Chapter 4 Notes — Evolutionary Origin of Cellswe
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Chapter 4 – Evolutionary Origin of Cells and Their General Features
Chapter Outline:
Origin of living cells on Earth
Microscopy
Overview of cell structure and function
The cytosol
The nucleus and endomembrane system
Semiautonomous organelles
Protein sorting to organelles
Extracellular matrix and plant cell walls
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4.1 Origin of Living Cells on Earth
Section 4.1 Learning Outcomes
Outline the 4 overlapping stages hypothesized to have led to the origin of living cells.
List various hypotheses about how complex organic molecules formed.
Explain the concept of an RNA world and describe how it could have evolved into a DNA/RNA/protein world.
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4.1 Origin of Living Cells on Earth
On modern Earth, every living cell is made from a pre-existing cell by cell division; but how did life get started?
The origin of life can be viewed as a process consisting of 4 overlapping stages:
1) Nucleotides and amino acids were produced first
2) Polymers formed (RNA and/or DNA, proteins)
3) Polymers became enclosed in membranes
4) Polymers enclosed in membranes acquired the properties of living cells
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4.1 Origin of Living Cells on Earth – Stage 1: Organic Molecules Formed Prior to the Existence of Cells
In the 1920s, it was proposed that organic molecules (nucleotides, amino acids) formed spontaneously under early Earth conditions.
These molecules are proposed to have accumulated in oceans to form a prebiotic soup.
Prominent hypotheses about how organic molecules formed:
Reducing atmosphere hypothesis
Extraterrestrial hypothesis
Deep-sea vent hypothesis
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4.1 Origin of Living Cells on Earth – Stage 1: Organic Molecules Formed Prior to the Existence of Cells
The reducing atmosphere hypothesis proposes that the early Earth atmosphere facilitated redox reactions required to form organic molecules; experimental work has supported this.
In the 1950s, the Miller–Urey experiment showed that organic molecules could be formed from simple precursors (H₂O, H₂, CH₄, NH₃).
This type of experiment documented formation of sugars, amino acids, lipids, and nitrogenous bases.
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4.1 Origin of Living Cells on Earth – Stage 1: Organic Molecules Formed Prior to the Existence of Cells
The extraterrestrial hypothesis proposes that organic molecules were carried to Earth's surface in meteorites.
Organic carbon, amino acids, and nucleic acid bases have been found in certain meteorites and may have been transported to Earth this way.
(Illustration credit note: Vecteezy.com)
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4.1 Origin of Living Cells on Earth – Stage 1: Organic Molecules Formed Prior to the Existence of Cells
The deep-sea vent hypothesis proposes that key organic molecules may have originated at deep-sea vents, where superheated water containing many dissolved gases and metal ions mixes with cold seawater.
Complex biological communities are found near modern deep-sea vents.
Note: These 3 hypotheses are not mutually exclusive.
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4.1 Origin of Living Cells on Earth – Stage 2: Organic Polymers May Have Formed on the Surface of Clay or in Water
The second stage in the origin of life was the formation of organic polymers (DNA, RNA, proteins).
Many clay minerals can bind organic molecules; experimentally, nucleic acid polymers and polypeptides can form on the surface of clay given the presence of monomers.
It has also been demonstrated experimentally that peptides can form from amino acids in aqueous solutions under mild conditions (in the presence of carbonyl sulfide, a gas present in volcanic gases and deep-sea vent emissions).
Experimental evidence supports hypotheses that polymers may have formed on clay surfaces or in the prebiotic soup.
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4.1 Origin of Living Cells on Earth – Stage 3: Cell-Like Structures May Have Originated When Polymers Were Enclosed by a Boundary
The term protobiont describes an aggregate of prebiotically produced molecules within a boundary.
Protobionts are envisioned as possible precursors of living cells, with characteristics:
A boundary separating internal contents from the external environment
Polymers inside containing information
Polymers inside having catalytic function
Protobionts eventually developing the capability to self-replicate
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4.1 Origin of Living Cells on Earth – Stage 3: Cell-Like Structures May Have Originated When Polymers Were Enclosed by a Boundary
Researchers hypothesized protobionts may have existed as liposomes, vesicles surrounded by a lipid bilayer.
Some lipids spontaneously form liposomes when dissolved in water, and the lipid bilayer is selectively permeable.
It has been demonstrated that clay can catalyze the formation of liposomes that grow and divide.
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4.1 Origin of Living Cells on Earth – Stage 4: Cellular Characteristics May Have Evolved via Chemical Selection, Beginning with an RNA World
RNA may have been the first macromolecule found in protobionts.
Unlike other polymers, RNA exhibits 3 key functions:
RNA can store information in its base sequence
Due to base pairing, its nucleotide sequence has the capacity for self-replication
RNA can perform a variety of catalytic functions; ribozymes are catalytic RNA molecules
RNA molecules may have developed cell-like characteristics through a process of chemical selection and chemical evolution.
Modern experiments have documented these processes for RNA molecules.
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4.1 Origin of Living Cells on Earth – Stage 4: Cellular Characteristics May Have Evolved via Chemical Selection, Beginning with an RNA World
Chemical selection occurs when a chemical within a mixture has special properties or advantages that cause it to increase in number; selection can lead to chemical evolution, where a population of molecules changes over time to become a new population with different chemical composition.
The RNA world is a hypothetical period on early Earth when both the information needed for life and the catalytic activity of living cells were contained in RNA molecules.
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4.1 Origin of Living Cells on Earth – The RNA World Was Superseded by the Modern RNA/DNA/Protein World
Why might the RNA world evolve into the modern RNA/DNA/protein world?
Incorporation of DNA may have allowed RNA to take on other roles (different binding and catalytic functions).
DNA is more stable than RNA.
Due to the different chemical properties of amino acids, proteins have greater catalytic ability than RNA.
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4.2 Microscopy
Section 4.2 Learning Outcomes
Describe the 3 key parameters in microscopy: resolution, contrast, and magnification.
Compare and contrast the different types of light and electron microscopes and their uses.
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4.2 Microscopy
The microscope is a magnification tool that allows visualization of cellular structures.
Important parameters in microscopy include:
Resolution: a measure of the clarity of an image (the ability to observe two adjacent objects as distinct from one another).
Contrast: relative differences in lightness, darkness, or color between adjacent regions in a sample (can enhance with dyes).
Magnification: the ratio between the size of an image produced by a microscope and the object’s actual size.
For reference values:
Light microscopes: resolution ≈ 0.2 ext{ µm}
Electron microscopes: resolution ≈ 2 ext{ nm} (100× better than light)
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4.2 Microscopy
There are different types of light microscopes.
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4.2 Microscopy – Electron Microscopy Types
There are 2 general types of electron microscopy; both types use heavy metals to “stain” the sample:
Transmission electron microscopy (TEM): A beam of electrons is transmitted through a sample; TEM gives the best resolution.
Scanning electron microscopy (SEM): A beam scans the surface to make a 3D image; the SEM image below has been colorized.
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4.3 Overview of Cell Structure and Function – Learning Outcomes
Compare and contrast the general structural features of prokaryotic and eukaryotic cells.
Explain how the proteome underlies the structure and function of cells.
Analyze how cell size and shape affect the ratio between surface area and volume.
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4.3 Overview of Cell Structure and Function
Cell structure and function are primarily determined by 4 factors:
Matter: each cell synthesizes a unique set of molecules/macromolecules contributing to its structure.
Energy: energy is needed to build molecules and carry out many functions.
Organization: the interior environment is highly organized; protein–protein interactions create intricate structures.
Information: each species has a unique genome (entire complement of genetic material).
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4.3 Overview of Cell Structure and Function – Prokaryotic Cells
Based on cell structure, cells are categorized as prokaryotic or eukaryotic; bacteria and archaea have prokaryotic cells.
Prokaryotic cells are relatively simple; they do not have a nucleus.
A typical bacterial cell is depicted below in the chapter materials.
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4.3 Overview of Cell Structure and Function – Eukaryotic Cells
Eukaryotic cells are compartmentalized by internal membranes to create organelles.
Protists, fungi, plants, and animals have eukaryotic cells.
A typical animal cell is depicted in the materials.
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4.3 Overview of Cell Structure and Function – Variation Among Cells
The shape, size, and organization of cells vary among species and among cell types in multicellular organisms.
Human skin cells and a human neuron illustrate that organelles are the same types, but structures and functions differ.
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4.3 Overview of Cell Structure and Function – Plant Cells
Plant cells contain organelles similar to those in animal cells.
Additional structures found in plant cells (not in animal cells): chloroplasts, a central vacuole, and a cell wall.
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4.3 Overview of Cell Structure and Function – Droplet Organelles
Droplet organelles are a category whose boundary is due to phase separation.
Most organelles are surrounded by a membrane; another mechanism is liquid–liquid phase separation, forming droplets with surface tension and viscosity.
The nucleolus is an example of a droplet organelle.
Inside a droplet organelle: molecules are close together, can assemble into complexes, and the environment is chemically different, affecting processes like RNA folding.
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4.3 Overview of Cell Structure and Function – Proteins and the Proteome
The characteristics of a cell are largely determined by the proteins it makes.
How can cells with the same genome be so different?
Only a subset of genes is expressed in any given cell type due to differential gene regulation.
The proteome is the complete protein composition of a cell or organism.
The set of proteins made by a cell varies in multiple ways:
Which proteins are expressed
Expression levels (low vs high abundance)
Which subtypes of proteins are expressed
Post-translational modifications (e.g., phosphorylation)
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4.3 Overview of Cell Structure and Function – Surface Area to Volume (SA/V) and Cell Size
SA and volume are critical parameters that affect cell sizes and shapes.
Small size is a nearly universal characteristic of cells because cells must exchange materials across their membrane.
The internal cell volume (V) and membrane surface area (SA) increase differently as cell radius increases.
Cells are small to maintain a large SA/V ratio, which supports sufficient exchange.
For a spherical cell, formulas to relate surface area and volume:
SA = 4πr^2,
\quad V = \frac{4}{3}\pi r^3,
\quad \frac{SA}{V} = \frac{3}{r}.
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4.4 The Cytosol – Learning Outcomes
Identify the location of the cytosol in a eukaryotic cell, and describe its general functions.
Compare and contrast the 3 types of protein filaments that form the cytoskeleton.
Explain how motor proteins interact with microtubules or actin filaments to promote cellular movements.
Compare and contrast cilia and flagella.
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4.4 The Cytosol
The cytosol is the region of a eukaryotic cell outside the organelles but inside the plasma membrane.
Cytosol is shown in tan in the figure; cytoplasm is a less specific term and includes everything inside the plasma membrane (cytosol, endomembrane system, semiautonomous organelles, and more).
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4.4 The Cytosol – Metabolism and Ribosomes
Synthesis and breakdown of molecules occur in the cytosol.
Metabolism is the sum of all chemical reactions in a cell/organism.
Reactions are organized into two major categories:
Catabolism (breakdown)
Anabolism (synthesis)
Both catabolic and anabolic reactions occur in the cytosol, though many reactions occur within specific organelles; the cytosol coordinates many metabolic activities.
Some ribosomes float freely within the cytosol; ribosomes are sites of protein synthesis.
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4.4 The Cytosol – The Cytoskeleton Provides Cell Shape, Organization, and Movement
The cytoskeleton is a network of 3 protein filament types, each built from many protein monomers:
Microtubules: long, hollow cylinders of tubulin; diameter ≈ 25 nm; undergo dynamic instability (growth/shrinkage); plus end and minus end.
Intermediate filaments: twisted, ropelike; diameter ≈ 10 nm; provide mechanical strength and tension-bearing support; anchored in the centrosome in animal cells.
Actin filaments (microfilaments): spiral, diameter ≈ 7 nm; provide shape and strength; dynamic; involved in muscle contraction and intracellular movement of cargo.
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4.4 The Cytosol – Cytoskeletal Filaments and Their Roles
Microtubules organize around the centrosome in animal cells; important for cell shape, organelle organization, chromosome sorting during division, intracellular cargo movement, and motility (cilia/flagella).
Intermediate filaments: mechanical strength, anchorage of cell and nuclear membranes.
Actin filaments: contribute to cell shape, mechanical support, and movement (e.g., amoeboid movement).
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4.4 The Cytosol – Motor Proteins
Motor proteins are a class of proteins that use ATP as energy to promote movement.
Three domains:
Head: ATP-binding/hydrolysis site.
Hinge: bends in response to ATP binding/hydrolysis and drives movement.
Tail: attaches to other proteins or molecules.
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4.4 The Cytosol – Motor Proteins in Action
Cells utilize motor proteins to drive different kinds of movement:
Movement of cargo along cytoskeletal tracks.
Movement of a filament (e.g., sliding of microtubules).
Bending of a filament (as used by cilia and flagella).
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4.4 The Cytosol – Cilia and Flagella
Cilia and flagella are cell appendages that bend to produce cell movement.
Flagella are usually longer; present singly or in pairs; propel a cell.
Cilia are usually shorter; numerous; cover all or part of the cell surface; can propel a cell or move fluid across the surface.
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4.4 The Cytosol – Structure of Cilia and Flagella
Both have the same internal structure called the axoneme.
Axoneme contains microtubules organized in a 9 + 2 array, the motor protein dynein, and linking proteins.
Microtubules extend from basal bodies anchored to the cytoplasmic side of the membrane.
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4.5 The Nucleus and Endomembrane System – Learning Outcomes
Describe the structure and organization of the cell nucleus.
Sketch the structures and explain the general functions of all components of the endomembrane system.
Distinguish between the rough endoplasmic reticulum, smooth endoplasmic reticulum, and Golgi apparatus.
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4.5 The Nucleus and Endomembrane System
The endomembrane system is a network of membranes that includes the nuclear envelope, endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles, peroxisomes, and plasma membrane.
Components may be directly connected or exchange materials via vesicles.
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4.5 The Nucleus and Endomembrane System – The Nucleus
The eukaryotic nucleus contains chromosomes.
The nuclear envelope is a double membrane with nuclear pores formed by the nuclear pore complex.
Chromosomes reside inside the nucleus as chromatin (DNA + proteins).
The nucleolus is a region of ribosome assembly.
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4.5 The Nucleus and Endomembrane System – Nuclear Structure and Organization
The structure of the nuclear envelope is supported by the nuclear matrix, a network of filamentous proteins.
The nuclear matrix also organizes chromosomes into distinct, non-overlapping chromosome territories.
Chromosomes can be labeled with chromosome-specific dyes to study organization.
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4.5 The Nucleus and Endomembrane System – Endoplasmic Reticulum (ER)
The ER is a network of membranes that forms flattened, fluid-filled tubules.
The ER membrane is continuous with the outer nuclear membrane.
Rough ER is studded with ribosomes; functions include protein sorting, insertion of membrane proteins, and glycosylation.
Smooth ER lacks ribosomes; functions include metabolism, detoxification, Ca^{2+} storage, and lipid synthesis/modification.
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4.5 The Nucleus and Endomembrane System – Golgi Apparatus
The Golgi apparatus consists of a stack of flattened membranous sacs; each enclosed compartment is a cisterna.
Vesicles transport materials between stacks, between the Golgi and ER, and between the Golgi and plasma membrane.
Functions include protein sorting, protein processing (glycosylation and proteolysis), and secretion.
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4.5 The Nucleus and Endomembrane System – Lysosomes
Lysosomes are small organelles in animal cells that break down macromolecules (carbohydrates, lipids, proteins, and nucleic acids).
Lysosomes contain many acid hydrolases that catalyze hydrolysis and function best at acidic pH.
Lysosomal pH is about 4.8.
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4.5 The Nucleus and Endomembrane System – Vacuoles
Vacuoles are compartments that may contain diverse fluids or solids; prominent in plants, fungi, and some protists.
Most vacuoles arise from fusion of smaller vesicles.
The central vacuole of plant cells provides storage and structure; contractile vacuoles regulate water balance; food vacuoles contain degradative enzymes.
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4.5 The Nucleus and Endomembrane System – Peroxisomes
Peroxisomes catalyze detoxifying reactions.
They are small organelles found in all eukaryotic cells.
Peroxisomes catalyze reactions that break down certain nutrients (fats, amino acids) and toxins.
A common by-product is hydrogen peroxide (H₂O₂), which is broken down by catalase into water and oxygen gas.
Peroxisome formation and maturation are depicted in the figures.
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4.6 Semiautonomous Organelles – Learning Outcomes
Sketch the structures and explain the general functions of mitochondria and chloroplasts.
Discuss the evidence for the endosymbiosis theory.
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4.6 Semiautonomous Organelles
Mitochondria and chloroplasts are semiautonomous; they grow and divide and contain distinct genetic material but rely on other parts of the cell for some functions.
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4.6 Semiautonomous Organelles – Mitochondria
Mitochondria provide most of the cell’s ATP.
Cells may contain hundreds to a few thousand mitochondria.
Primary function: to make ATP.
Mitochondria do not create energy themselves; they convert chemical energy stored in the bonds of sugars, fats, and amino acids into chemical energy stored in ATP.
Structures include: outer membrane, intermembrane space, inner membrane with cristae, and the mitochondrial matrix.
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4.6 Semiautonomous Organelles – Chloroplasts
Chloroplasts carry out photosynthesis; they capture light energy and use some of that energy to synthesize organic molecules like glucose.
Found in plants and algae.
Structures include: outer membrane, intermembrane space, inner membrane, stroma, and thylakoid membranes (stacked to form grana) and the thylakoid lumen.
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4.6 Semiautonomous Organelles – Genetic Material and Division
Mitochondria and chloroplasts contain their own genetic material and divide by binary fission.
The mitochondrial genome and chloroplast genome are distinct chromosomes found in these organelles.
Like bacteria, their genomes are typically circular and small compared with the nuclear genome.
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4.6 Semiautonomous Organelles – Endosymbiosis Basis
Mitochondria and chloroplasts are derived from ancient symbiotic relationships.
The endosymbiosis theory proposes that mitochondria and chloroplasts originated from bacteria living inside a primordial eukaryotic cell.
Genes in mitochondria and chloroplasts resemble bacterial genes.
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4.7 Protein Sorting to Organelles – Learning Outcomes
List the categories of proteins that are sorted cotranslationally and post-translationally.
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4.7 protein Sorting to Organelles – General Sorting Concepts
Most eukaryotic proteins contain sorting signals, short amino acid sequences that direct them to the proper location.
In cotranslational sorting, sorting occurs during translation; used for proteins destined for the ER, Golgi, lysosomes, vacuoles, plasma membrane, and secreted proteins.
Protein synthesis begins in the cytosol; signals recruit the ribosome to the rough ER, then vesicles transport to other organelles.
In post-translational sorting, sorting occurs after protein synthesis; the protein is built in the cytosol and then moved to the target organelles.
Used for most proteins destined for the nucleus, mitochondria, chloroplasts, and peroxisomes.
Proteins without sorting signals remain in the cytosol.
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4.7 Protein Sorting to Organelles – Diagrammatic Summary
Cotranslational sorting to ER: ribosome associates with ER, polypeptide enters the ER lumen, some proteins remain in the ER, others go to Golgi via vesicles.
Post-translational sorting to nucleus, mitochondria, chloroplasts, peroxisomes: completed polypeptide in cytosol; sorting signals route to respective organelles.
Cytosolic proteins with no sorting signals remain in cytosol.
Sorting signals include ER signal peptide and various retention/retrieval signals for Golgi, lysosome/vacuole, plasma membrane, and extracellular secretion.
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4.8 Extracellular Matrix and Plant Cell Walls – Learning Outcomes
Explain the functional roles of the extracellular matrix (ECM) in animals.
Describe the major structural components of the ECM of animals.
Describe the structure and function of plant cell walls.
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4.8 Extracellular Matrix and Plant Cell Walls – ECM and Plant Cell Walls Overview
Animal and plant cells secrete materials that form a meshwork outside the cell’s membrane.
Animal cells are surrounded by the extracellular matrix (ECM).
Bone and cartilage are mostly ECM, with only a few scattered cells.
Plant cells are surrounded by the cell wall; the wall is extremely rigid and strong; woody portions of plants are mostly cell wall.
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4.8 Extracellular Matrix and Plant Cell Walls – ECM Functions
The ECM in animals supports and organizes cells and plays a role in cell signaling.
The ECM is mostly composed of fibrous proteins and polysaccharides (give a gel-like character)
Functions include:
Providing strength (e.g., skin, cartilage)
Structural support (bone)
Organization (attachment to ECM)
Cell signaling (cells respond to ECM changes in multicellular organisms)
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4.8 Extracellular Matrix and Plant Cell Walls – ECM Components
Adhesive and structural proteins are major components of the ECM of animals; they help join ECM components and attach to the cell surface.
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4.8 Extracellular Matrix and Plant Cell Walls – ECM Polysaccharides
Animals secrete polysaccharides into the ECM as the second major component (after proteins).
The most abundant polysaccharides are glycosaminoglycans (GAGs): long, unbranched.
Most GAGs are linked to core proteins, forming proteoglycans.
GAGs are highly negatively charged and attract water, contributing to resistance to compression and protection of cells.
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4.8 Extracellular Matrix and Plant Cell Walls – Plant Cell Walls
The plant cell wall provides strength and resistance to compression.
The primary cell wall is made first and is flexible to allow growth; contains cellulose and other polysaccharides.
The secondary cell wall is deposited after maturation, between the membrane and primary cell wall; it mainly contains cellulose.
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4.9 Systems Biology of Cells: A Summary – Learning Outcomes
Outline the differences in complexity among bacteria, animal cells, and plant cells.
Describe how a eukaryotic cell can be viewed as 4 interacting systems: the nucleus, cytosol, endomembrane system, and semiautonomous organelles.
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4.9 Systems Biology of Cells: A Summary – Bacteria vs. Eukaryotic Systems
Bacterial cells are relatively simple systems.
Eukaryotic cells are a system of 4 interacting parts: the nucleus, cytosol, endomembrane system, and semiautonomous organelles.
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4.9 Systems Biology of Cells: A Summary – Eukaryotic Cell as a 4-Part System
A eukaryotic cell can be viewed as a system of 4 interacting parts (nucleus, cytosol, endomembrane system, semiautonomous organelles).
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Chapter 4 Summary
4.1 Origin of living cells on Earth:
Stage 1: Organic molecules formed prior to the existence of cells (reducing atmosphere, extraterrestrial, deep-sea vent hypotheses).
Stage 2: Organic polymers may have formed on the surface of clay or in water.
Stage 3: Cell-like structures may have originated when polymers were enclosed by a boundary (liposomes).
Stage 4: Cellular characteristics may have evolved via chemical selection, beginning with an RNA world.
The RNA world was superseded by the modern DNA/RNA/protein world.
4.2 Microscopy: Light and electron microscopes visualize cells; key parameters include resolution, contrast, and magnification.
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Chapter 4 Summary (continued)
4.3 Overview of cell structure and function:
Prokaryotic cells are relatively simple; eukaryotic cells are compartmentalized by internal membranes to create organelles.
Droplet organelles (e.g., nucleolus) arise via phase separation.
The proteome largely determines cell characteristics.
SA/V ratio is critical for cell exchange and size.
4.4 The cytosol:
Metabolism occurs in the cytosol; the cytoskeleton provides shape, organization, and movement; motor proteins drive movement along cytoskeletal tracks.
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Chapter 4 Summary (continued)
4.5 The nucleus and endomembrane system:
The nucleus contains chromosomes; the endomembrane system includes the ER, Golgi, lysosomes, vacuoles, peroxisomes, and plasma membrane.
4.6 Semiautonomous organelles:
Mitochondria provide ATP; chloroplasts perform photosynthesis; both contain their own DNA and divide by binary fission; derived from ancient symbiosis.
4.7 Protein sorting to organelles:
Sorting signals direct proteins to destinations; cotranslational sorting targets ER, Golgi, lysosomes, vacuoles, plasma membrane, and secreted proteins; post-translational sorting targets nucleus, mitochondria, chloroplasts, peroxisomes; cytosolic proteins lack sorting signals.
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Chapter 4 Summary (continued)
4.8 ECM and plant cell walls:
ECM supports and organizes cells and participates in signaling; ECM components include adhesive/structural proteins and proteoglycans.
Plant cell walls provide structural strength and rigidity via cellulose-containing layers (primary and secondary).
4.9 Systems biology of cells: a summary:
Bacteria are simpler; eukaryotic cells comprise four interacting parts: nucleus, cytosol, endomembrane system, and semiautonomous organelles.
Page 63–66 (Chapter Endnotes)
Chapter 4 Summary highlights across sections; essential takeaways mirror the page-by-page summaries above.