TOPIC 1: The Cell

The sources define the 3 Domains of life as a key learning objective within Topic 1: The Cell, which is the first topic covered in Unit 1: Cells and Energy Transformations.

The primary objective regarding classification is to describe the 3 Domains of life and explain why this system has replaced the 5 Kingdom system.

Shift from 5 Kingdoms to 3 Domains

Historically, the standard classification system in Western science was the 5-Kingdom taxonomic hierarchy (classification system), established by Carolus Linnaeus in the 1700s. This system included Monera, Protista, Fungi, Plantae, and Animalia.

The sources indicate that Molecular Biology brought about the change in classification. All life stores genetic information in DNA molecules and uses ribosomes (rRNA) to translate this information into proteins, making ribosomes essential components of all life. The new system, the 3-Domain Classification System, is based on comparing the nucleotide sequences of the ribosome gene among species.

Describing the 3 Domains

The three recognized domains of life are Bacteria, Archaea, and Eukarya. All life on Earth has a shared ancestry, originating from a Last Universal Common Ancestor (LUCA).

1. Domain Bacteria: These are prokaryotic organisms. A distinguishing feature of Bacteria that differentiates them from Archaea and Eukarya is that most bacteria have a cell wall made from peptidoglycan. All bacteria are prokaryotic organisms.

2. Domain Archaea: These are also prokaryotic organisms.

3. Domain Eukarya: These organisms are characterized by eukaryotic cells.

Cellular Context: Prokaryotes vs. Eukaryotes

The classification system is intrinsically linked to the comparison between prokaryotic and eukaryotic cells, another key learning objective of Topic 1.

• Defining Feature: The fundamental distinction between a prokaryotic cell and a eukaryotic cell is the presence or absence of a nucleus.

• Size Constraints: Eukaryotic cells can be large, whereas prokaryotic cells are typically small. This size difference is tied to geometry and diffusion; as a cell doubles in size, its surface area to volume ratio decreases by half (e.g., from 6:1 to 3:1), meaning the cell membrane (site of nutrient exchange and energy generation) must support the internal volume.

• Origin of Eukaryotes (Endosymbiosis): The sources connect the domains via the Endosymbiotic Theory. Some eukaryotic organelles, specifically mitochondria and chloroplasts, were originally independent prokaryotic cells.

  • Eukaryotic cells are described as Bacteria-Archaea hybrids.

  • The host cell in the endosymbiotic relationship was an Archaea-like host cell.

  • For chloroplasts, the endosymbiotic event may have been an early eukaryotic cell engulfing a bacteria that was efficient at photosynthesis. The resulting relationship was beneficial to both organisms and became permanent. The host cell used its resources while the bacteria (the endosymbiont) received resources.

In summary, the classification system of the 3 Domains (Bacteria, Archaea, Eukarya) is based on molecular evidence (rRNA sequence comparison), replacing the older 5-Kingdom system, and provides the framework for understanding the fundamental cellular differences, particularly the presence of a nucleus (eukaryotic vs. prokaryotic) and the evolutionary origin of eukaryotes through endosymbiosis.\

The sources clearly identify the comparison between prokaryotic and eukaryotic cells as a crucial component of Topic 1: The Cell within Unit 1: Cells and Energy Transformations.

The learning objectives specifically require students to compare and contrast prokaryotic and eukaryotic cells. This comparison includes explaining the importance of the Surface Area to Volume (SA:V) ratios to cells and describing the origin of eukaryotic cells, including endosymbiosis.

Distinguishing Feature: The Nucleus

The most fundamental difference used to distinguish prokaryotic cells from eukaryotic cells is the presence or absence of a nucleus.

• Prokaryotic Cells: Lack a nucleus. The Domains Bacteria and Archaea are comprised of prokaryotic organisms.

• Eukaryotic Cells: Possess a nucleus. The Domain Eukarya is comprised of eukaryotic organisms.

Size Constraints and SA:V Ratio

Prokaryotic cells are typically small, and the sources explain this limitation based on geometry and diffusion.

1. Geometry and Scaling: Every time a cell doubles in size, the surface area to volume ratio decreases by half. For example, if the initial SA:V ratio is 6:1, doubling the cell's dimension reduces the ratio to 3:1.

2. Diffusion Constraint: The cell's surface area, which is the cell membrane, is the site of nutrient exchange and energy generation. This surface area must be large enough to support the internal volume.

3. Consequence of Growth: As cells get larger, their SA:V ratio decreases. If a cell grows too large, the surface area cannot supply nutrients and remove waste efficiently enough for the increased volume, limiting the cell size. The rates of diffusion and ATP synthesis must be sufficient to support the internal volume.

The sources also ask the question: "How can Eukaryotes be large?". Eukaryotic cells overcome size constraints partially through their endomembrane system.

Origin of Eukaryotes (Endosymbiotic Theory)

The differences between these cell types are explained by the Endosymbiotic Theory, which describes the origin of eukaryotic cells.

• Shared Ancestry: All life on Earth has a shared ancestry, originating from a Last Universal Common Ancestor (LUCA).

• Organelle Origin: Some eukaryotic organelles, specifically mitochondria and chloroplasts, were originally independent prokaryotic cells.

• Host and Endosymbiont: These organelles formed when two organisms (now extinct) formed a permanent relationship that was beneficial to both.

  • The host cell was an Archaea-like host cell.

  • The mitochondria originated from an aerobic bacteria.

  • Chloroplasts may be the result of an early eukaryotic cell engulfing a bacteria that was efficient at photosynthesis.

• Hybrid Nature: According to the theory, eukaryotic cells are Bacteria-Archaea hybrids. The host cell used its resources, while the endosymbiont (the bacteria) received resources.

Additional Comparisons

The Domains Bacteria and Archaea are both prokaryotic. A key feature that differentiates Bacteria from Archaea and Eukarya is that most bacteria have a cell wall made from peptidoglycan.

The sources emphasize the explanation of the importance of Surface Area to Volume (SA:V) ratios to cells as a core learning objective within **Topic 1:The sources emphasize the explanation of the importance of Surface Area to Volume (SA:V) ratios to cells as a core learning objective within Topic 1: The Cell. This concept is crucial for understanding a fundamental difference between prokaryotic and eukaryotic cells, specifically concerning their typical size limitations.

Importance of SA:V Ratios

The importance of the SA:V ratio is explained primarily through the geometric and physiological constraints it imposes on cell size:

1. Geometric Constraint (Why Prokaryotic cells are small): Prokaryotic cells are typically small, and this limitation is tied directly to geometry.

   • Scaling Effect: Every time a cell doubles in size, the surface area to volume ratio decreases by half. For example, if a cell with dimension 'x' has a ratio of 6:1, a cell with dimension '2x' (double the size) has a ratio of 3:1.

   • Consequence: As cells get larger, their SA:V ratio decreases.

2. Physiological Constraint (Diffusion): The cell's function depends on efficient exchange with the surroundings, which is governed by the SA:V ratio.

   • Cell Membrane Function: A cell's surface area is its cell membrane, which is the site of nutrient exchange and energy generation.

   • Support Requirement: The surface area (membrane) must support the internal volume of the cell.

   • Rate Limitation: If the cell grows too large, the surface area will be insufficient relative to the volume. The rates of diffusion and ATP synthesis must be adequate to support the internal volume.

Therefore, the low SA:V ratio limits prokaryotic cells from growing large because the cell membrane cannot efficiently supply nutrients and exchange waste for the entire volume.

Context in Topic 1: The Cell

The explanation of SA:V ratios is presented within the learning objective that requires students to compare and contrast prokaryotic and eukaryotic cells.

• Prokaryotes: They are constrained to small sizes by the SA:V principle.

• Eukaryotes: The sources pose the question, "How can Eukaryotes be large?". Eukaryotic cells overcome the geometric limitations of size partly because they possess an endomembrane system, including internal membranes and organelles. These internal structures effectively compartmentalize the cell, creating additional cellular regions and providing greater internal surface area to handle the metabolic demands of a larger volume.

The description of the origin of eukaryotic cells, specifically including endosymbiosis, is clearly designated as a required learning objective (Objective 3) within **Topic 1The description of the origin of eukaryotic cells, specifically including endosymbiosis, is clearly designated as a required learning objective (Objective 3) within Topic 1: The Cell. This concept explains how the complex eukaryotic cell structure evolved from simpler prokaryotic ancestors, linking the domains of life.

The Origin of Eukaryotic Cells via Endosymbiosis

The central explanation provided by the sources is the Endosymbiotic Theory.

1. Shared Ancestry: The theory acknowledges that all life on Earth has a shared ancestry, originating from a Last Universal Common Ancestor (LUCA). Eukaryotic cells themselves are described as Bacteria-Archaea hybrids.

2. Organelle Origin: Endosymbiosis posits that some eukaryotic organelles, specifically mitochondria and chloroplasts, were originally independent prokaryotic cells.

3. Establishment of the Relationship: These organelles formed when two organisms (now extinct) formed a relationship that was beneficial to both and is now permanent.

Details of the Endosymbiotic Events

The sources detail the types of cells involved in this relationship:

• The Host Cell: The host cell in the endosymbiotic process was an Archaea-like host cell.

• The Endosymbiont: The endosymbiont was a bacteria-like cell. The sources describe the specific origins of key organelles:

  • Mitochondria: Mitochondria originated from an aerobic bacteria.

  • Chloroplasts: Chloroplasts may be a result of an early eukaryotic cell engulfing a bacteria that was efficient at photosynthesis.

The relationship was permanent and mutually beneficial. The host cell used its resources, and the endosymbiont (the bacteria) received resources. The Archaea received something, and the Bacteria received something.

Evidence for Endosymbiotic Theory

The sources cite several lines of evidence supporting the Endosymbiotic Theory:

• Size: Mitochondria and chloroplasts are the same size as modern prokaryotes.

• Ribosome/DNA Sequence: The ribosome DNA sequences (rRNA) of these organelles resemble those of modern prokaryotes, distinct from the rRNA sequence found in the eukaryotic nucleus. For example, Eukaryote rRNA, Mitochondrial rRNA, and Prokaryote rRNA all have different sequences.

• Existing Associations: The fact that many other (endo)symbiotic associations exist is also cited as evidence.

Context within Topic 1

The understanding of endosymbiosis is critical for Topic 1 because it directly explains how Eukarya—one of the 3 Domains of life—acquired its defining characteristics, such as membrane-bound organelles. Furthermore, the theory explains how eukaryotic cells overcame the size constraints imposed by Surface Area to Volume ratios typical of prokaryotic cells, allowing them to be larger and more complex due to the internal compartments provided by the acquired organelles.

The sources explicitly include the comparison of Cytoskeleton structures (Microtubules, Intermediate Filaments, and Microfilaments) as a key learning objective within Topic 1: The Cell.

Learning Objective

The objective is to compare the structure and function of microtubules, intermediate filaments, and microfilaments (MT, IF, MF).

Structure and Composition Comparison

The sources provide visual and textual information detailing the structural components and typical sizes of the three cytoskeleton structures:

• Microtubules (MT): These structures are the largest, measuring 25 nm. They are composed of Tubulin dimers, which include $\alpha$-tubulin and $\beta$-tubulin. Their structure is shown as thirteen filaments side by side.

• Intermediate Filaments (IF): These structures fall in the middle size range, between 8–12 nm. They are composed of intermediate filament protein.

• Microfilaments (MF): These are the smallest, measuring 5–7 nm. They are composed of Actin subunits.

Function and Cellular Context

In the larger context of Topic 1: The Cell, the cytoskeleton plays a fundamental role in maintaining and facilitating cell processes:

• General Role: The cytoskeleton supports and is involved in cell division.

• Cell Location: All three structures—microfilaments, intermediate filaments, and microtubules—are depicted within diagrams illustrating both animal cell and plant cell structures, specifically within the cytosol.

• Associated Structures: Microtubules are shown to be components of centrioles. Microfilaments, intermediate filaments, and microtubules are all visible components of the cellular architecture, providing internal framework and facilitating movement, such as the movement of a vesicle along a microtubule.

Understanding the cytoskeleton is essential for Topic 1, as it contributes to the comparison of plant versus animal cell structure (another learning objective) and the overall understanding of the internal organization and mechanics of the eukaryotic cell.

The sources establish that the comparison of key elements of plant versus animal cell structure is a required learning objective (Objective 5) within Topic 1: The Cell. This comparison utilizes the understanding of eukaryotic cellular components and architecture developed earlier in the topic.

The sources provide visual representations (diagrams) of both an Animal Cell and a Plant Cell, highlighting specific components present in each.

Key Components Distinguished in Plant vs. Animal Cells

The diagrams and associated content point to several structures that differentiate plant and animal cells, although the sources do not provide a detailed textual comparison list:

Shared Eukaryotic Structures: Both diagrams depict core eukaryotic structures, underscoring their shared classification within the Domain Eukarya:

• Nucleus: Contains the Nuclear envelope, Chromatin, and Nucleolus.

• Endomembrane System: Both cells contain Rough ER, Smooth ER, and the Golgi complex.

• Energy Organelle: Both contain the Mitochondrion.

• General Structures: Both have a Plasma membrane, Cytosol, Ribosomes (free in cytosol), Microbody, and Cytoskeleton elements (Microfilaments and Microtubules).

Context within Topic 1

This comparison builds upon the prior learning objectives:

1. Eukaryotic Status: Both are Eukaryotic cells, defined by the presence of a nucleus. Their complexity allows them to be large, partly due to the presence of organelles and the endomembrane system.

2. Organelle Origin: The presence of chloroplasts in plant cells (and mitochondria in both) relates directly to the Endosymbiotic Theory, explaining the origin of these organelles from independent prokaryotic cells.

3. Cytoskeleton: Both cell types contain components of the cytoskeleton, specifically microfilaments and microtubules. In plant cells, the cell wall provides structural support alongside the cytoskeleton.

4. Nutritional Classification: The presence of chloroplasts in plant cells links to the learning objective of defining organisms based on nutritional requirements. Plants, which perform photosynthesis, are classified as Photoautotrophs (using light for energy and inorganic carbon).

The sources clearly establish that defining organisms based on their energy and carbon nutritional requirements is the final learning objective (Objective 6) for **Topic 1The sources clearly establish that defining organisms based on their energy and carbon nutritional requirements is the final learning objective (Objective 6) for Topic 1: The Cell. This classification system provides a functional categorization of life that complements the structural and evolutionary classification provided by the 3 Domains and endosymbiosis.

Classification by Nutritional Requirements

Organisms are classified based on two criteria: their Energy Source and their Carbon Source.

1. Energy Source

Organisms must have a source of energy. The sources list two main categories for energy acquisition:

• Chemical (Chemo-): Organisms that use chemical sources for energy.

• Light (Photo-): Organisms that use light (sunlight) for energy.

2. Carbon Source (C Source)

Organisms must also have a source of carbon. The sources list two main categories for carbon acquisition:

• Organic: Carbon acquired from organic molecules (typically other organisms or their byproducts).

• Inorganic: Carbon acquired from inorganic molecules (like $\text{CO}_2$).

The Four Main Categories of Organisms

Combining these two sources results in four primary nutritional classifications, presented in a table format in the sources:

The sources also show hypothetical classifications involving organic and inorganic sources that are not typically the primary method, such as Chemoorganoautotroph and Chemolithoheterotroph.

Applying the Classification

The sources provide examples and exercises to ensure understanding of this objective:

• Chemolithoautotroph: An organism that gets carbon from fixing $\text{CO}_2$ (inorganic) and energy from oxidizing iron (chemical) is called a Chemolithoautotroph.

• Chemoorganoautotroph: A new species that uses organic molecules from its environment for energy generation (Chemoorgano) and inorganic molecules as a source of carbon (Autotroph) is classified as a Chemoorganoautotroph.

• Chemolithoheterotroph: A Chemolithoheterotroph acquires its Carbon from Organic molecules.

Context in Topic 1: The Cell

This objective is related to the fundamental understanding of life's diversity and function, established earlier in Topic 1:

• Eukaryotic Organelles: The existence of chloroplasts in plant cells is directly linked to the Photoautotroph classification, as chloroplasts enable the use of light (Photo-) and the fixation of inorganic carbon ($\text{CO}_2$, Auto-) via photosynthesis. The origin of chloroplasts is explained by the Endosymbiotic Theory, where an early eukaryotic cell engulfed a bacteria efficient at photosynthesis.

• Energy Requirement: This classification system sets the stage for future topics (Topics 5 and 6), which deal extensively with Cellular Respiration (Chemo- energy source) and Photosynthesis (Photo- energy source). Biological systems are defined as open systems that must acquire energy and matter from their surroundings. These nutritional requirements determine how organisms fulfill this need.