Chapter 4 – Evolutionary Origin of Cells and Their General Features

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:

  • Nucleotides and amino acids were produced first.

  • Polymers formed (RNA and/or DNA, proteins).

  • Polymers became enclosed in membranes.

  • Polymers enclosed in membranes acquired the properties of living cells.

Stage 1: Organic Molecules Formed Prior to the Existence of Cells

• In the 1920s, it was proposed that organic molecules, such as nucleotides and amino acids, formed spontaneously under the conditions that occurred on early Earth.

• It is proposed that organic molecules accumulated in oceans to form a prebiotic soup.

• A few prominent hypotheses about how organic molecules formed include:

  • Reducing atmosphere hypothesis

  • Extraterrestrial hypothesis

  • Deep-sea vent hypothesis

• The reducing atmosphere hypothesis proposes that the early Earth atmosphere facilitated the redox reactions required to form organic molecules; experimental work has supported this hypothesis.

• In the 1950s, the Miller-Urey experiment showed organic molecules could be formed from simple precursors (H2O, H2, CH4, and NH3).

• This type of experiment has documented the formation of sugars, amino acids, lipids, and nitrogenous bases.

• The extraterrestrial hypothesis proposes that organic molecules were carried to the surface of the Earth in meteorites.

• Organic carbon, amino acids, and nucleic acid bases have been found in certain types of meteorites and may have been transported to Earth this way.

• 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 that these 3 hypotheses are not mutually exclusive.

Stage 2: Organic Polymers May Have Formed on the Surface of Clay or in Water

• Scientists hypothesize that the second stage in the origin of life was the formation of organic polymers (DNA, RNA, proteins).

• Many clay minerals are known to bind organic molecules, and it has been demonstrated experimentally that 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 be formed 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 the hypotheses that polymers may have formed on clay surfaces or in the prebiotic soup.

Stage 3: Cell-Like Structures May Have Originated When Polymers Were Enclosed by a Boundary

• The term protobiont is used to describe an aggregate of prebiotically produced molecules within a boundary.

• Protobionts are envisioned as possible precursors of living cells, given the following characteristics:

  • A boundary separated internal contents from the external environment.

  • Polymers inside the protobiont contained information.

  • Polymers inside the protobiont had catalytic function.

  • Protobionts eventually developed the capability to self-replicate.

• Researchers have hypothesized that protobionts may have existed as liposomes, which are 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.

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 has the ability to 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 the occurrence of these processes for RNA molecules.

• 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.

• 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 the amino acids, proteins have greater catalytic ability than RNA.

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.

• Light microscopes use light for illumination; resolution is 0.2 µm.

• Electron microscopes use a beam of electrons for illumination; resolution is 2 nm (100 times better).

• 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 surface to make 3D image; the SEM image below has been colorized.

4.3 Overview of Cell Structure and Function

• Cell structure and function are primarily determined by 4 factors:

  • Matter: each type of cell synthesizes a unique set of molecules/macromolecules that contribute to cell structure.

  • Energy: energy is needed to build molecules and carry out many other cellular functions.

  • Organization: the interior environment of a cell is highly organized; protein-protein interactions create intricate structures within cells.

  • Information: each species has a unique genome (entire complement of genetic material).

• Based on cell structure, cells are categorized as either prokaryotic or eukaryotic; bacteria and archaea have prokaryotic cells.

• Prokaryotic cells are relatively simple; they do not have a nucleus.

• Eukaryotic cells contain a nucleus and other membrane-bound organelles; eukaryotic cells exhibit extensive compartmentalization.

• Protists, fungi, plants, and animals have eukaryotic cells.

• The shape, size, and organization of cells vary among species and among cell types in multicellular organisms (not all cells look like the typical cells shown in figures and 3-D models).

• Plant cells contain organelles similar to those in animal cells.

• Additional structures found in plant cells (but not in animal cells) include chloroplasts, a central vacuole, and a cell wall.

• Most organelles are surrounded by a single or double membrane.

• Another mechanism of compartmentalization is liquid-liquid phase separation, in which aggregated solutes (such as proteins and RNA molecules) separate from the bulk solvent and form a droplet.

• The droplet has a spherical shape with a measurable surface tension and viscosity.

• Molecules can diffuse within the droplet and can pass from the droplet to the surrounding liquid phase.

• The nucleolus is an example of a droplet organelle.

  • Within a droplet organelle:

    • Molecules are close together and can assemble into complexes.

    • The environment is chemically different than the surrounding medium (can affect events such as RNA folding).

• 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 largely determines the characteristics of that cell, and protein profiles vary in many ways:

  • Which proteins are expressed.

  • Levels of expression (low vs. high amount of a specific protein).

  • Which subtypes of proteins are expressed.

  • Post-translational modifications like phosphorylation.

• Cells must exchange materials (nutrients, wastes) across their membrane to survive, and the rate of transport is limited by the surface area of the membrane.

• Internal cell volume (V) and membrane surface area (SA) increase differently as the radius of the cell increases.

• Cells are small because a large SA/V ratio is needed to support sufficient exchange.

4.4 The Cytosol

• The cytosol is the region of a eukaryotic cell that is outside the cell organelles but inside the plasma membrane.

• Cytoplasm is a less specific term; cytoplasm includes everything inside the plasma membrane (cytosol, endomembrane system, semiautonomous organelles, and more).

• Metabolism is the sum of all the chemical reactions occurring in a cell/organism.

• Reactions are organized into 2 major categories: catabolism (breakdown) and anabolism (synthesis).

• Both catabolic and anabolic reactions occur in the cytosol.

• Although many reactions occur within specific organelles, the cytosol is a central coordinating region for many metabolic activities.

• Some ribosomes float freely within the cytosol; ribosomes are sites of protein synthesis.

• The cytoskeleton is a network of 3 different types of protein filaments; each type is constructed from many protein monomers:

  • Microtubules are long, hollow cylinders composed of tubulin subunits; they regularly grow and shorten (dynamic instability).

    • In animal cells, microtubules are organized around the centrosome.

    • Microtubules are important for cell shape and organization (anchor some organelles) as well as chromosome sorting during cell division.

  • Intermediate filaments can be built from several types of proteins; the proteins assemble in a staggered manner to form a twisted, ropelike structure.

    • They are relatively permanent and function as tension-bearing fibers.

  • Actin filaments (microfilaments) are composed of actin subunits; two strands spiral around each other.

    • Actin filaments are also dynamic and provide shape and strength.

• Motor proteins are a type of protein that use ATP as a source of energy to promote various types of movement.

• Motor proteins have 3 domains:

  • A head, the site of ATP binding and hydrolysis

  • A hinge that bends in response to ATP binding/hydrolysis and drives movement

  • A tail, an elongated region attached to other proteins/molecules

• Cells utilize motor proteins to drive different kinds of movement:

  • Movement of cargo

  • Movement of a filament

  • Bending of a filament (used by cilia and flagella)

• Cilia and flagella are cell appendages that bend to produce different types of cell movement.

• Flagella are usually longer than cilia.

  • Present singly or in pairs; propel a cell.

• Cilia are often shorter structures.

  • Numerous; tend to cover all or part of the cell surface; can propel a cell or move fluid across the surface of a cell.

• Both cilia and flagella have the same internal structure, called the axoneme.

  • Contains microtubules (organized in a 9 + 2 array), the motor protein dynein, and linking proteins.

  • Microtubules extend from basal bodies that are anchored to the cytoplasmic side of the membrane.

4.5 The Nucleus and Endomembrane System

• The endomembrane system is a network of membranes that includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, peroxisomes, and plasma membrane.

• Components may be directly connected to each other or pass materials via vesicles.

• The nuclear envelope is the double-membrane enclosing the nucleus; nuclear pores are openings across the nuclear envelope that are formed by the proteins of the nuclear pore complex.

• Chromosomes are inside the nucleus; chromosomes are formed of chromatin, a complex of DNA and proteins.

• The nucleolus is a region of ribosome assembly.

• 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.

• The endoplasmic reticulum (ER) is a network of membranes that form 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 and modification.

• 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 (including glycosylation and proteolysis), and secretion.

• Lysosomes are small organelles found in animal cells that break down macromolecules (carbs, lipids, proteins, and nucleic acids).

• Lysosomes contain many acid hydrolases, enzymes that catalyze hydrolysis reactions and function optimally at an acidic pH.

• Lysosomal pH is about 4.8.

• Vacuoles are compartments that may contain diverse fluid or solid substances; they are prominent in plants, fungi, and certain protists.

• Most vacuoles are made by the fusion of many smaller vesicles.

• The central vacuole of plant cells provides storage and structure, contractile vacuoles provide water balance to maintain cell volume, and food vacuoles contain degradative enzymes.

• Peroxisomes are small organelles found in all eukaryotic cells.

• Peroxisomes catalyze a variety of reactions, including reactions that break down some nutrients (fats and amino acids) and toxins.

• A common by-product is hydrogen peroxide H2O2, which is broken down by the catalase enzyme into water and oxygen gas.

4.6 Semiautonomous Organelles

• Mitochondria and chloroplasts are considered semiautonomous; they grow and divide and contain distinct genetic material however they rely on other parts of the cell for some functions.

• Cells may contain hundreds to a few thousand mitochondria.

• The primary function of mitochondria is to make ATP.

• Mitochondria do not create energy, rather they convert chemical energy stored in the bonds of sugars, fats, and amino acids into chemical energy stored in the bonds of ATP.

• Structures include the outer membrane, intermembrane space, inner membrane with folds called cristae, and the mitochondrial matrix.

• Chloroplasts perform photosynthesis; they capture light energy and use some of that energy to synthesize organic molecules like glucose.

• Found in plants and algae.

• Structures include the outer membrane, intermembrane space, inner membrane, stroma, thylakoid membranes (stacked to form grana), and the thylakoid lumen.

• The mitochondrial genome and the chloroplast genome are the distinct chromosomes found in these organelles.

• Like bacteria, the genomes of these organelles are typically composed of 1 circular chromosome.

• Compared with the nuclear genome, they are very small.

• Mitochondria and chloroplasts increase in number by binary fission; the chromosome is duplicated then the organelle divides into 2 organelles.

• The endosymbiosis theory proposes that mitochondria and chloroplasts originated from bacteria that started living inside a primordial eukaryotic cell.

• Genes in mitochondria and chloroplasts are very similar to bacterial genes.

4.7 Protein Sorting to Organelles

• Most eukaryotic proteins contain sorting signals, short sequences of amino acids that direct them to the proper cellular location.

• In cotranslational sorting, the sorting occurs at the same time as translation (protein synthesis).

  • Used for proteins destined for the ER, Golgi, lysosomes, vacuoles, plasma membrane, as well as secreted proteins.

  • Protein synthesis begins in cytosol, signals recruit the ribosome to the rough ER, then vesicles transport to other organelles.

• In post-translational sorting, the sorting occurs after protein synthesis; the protein is built in the cytosol then moved.

  • Used for most proteins for the nucleus, mitochondria, chloroplasts, and peroxisomes.

• Proteins without any sorting signals remain in the cytosol.

4.8 Extracellular Matrix and Plant Cell Walls

• Animal and plant cells secrete materials that form a meshwork outside of 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.

  • Extremely rigid and strong; woody portions of plants are mostly cell wall.

• The ECM is mostly composed of fibrous proteins and polysaccharides (give a gel-like character).

• ECM functions include:

  • providing strength (like in skin and cartilage).

  • structural support (bone).

  • organization (like when cells are arranged through attachment to ECM).

  • cell signaling (cells in a multicellular organism can respond to changes in the ECM).

• Adhesive proteins adhere ECM components together and to the cell surface; some structural proteins provide tensile strength while others provide elasticity.

• Polysaccharides are the second major component of the ECM (proteins are the first).

• The most abundant types of polysaccharides are glycosaminoglycans (GAGs); they are long and unbranched.

• Most GAGs are linked to core proteins, forming proteoglycans.

• GAGs are highly negatively charged and attract water.

• The primary function of GAGs and proteoglycans is to resist compression, thereby protecting cells.

• The cell walls of plants are usually thicker, stronger, and more rigid than the ECM around animal cells.

• The primary cell wall is made first and is flexible so cells can grow.

  • It contains cellulose as well as other polysaccharides.

• The secondary cell wall is made second, after a plant cell matures; it is deposited between the membrane and the primary cell wall.

  • It mainly contains cellulose.

4.9 Systems Biology of Cells: A Summary

• A eukaryotic cell can be viewed as a system of 4 interacting parts:

  • Nucleus

  • Cytosol

  • Endomembrane system

  • Semiautonomous organelles