATP
Electrons drop in free energy as they go down the chain.
The energy released causes proteins to pump H+ from the mitochondrial matrix to the intermembrane space.
Electrons are finally passed to O2 forming H2O; Oxygen is the final electron acceptor of the electron transport chain
ATP Synthase: H+ then moves back across the membrane, passing through the proton.
lets hydrogen ions flow from the high concentration in the intermembrane space to the low concentration in the matrix. But when they flow through this protein (which is a source of energy), the protein spins like a turbine taking ADP (2-phosphate) and another phosphate to turn it into ATP.
ATP synthase uses the exergonic flow of H+ to drive phosphorylation of ATP.
Chemiosmosis: the use of energy in a H+ gradient to drive cellular work.
These reduced electron carriers are going to give away there energy by giving away their electrons to the proteins of the electron transport chain that are embedded in the inner membrane of the mitochondria.
The electron transport chain is going to transport the electrons from one protein to the next, and as they’re being passed, they’re releasing energy that is used for active transport to pump protons from a low concentration in the matrix to a high concentration in the intermembrane space.
In the end, the electrons go to oxygen and combine with hydrogen ions to create water.
o Oxygen is the final electron acceptor of the electron transport chain. So, you need oxygen in the matrix.
Now, there’s a lot of hydrogen ions in the intermembrane space but a few in the matrix. To fix that, the protons will use the ATP Synthase (protein) to cross back to the low concentration side.
When the protons flow through this protein, it causes a phosphate to attach to an ADP, which creates ATP.
Products of Oxidative Phosphorylation: 28 ATP
Aerobic Cellular Respiration (Big Picture)
During cellular respiration, most energy flows in this sequence:
Glucose to NADH to Electron Transport Chain to Proton-Motive Force to ATP
Making 32 ATP per Glucose
Substrate-Level Phosphorylation: a way cells make ATP directly by transferring a phosphate group from a phosphorylated substrate to ADP (uses an enzyme)
This process does not require oxygen or the electron transport chain
It happens inside the cytoplasm during glycolysis and in the mitochondrial matrix during the citric acid cycle (Krebs cycle).
Oxidative phosphorylation accounts for about 28 of the ATP generated by cellular respiration.
Substrate-level phosphorylation (used during glycolysis and the citric acid cycle) accounts for only 4 of the ATP generated by cellular respiration.
When is it used?
During glycolysis (in the cytoplasm)
During the citric acid cycle (in the mitochondria)
Fermentation (the purpose is to reoxidize the electron carrier, by reducing either pyruvate to ace. to ethanol, or pyruvate to lactid acid)
Fermentation allows cells to produce ATP without oxygen by regenerating NAD+.
Fermentation consists of glycolysis plus reactions that regenerate NAD+ (is needed to keep doing glycolysis over and over again), which can be reused by glycolysis.
Alcohol Fermentation: Converts pyruvate to ethanol and CO2.
occurs in 2 steps.
you take glucose and then do the process of glycolysis to turn it into pyruvate. You also turn 2 NAD+ into 2 NADH, and charge up 2 Net ATP.
Input: 1 glucose, Output 2 ATP, Waste 2 CO2 and 2 Ethanol
Lactic Acid Fermentation: Converts pyruvate to lactate.
Pyruvate is reduced to NADH, forming lactate.
The whole point of lactic acid fermentation is to oxidize NADH into NAD+ so that glycolysis can continuously repeat to make more ATP.
Input 1 glucose, Output: 2 NET ATP, Waste: 2 lactate
humans can do lactic acid fermentation as a supplement to gain a bit more energy.
Location: Both occur in the cytoplasm.
Only 2 ATP per glucose is produced (in the glycolysis)
Obligate anaerobes carry out fermentation and cannot survive in the presence of O2.
Yeast and many bacteria are facultative anaerobes, meaning that they can survive using either fermentation or cellular respiration.
Alcohol fermentation and lactic acid fermentation are both anaerobic processes (they occur without oxygen).
Their main function is to regenerate NAD+ from NADH, allowing glycolysis to continue and produce ATP when oxygen is not available.
Alcohol fermentation:
Occurs in yeast and some bacteria.
Converts pyruvate into ethanol and CO2.
Regenerates NAD+ so glycolysis can keep going.
Lactic acid fermentation:
Occurs in muscle cells and some bacteria.
Converts pyruvate into lactic acid (lactate).
Also regenerates NAD+ for glycolysis.
Summary:Both types of fermentation allow cells to keep making ATP by glycolysis when oxygen is not available, by recycling NAD+!
Important!!!
No matter what type of organism you are, you’re going to start with glucose and do glycolysis to make pyruvate.
Then if you have access to oxygen, you’re going to do aerobic cellular respiration using the mitochondria to get 32 ATP per glucose molecule.
However, if you don’t have access to oxygen, you’re going to do fermentation (after glycolysis) using the cytoplasm to get 2 ATP per glucose molecule.
For all of these processes, glucose comes from photosynthesis.
Electron Transport Chain and Chemiosmosis
The electron transport chain (ETC) is a series of protein complexes in the inner mitochondrial membrane that transfer electrons and pump protons to create a gradient.
ATP Synthase: Uses the proton gradient to synthesize ATP from ADP and Pi.
Equation:
Comparing Fermentation and Cellular Respiration
Process | Oxygen Required | ATP Yield (per glucose) | End Products |
|---|---|---|---|
Cellular Respiration | Yes | ~30-32 | CO2, H2O |
Alcohol Fermentation | No | 2 | Ethanol, CO2 |
Lactic Acid Fermentation | No | 2 | Lactate |
Chapter 10: Photosynthesis
Overview of Photosynthesis
Photosynthesis is the process by which plants, algae, and some bacteria convert light energy into chemical energy stored in glucose.
Location: Occurs in chloroplasts, primarily in the leaves.
Calvin Cycle: The set of light-independent reactions that synthesize glucose from CO2.
ATP Synthase: Also present in chloroplasts, producing ATP during photosynthesis.
located in the thylakoid membrane of the chloroplast
Light Reactions
Light reactions capture solar energy and convert it into chemical energy (ATP and NADPH).
ATP and NADPH are produced on the side facing the stroma
In summary, light reactions generate ATP and increase the potential energy of electrons by moving them from H2O to NADPH
Occurs in the thylakoids
Inputs: Light, water, ADP, NADP+
Outputs: Oxygen, ATP, NADPH
The light reactions:
o Split H2O
o Release O2
o Reduce NADP+ to NADPH
o Generate ATP from ADP by photophosphorylation.
- When a pigment absorbs light, it goes from a ground state to an excited state. When this happens, electrons are given energy.
- Light energy results in removal of electrons from chlorophyll molecules.
o The electrons gain so much energy that they jump away from the chlorophyll molecule and leave it.
Photophosphorylation: The process of ATP formation using light energy.
Light-Independent Reactions (Calvin Cycle)
The Calvin cycle uses ATP and NADPH to build glucose from CO2
occurs in the stroma
begins with carbon fixation.
Inputs: CO2, ATP, NADPH
Outputs: Glucose, ADP, NADP+
The Calvin Cycle:
o Forms sugar from CO2, using ATP and NADPH
o The Calvin cycle begins with carbon fixation, incorporating CO2 into organic molecules.
The reactions that require CO2 in photosynthesis happen during the Calvin cycle in the stroma of the chloroplast
Primary Function: Carbon fixation and sugar synthesis.
Carbon fixation: you take the carbon from the inorganic CO2 and put it into organic molecules
Photosystems
Embedded in the Thylakoid membrane are photosystems.
Inside the photosystem, you have the green chlorophyll molecules, they are going to absorb light energy, and the energy is going to go to the electrons in the chlorophyll.
The electrons are going to keep gaining energy until they gain so much energy that they leave the chlorophyll molecule.
there are 2 photosystems
in PS2, the green chlorophyll pigment absorbs the light energy. The energy is going to the electrons. The electrons will get excited, gain a ton of energy and leave the chlorophyll.
The electrons leaving the chlorophyll have to pass through an electron transport chain (electrons pass through the chain, releasing energy). The released energy then powers active transport to take hydrogen ions from a place of low concentration in the stroma, to a place of high concentration in the thylakoid lumen (space). Then, using ATP Synthase (the protein), the protons travel back to a place of low concentration. Also, during the use of ATP synthase, ATP is made.
in PS1, the green chlorophyll pigment absorbs the light energy. The energy is going to the electrons. The electrons will get excited, gain a ton of energy and leave the chlorophyll.
This time, the electrons leaving the chlorophyll go to an electron carrier. So, that carrier is now carrying those electrons which means that it is carrying energy
Autotrophs vs. Heterotrophs
Organisms are classified based on how they obtain energy and carbon.
Autotrophs: Produce their own food from inorganic sources (e.g., plants).
Heterotrophs: Obtain energy by consuming other organisms.
Example: Animals are heterotrophs; plants are autotrophs.
Processes Driven by Light Energy
Photosynthesis is the primary biological process directly driven by light energy. (the light energy is giving electrons to chlorophyll causing them to leave the chlorophyll).
Photosystems: Protein complexes that absorb light and initiate electron transfer.
Photophosphorylation: Most similar to oxidative phosphorylation in mitochondria, but uses light energy.
The processes most directly driven by light energy in photosynthesis are the light reactions, including electron excitation, water splitting, and ATP/NADPH formation!
Oxidative Phosphorylation vs. Photophosphorylation
Chloroplasts and mitochondria generate ATP by chemiosmosis, but use different sources of energy.
Mitochondria transfer chemical energy from food to ATP; chloroplasts transform light energy into the chemical energy of ATP
In mitochondria, protons are pumped to the intermembrane space and drive ATP synthesis as they diffuse back into the mitochondrial matrix.
In chloroplasts, protons are pumped into the thylakoid space and drive ATP synthesis as they diffuse back into the stroma
Electron Transport Chain & ATP Synthases
In animals, the electron transport chain and ATP Synthase are found embedded in the inner membrane of the mitochondria.
In plants, the electron transport chain and ATP Synthase are found embedded in the thylakoid membrane of the chloroplasts AND embedded in the inner membrane of the mitochondria.
