Theme 1 Module 2: Organelles and Energy

How did the appearance of photosynthetic cells, particularly photosynthetic eukaryotes during the Proterozoic eon, transform Earth’s environment and influence the evolution of life from unicellular organisms to more complex forms?

Life began about 4 billion years ago, and for most of Earth’s history, it was made up of unicellular organisms living in an environment with almost no oxygen. Conditions were harsh and inhospitable. The big turning point came when the first photosynthetic cells appeared—they could produce oxygen, which changed the environment and allowed life to diversify. Later, during the Proterozoic eon, the first photosynthetic eukaryotes evolved. Over time, many unicellular organisms started working together to survive tough conditions, forming co-dependent relationships. These interactions eventually led to more complex life forms, which we can understand better by comparing prokaryotes and eukaryotes today

What is the structural differences: eukaryotic and prokaryotic cells?

Eukaryotic and prokaryotic cells have many structural components that are similar and others that differ.  

• Similarity: For example, both eukaryotic and prokaryotic cells have an external membrane that separates the inside of the cell from the outside of the cell.  

• Differ: These two cell types differ in that eukaryotic cells alone have an internal network of membranes. In particular, eukaryotic cells have a double membrane bound nucleus that serves as an internal compartment to separate the genetic material of the cell (chromosomes) from the rest of the cell interior. The transition from prokaryotes that lack a distinct nucleus and eukaryotes, with a true compartmentalized nucleus is considered to be a significant change in evolutionary history. 

Life on Earth was mostly unicellular and oxygen was absent until photosynthetic cells appeared. Fossil records show prokaryotes existed the longest, while eukaryotes appeared about 2 billion years ago. How did these two groups originate, and what differences between prokaryotes and eukaryotes help explain their evolution?

Interestingly, life on earth was almost exclusively unicellular for most of Earth's history and oxygen was virtually absent from the oceans and atmosphere until the appearance of the first photosynthetic cells. What we find from the fossil record is that prokaryotic cells have been around for the longest time. Eukaryotic cells, however, appear in our tree of life about 2 billion years ago. How is it that these 2 different groups came to be? To understand this, it is important to consider the differences between prokaryotes and eukaryotes. 

Prokaryotes and eukaryotes originated through evolutionary processes shaped by environmental changes. Early Earth had almost no oxygen, so life began as simple unicellular prokaryotes. When photosynthetic prokaryotes appeared, they started producing oxygen, which transformed the environment. This oxygen allowed for more complex life forms to evolve. About 2 billion years ago, eukaryotic cells appeared, likely through endosymbiosis, where one prokaryotic cell lived inside another and they became co-dependent.

Key differences:

• Prokaryotes: Simple cells, no nucleus, no membrane-bound organelles.

• Eukaryotes: Complex cells, have a nucleus and membrane-bound organelles (like mitochondria and chloroplasts).

These differences reflect how eukaryotes evolved from prokaryotes to handle new conditions and energy needs

What are Organelles?

Organelles: are membrane- bound structures inside the cell. 

• Chloroplasts in plant cells 

• Mitochondria in animal and plant cells 

Biologists hypothesize that the earliest eukaryotes were likely single-celled organisms that contained organelles and internal membrane systems with distinct structures and functions. In modern-day cells, we know that mitochondria are the organelles that generate energy in the form of ATP. We also know that plant cells and photosynthetic protists contain chloroplasts which actively engage in photosynthesis, producing chemical energy from light energy. These organelles are essential contributors to normal cell function. 

What is mitochondria?

Mitochondria convert the energy from the food we eat into energy that powers most cellular functions in our bodies. A grave consequence that can come about with mitochondrial malfunction is exhaustion. This is a common symptom of mitochondrial diseases. As we progress through this module, we will consider a few questions.... these include: What are mitochondria? Where did they come from? What do they do? 

What is Photosynthesis? what is inside the chloroplast?

Photosynthesis: a process in plant cells and other organisms to convert light energy into chemical energy Chemical energy is stored in the  bonds of carbohydrate molecule 

 

As part of our daily nutrition, we depend on the activity of chloroplasts in plant cells to engage in photosynthesis and produce sugars that we consume in our diets. In this figure, we see a high-resolution electron micrograph that shows the structure of a typical chloroplast.

• The chloroplast has a double membrane around its exterior and an interior that is filled with hundreds of flattened and stacked membranes called thylakoids. These thylakoid stacks are organized into piles called grana. It is within these membranes, that pigments and enzymes participate in photosynthesis. 

What is Cellular respiration?

Cellular respiration: a process used by plants and animals to release the chemical energy stored in bonds of carbohydrate molecules and partially capture it in the form of ATP 

The chemical energy requirements of our cells can be obtained from the sugars we consume through processing by mitochondria distributed throughout a cell.  

• Amazingly, depending on the type of cell, we have between 50 to over a million mitochondria present in a cell.  

• Chemical energy in the form of ATP is generated in the mitochondria through breakdown of sugars. As seen in the high-resolution electron micrograph in this figure, each mitochondrion has two membranes.  

  • The outer membrane surrounds the organelle 

  • inner membrane is connected to a series of sac-like structures called cristae. It is in these membranes that most of the ATP is synthesized in eukaryotic cells. But the question remains.... how did these organelles form inside our cells? 

Some properties of mitochondria?

• Look like bacterial cells 

• About the same size as bacterial cells 

• Have their own circular genome 

• Produce the enzymes necessary for protein synthesis 

Are Bacteria in our cells?

As discussed earlier, we know that bacteria reside on our cells, but are they also inside our cells? In 1981, Dr. Lynn Margulis proposed the theory that eukaryotic cells originated as communities of interacting entities that are joined together. Specifically, she proposed that prokaryotic cells could have perhaps been ingested or entered into a host cell, where over time, the guest prokaryotes and eukaryotes may have developed mutually beneficial interactions that then became obligatory for survival of the host cell. Mitochondria and chloroplasts are examples of distinct membrane-bound compartments in the cell that may have entered the cell from external origins. 

why it might be advantageous to develop this type of endosymbiotic relationship?

Why would cells want this kind of partnership? Let’s look at mitochondria as an example. Early Earth was a tough place to live. Ancient eukaryotic cells could only make a little energy (ATP) without oxygen. Then, they encountered aerobic bacteria that could make a lot of energy using oxygen. So, the eukaryotic cell likely engulfed the bacteria. This was a win-win:

• The bacteria gave the host cell lots of energy.

• The host cell gave the bacteria a safe home and food.

Over time, this partnership became permanent, and those bacteria evolved into mitochondria inside eukaryotic cells.

What is prediction?

Prediction: You might see living examples of acquired endosymbiotic relationships which can be seen in eukaryotic organisms

A hypothesis or theory leads to a set of predictions. What are these? Are these different from the predictions of other theories? What predictions would we make if the endosymbiotic theory were an accurate representation of the evolution of organelles such as the chloroplast and mitochondria? One prediction may be that: You might see living examples of acquired endosymbiotic relationships which can be seen in eukaryotic organisms

explain how green algae Cymbaloms is an example of eukaryotic organisms that in their lifetime acquire the ability to engage in photosynthesis only after they have engulfed photosynthetic bacteria

Some eukaryotic organisms can only do photosynthesis after they swallow photosynthetic bacteria. For example, the green algae Cymbaloms keeps living bacteria inside it. These bacteria make food through photosynthesis and share it with the algae. In return, the algae gives the bacteria a safe place to live. Both benefit from this partnership.

Describe what is happening in this diagram

This image illustrates the concept of endosymbiosis in action, specifically how plastids (like chloroplasts) may have originated.

Here’s what is happening:

• Title: “Endosymbiosis in action” – This refers to the process where one organism lives inside another in a mutually beneficial relationship.

• Text on the left:
  Phagocytosis by an early eukaryote: a first step in the origin of plastids.
  This means an early eukaryotic cell engulfed another organism (phagocytosis) as the first step toward forming plastids.

• Diagram on the right:

  • Shows an early eukaryotic cell with a nucleus (blue oval) and a feeding channel.

  • A cyanobacterium (green oval), which is the ancestor of modern chloroplasts, is being engulfed by the eukaryotic cell.

  • The cyanobacterium ends up inside a permanent food vacuole.

  • Green arrows point to trees and plants, symbolizing that this process eventually led to photosynthetic eukaryotes (plants and algae).

• Key idea:
  The cyanobacterium provided photosynthesis (food production) for the host cell, while the host cell gave the cyanobacterium protection and nutrients. Over time, this relationship became permanent, and the cyanobacterium evolved into a plastid (chloroplast) inside the eukaryotic cell.

describe Endosymbiosis in action with coral

This relationship is also seen in other animals. Corals live symbiotically with microbes called dinoflagellates. These dinoflagellates photosynthesize, as long as they have light and nutrients. However, they do not keep the products of photosynthesis for themselves. They release almost all of the products to the coral. In the sea slug, this relationship is taken one step further. 

Corals are animals that live symbiotically with microbes. This is similar to the human microbiome 

describe Endosymbiosis in action with sea slugs

The sea slug consumes photosynthetic algae and harvests the chloroplasts from the algal cells. The chloroplasts are maintained in the cells of the sea slug. These are temporary endosymbiotic relationships that can be acquired and perhaps lost during the lifetime of the organism. 

 

This sea slug is an animal that can consume photosynthetic algae and keep only the chloroplast 

What is the Endosymbiotic Theory? What is some evidence?

Simplified Explanation:
For endosymbiosis to lead to organelles like mitochondria and chloroplasts, the relationship must become permanent and heritable. This means when the host cell divides, the organelles are passed on to the new cells.

• In other words, when the host cell divides then the organelles are distributed relatively evenly between the two daughter cells.

Evidence for this theory includes:

• Mitochondria and chloroplasts have their own circular DNA, similar to bacteria.

• Their genes and proteins are very similar to those found in bacteria.

This supports the idea that these organelles originally came from bacteria living inside early eukaryotic cells.

Why are organelles important?

Simplified Explanation:
Cells have different organelles (special compartments) to keep different jobs separate.

Why is this helpful?

1. Efficiency: Each organelle has the right enzymes and materials for its job.

   • Example:

     • Chloroplasts have everything needed for photosynthesis.

     • Mitochondria have everything needed for aerobic respiration.

   • Keeping enzymes, substrates, and products together makes reactions faster.

2. Separation of processes: Some processes don’t mix well (like building molecules vs. breaking them down). Organelles keep these processes apart so they don’t interfere with each other.

original explanation: The existence of different organelles within the cell allows for the compartmentalization of different cellular functions.  

Why is this advantageous to the cell?  

• One reason is that specific sets of enzymes responsible for specific biochemical functions can be kept in close proximity to each other.  

  • For example, the chloroplast contains all the enzymes necessary for photosynthesis, the mitochondria for aerobic respiration. The efficiency of the chemical reactions is increased if enzymes, substrates and products are concentrated in an organelle.  

  • Another reason could be that incompatible processes such as synthesis and degradation can be kept separate and not interfere with each other.

How does energy flow in biological systems?

Simplified Notes: How Energy Flows in Biological Systems 

• Photosynthesis in chloroplasts: 
  Plants use light energy and CO₂ + H₂O to make organic molecules (like sugars) and oxygen (O₂). 

• Why is this important? 

  • These sugars store energy that flows through the ecosystem. 

  • Non-photosynthetic organisms (like animals and humans) cannot make their own food, so they rely on plants (or animals that eat plants) for energy. 

  • Cellular respiration in mitochondria: 

    • Organisms use these sugars and oxygen to make ATP, the energy molecule that powers most cellular work. 

    • This process also releases CO₂ and H₂O, which plants use again for photosynthesis. 

    • Energy cycle: 

      1. Light energy → Photosynthesis → Organic molecules + O₂ 

      2. Organic molecules + O₂ → Cellular respiration → ATP + CO₂ + H₂O 

      3. ATP powers activities (like a cyclist pedaling) 

      4. Some energy is lost as heat. 

 

original explanation: If we look at a chloroplast that is actively engaging in photosynthesis, we see that these organelles harness light energy, and together with atmospheric carbon dioxide, make important organic sugars and gaseous oxygen. The energy present in the sugars can then flow within the remaining ecosystem. What do we mean by this? Well, consider that living cells need energy from outside sources. Non-photosynthetic organisms, because they lack chloroplasts, cannot harness light energy to make organic molecules. As a result, much energy is provided through metabolism of organic molecules that are produced by chloroplasts in the plants that we consume either directly or by feeding on animals that feed on plants. Consider that food provided by photosynthetic plants that stockpile sugars can be used as sources of energy for our day-to –day activities. For example, a cyclist, can use the sugars from a consumed meal to synthesize ATP in his or her cells which will power the cyclist's muscle cells. 

How does Cholorplast make chemical energy?

Here’s an easy-to-understand version of the text and image combined:

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Simplified Notes: How Chloroplasts Make Chemical Energy

• What do chloroplasts do?

  • In plants, chloroplasts use sunlight, carbon dioxide (CO₂), and water (H₂O) to make carbohydrates (like glucose).

  • Oxygen (O₂) is produced as a by-product.

• Two main stages of photosynthesis:

  1. Light Reactions (Photosynthetic Electron Transport Chain):

     • Light energy is captured by chlorophyll.

     • Water is split → releases O₂.

     • Energy is stored in ATP and NADPH.

  2. Calvin Cycle:

     • Uses ATP and NADPH from light reactions.

     • Converts CO₂ into carbohydrates (sugars).

• Why is this important?

  • Sugars store energy for plants and all organisms that eat plants.

  • Oxygen is essential for life.

• Photosynthesis equation:
  [ 6CO₂ + 12H₂O + light energy → C₆H₁₂O₆ + 6H₂O + 6O₂ ]

How are carbohydrates formed, and what types of bonds and enzymes are involved in linking monosaccharides together?

Carbohydrates are the most abundant sources of ATP that fuel our bodily processes. These carbohydrates are formed by the polymerization of monosaccharides through glycosidic bonds to form complex sugars.  

• Examples of monosaccharides include glucose, fructose and galactose.  

• Special proteins called enzymes are able to catalyze (or speed up) the condensation reaction between specific hydroxyl groups of certain monosaccharides to produce disaccharides such as lactose, sucrose, maltose and others.  

• Usually, the reaction occurs between the OH group on carbon 1 of one molecule and carbon 4 of another monosaccharide to give either the alpha1-4 glycosidic linkage or beta1-4 glycosidic linkage. 

How do plants and animals store polysaccharides for energy?

Polysaccharides are the structures that form when many monosaccharides are linked together. These can include simple disaccharides, or larger and more common polysaccharides found in organisms that include starch and glycogen.  

• Starch is the storage polysaccharide that is found in all photosynthetic plants and is made up of alpha1-4 glycosidic linkages between alpha-glucose monomers. The two types of starch include two types of polysaccharides: unbranched amylose and branched amylopectin. ** These differences in structure vary only based on the interactions between neighboring carbon atoms of each glucose monomer,  

  • amylopectin the branches form by glycosidic linkages between the carbon 1 of one glucose molecule and carbon 6 of another.

  • It is often these starches that we consume and use as energy in our own bodies. When starches are consumed, we store the digested carbohydrates as highly branched glycogen polysaccharide helices. This stored glycogen energy can be broken down into glucose through cellular respiration to produce ATP for vital  cellular processes. 

Why do we need ato? What are the 4 steps? How much atp is produced?

 

Simplified Notes: How Glucose Processing Produces ATP 

• Why do we need ATP? 

  • ATP is the energy molecule that powers all cellular activities. 

  • Our cells only store enough ATP for 30–60 seconds, so they must constantly make more. 

  • How is ATP made? 

    • Through cellular respiration, which breaks down glucose in 4 steps. 

    • The first three steps shown here are: 

      1. Glycolysis (in cytosol): 

         • Glucose → 2 Pyruvate 

         • Produces 2 ATP and 2 NADH (electron carriers). 

      2. Pyruvate Processing (in mitochondria): 

         • Pyruvate → Acetyl CoA 

         • Produces CO₂ and NADH. 

      3. Citric Acid Cycle (Krebs Cycle): 

         • Acetyl CoA → more ATP, CO₂, and electron carriers (NADH, FADH₂). 

         • Produces 2 ATP, 6 NADH, 2 FADH₂, and 4 CO₂. 

         • Why are electron carriers important? 

           • NADH and FADH₂ will be used in the next step (Electron Transport Chain) to make lots of ATP. 

Original Explanation:  

• Throughout the first 3 steps of glucose processing, it appears that there is not a whole lot of ATP synthesized. The reality is that the bulk of the electron donors are used in the electron transport chain present in the inner mitochondrial membranes or cristae, to produce another 32 molecules of ATP.  

• As a result, for every glucose molecule that we process in our cells, we produce 36 theoretical ATP, with negligible amounts coming from glycolysis and the Krebs cycle and most ATP forming when the electron donors NADH and FADH2 move through the protein complexes of the electron transport chain residing in the extensive inner mitochondrial membranes.  

  • As a result of this transfer of electrons through the complexes of the electron transport chain, as these electrons move through  the membranes, protons are pumped into the intermembrane spaces of the mitochondria.  

  • This creates an electrochemical concentration gradient across the inner mitochondrial membranes that drives protons through the ATP synthase protein channels that are embedded in the membranes. This results in the synthesis of an additional 32 ATP.  

  • Until recently, it was believed that 36 molecules of ATP were synthesized for every molecule of glucose, the theoretical maximum, but recent research using more precise measurements of energy expenditure suggests that the actual yield is closer to 30 ATP molecules per molecule of glucose. 

Carbohydrates are not the only source of energy. What else can be used and how?

Proteins and Fats as Fuel

Cells can use carbohydrates, fats, and proteins for energy by converting them into molecules that enter cellular respiration.

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Carbohydrates

• Start as sugars (e.g., glucose).

• Glucose goes through glycolysis → forms pyruvate.

• Pyruvate is converted into Acetyl-CoA.

• Acetyl-CoA enters the Krebs cycle → produces ATP and electron carriers.

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Fats

• Broken down into:

  • Fatty acids → converted directly into Acetyl-CoA.

  • Glycerol → enters glycolysis → then follows the same path as glucose.

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Proteins

• Broken down into amino acids.

• Amino acids are converted into intermediates that enter:

  • Pyruvate stage or

  • Acetyl-CoA stage → then into the Krebs cycle.

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Key Idea

• All three macronutrients (carbs, fats, proteins) eventually feed into cellular respiration at different points:

  • Glycolysis (for glucose and glycerol).

  • Acetyl-CoA (for fatty acids and some amino acids).

  • Krebs cycle (final common pathway)

Original explanation: Carbohydrates are not the only source of energy that can be used to make ATP. Proteins and lipids that are consumed as part of our diet can also be converted to components that enter into the cellular respiration pathway and lead to the production of ATP. As a result, all three of these macromolecules can contribute to ATP production. The rule of thumb though is that when all 3 of these macromolecules are available in a cell, carbohydrates are metabolized first, followed by fats and then proteins. 

How can energy be released by hydrolysis of ATP?

Here are detailed, easy-to-understand notes based on your text and the image:

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Why is ATP a Source of Molecular Energy? Structure of ATP

• ATP (Adenosine Triphosphate) consists of:

  • Adenine (nitrogenous base)

  • Ribose sugar

  • Three phosphate groups (P-P-P)

Why does ATP have high potential energy?

• The three phosphate groups carry four negative charges close together.

• These negative charges repel each other, creating instability.

• This repulsion gives the molecule high potential energy.

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How is Energy Released?

• ATP hydrolysis = ATP reacts with water (H₂O) → breaks the bond between the outermost phosphate group and its neighbor.

• Products:

  • ADP (Adenosine Diphosphate)

  • Inorganic phosphate (Pi)

  • Energy (~30.5 kJ/mol)

• This reaction is highly exergonic (releases energy), which cells use to power processes like:

  • Muscle contraction

  • Active transport

  • Biosynthesis

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Image Explanation

• Left: ATP + H₂O

• Middle: ADP + Pi

• Right: Energy released (30.5 kJ/mol ATP)

• Caption: ATP hydrolysis is an exergonic reaction.

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Key Points to Remember

• ATP = energy currency of the cell.

• Energy comes from breaking the high-energy phosphate bond.

• Hydrolysis of ATP → ADP + Pi + Energy.

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orignal explanation:
Why is ATP a source of molecular energy? ATP fuels cellular processes because it has a high potential energy. Adenosine triphosphate (ATP) consists of 3 phosphate groups attached to a ribose sugar and an adenine. The 3 phosphate groups have 4 negative charges in close proximity, so these negatively charged phosphate groups repel each other giving the electrons of the phosphate groups a very high potential energy and are the source of the potential energy in this molecule. The potential energy of ATP can be released and harnessed during a hydrolysis reaction, where ATP can react with water, breaking the bond between the outermost phosphate group and its neighbor, resulting in the formation of ADP and inorganic phosphate. The hydrolysis of ATP is a highly exergonic reaction. 

What sort of Cellular processes is ATP used for?

The cell's interior machinery takes advantage of the energy that is released during ATP hydrolysis to perform mechanical, transport, and chemical work.  

• For example, the cyclist that is pedaling along, uses ATP hydrolysis to fuel the contraction of his or her muscles during this strenuous exercise.  

• As we saw in the first module, ATP is also important for transport of substances across the cell membrane AGAINST a concentration gradient 

• Finally, many enzymes within a cell require energy to perform their functions and so the cell is also able to use ATP-derived energy to help drive those endergonic (or energy requiring) reactions. 

What is the endomembrane system?

What does the endosymbiotic theory state?

As outlined in this module, it is likely that today's eukaryotes were derived and modified from an ancestral prokaryote that contained genetic material of inheritance. 

 The endosymbiotic theory states that these early eukaryotes became hosts to aerobic and photosynthetic prokaryotes, which we now know as mitochondria and chloroplasts respectively.

Where does Glycolysis happen? what is the chemical reaction?

Cytosol

C6H12O6 + 2NAD+ +2ADP +2pi → 2C3H4O3 (pyruvate) + 2NADH +2H+ +2ATP + 2H2O

Where does pyruvate happen? what is the chemical reaction?

mitochondrial matrix

2C3H4O3 (Pyruvate) + NAD+ + COA → Acetyl-CoA +NADH +CO2

Where does citric acid cycle happen? what is the chemical reaction?

matrix of the mitochondria

Acetyle- COA + 3NAD+ + FAD +GDP + pi +2H2O → COA-SH + 3NADH + FADH2 + 3H+

light cycle happen? what is the chemical reaction?

within the thylakoid membranes of chloroplasts in eukaryotic cells
2H2O+ 2NADP+ + 3AP + 3pi + light -> O2 + 2NADPH + 3ATP

Calvin cycle happen? what is the chemical reaction?

Stroma
3CO2 + 6NADPH + 9ATP -> G3P + 6NADP+ 9ADP +8Pi + 3H2O