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Chapter 4

Lecture Outline

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Chapter 4

General Features of Cells

Key Concepts:

• Origin of Living Cells on Earth • Microscopy • Overview of Cell Structure • The Cytosol • The Nucleus and Endomembrane System • Semiautonomous Organelles • Protein Sorting to Organelles • Systems Biology of Cells: A Summary

Origin of life – four overlapping stages

• Nucleotides and amino acids produced prior to the existence of cells

• Nucleotides and amino acids became polymerized to form DNA, RNA and proteins

• Polymers became enclosed in membranes

• Polymers enclosed in membranes acquired cellular properties

Stage 1: Origin of organic molecules

• Conditions on primitive Earth may have been more conducive to spontaneous formation of organic molecules

• Prebiotic or abiotic synthesis Little free oxygen gas

Formed prebiotic soup

• Several hypotheses on where and how organic molecules originated

Origin of organic molecules 1

Reducing atmosphere hypothesis Based on geological data

Atmosphere rich in water vapor, H2, CH4, NH3 (and little O2)

Stanley Miller used a chamber apparatus to simulate this atmosphere and bolts of lightning

Formed precursors, amino acids, sugars and nitrogenous bases

First attempt to apply scientific experiments to understand origin of life

Since 1950s, ideas about early Earth atmosphere changed

• Still, similar results

Figure 4.1

Origin of organic molecules 2

Extraterrestrial hypothesis

Meteorites brought organic carbon to Earth

• Includes amino acids and nucleic acid bases

Opponents argue that most of this would be destroyed in the intense heating and collision

Deep-sea vent hypothesis

Biologically important molecules may have been formed in the temperature gradient between extremely hot vent water and cold ocean water Supported by experiments Complex biological communities found here that derive energy from chemicals in the vent (not the sun)

Figure 4.2a

a) Deep-sea vent hypothesis

Figure 4.2b

b) A deep-sea vent community

b: ©CSSF/Neptune Canada

Stage 2: Organic polymers

• Experimentally, prebiotic synthesis of polymers not possible in aqueous solutions

Hydrolysis competes with polymerization

• Experiments have shown formation of nucleic acid polymers and polypeptides on clay surface

Stage 3: Formation of boundaries

Protobiont

• An aggregate of prebiotically produced molecules and macromolecules

• Have acquired a boundary, such as a lipid bilayer, that allow it to maintain an internal chemical environment distinct from that of its surroundings

Formation of boundaries

Four characteristics of a protobiont:

• Boundary separated external environment from internal contents

• Polymers inside the protobiont contained information

• Polymers inside the protobiont had catalytic function

• Protobionts capable of self-replication

Living cells may have evolved from

• Coacervates Droplets that form spontaneously from the association of charged polymers

Enzymes trapped inside can perform primitive metabolic functions

• Liposomes Vesicles surrounded by a lipid layer

Clay can catalyze formation of liposomes that grow and divide

Can enclose RNA

Figure 4.3

a: Source: A. l. Oparin. From The Origin of Life, New York: Dover, 1952; b: ©Mary Kraft

Stage 4: RNA world

Majority of scientists favor RNA as the first macromolecule of protobionts

Three key RNA functions:

• Ability to store information

• Capacity for self-replication

• Enzymatic function (ribozymes)

DNA and proteins cannot do all 3 functions

Chemical selection

A chemical within a mixture has special properties that cause it to increase in number compared to other chemicals in the mixture

Hypothetical scenario with two steps:

• One of the RNA molecules mutates and has enzymatic ability to attach nucleotides together • Advantage of faster replication

• Second mutation produces enzymatic ability to synthesize nucleotides • No reliance on prebiotic synthesis

Figure 4.4

1a Mutation: A mutation provides an RNA molecule with the catalytic ability to synthesize new RNA molecules using pre-existing RNA molecules as templates.

1b Chemical selection: The amount of this mutant RNA with catalytic function increases because it can self-replicate faster.

2a Mutation: A second mutation provides an RNA molecule with the ability to catalyze a step in the synthesis of ribonucleotides.

2b Chemical selection: The second mutation is also favored, so after many generations, the protobionts have 2 catalytic functions— self-replication and ribonucleotide synthesis.

Advantages of DNA / RNA / protein world

• Information storage DNA would have relieved RNA of informational role and allowed RNA to do other functions

DNA is less likely to suffer mutations

• Metabolism and other cellular functions Proteins have a greater catalytic potential and efficiency

Proteins can perform other tasks – cytoskeleton, transport, etc.

Cell theory

• All living organisms are composed of one or more cells

• Cells are the smallest units of life

• New cells come only from pre-existing cells by cell division

Microscopy

• Resolution Ability to observe two adjacent objects as distinct from one another

• Contrast How different one structure looks from another

Contrast can be enhanced by special dyes to reveal cellular structure

• Magnification Ratio between the size of an image produced by a microscope and its actual size

Two kinds of microscopes

Type of microscope is based on the source of illumination

• Light microscope • Uses light for illumination • Resolution 0.2 micrometer

• Electron microscope • Uses a beam of electrons for illumination • Resolution 2 nanometer (100 times better)

Figure 4.5

Types of Light Microscopy

• Standard (bright field) Light is focused with glass lenses Light passes directly through sample

• Phase contrast Microscope amplifies differences in phase of light transmitted or reflected by sample Improved contrast of denser structures

• Differential interference contrast (DIC or Nomarski microscopy) Another method using optics to improve contrast Good for internal cellular structures

Figure 4.6a

a) Three different methods of light microscopy on the same unstained sample

Standard light microscopy (bright field, unstained sample). Light is passed directly through a sample, and the light is focused using glass lenses. Simple, inexpensive, and easy to use but offers little contrast with unstained samples.

Phase contrast microscopy. As an alternative to staining, this microscope controls the path of light and amplifies differences in the phase of light transmitted or reflected by a sample. The dense structures appear darker than the background, thereby improving the contrast in different parts of the specimen. Can be used to view living, unstained cells.

Differential interference contrast (Nomarski) microscopy. Similar to a phase contrast microscope in that it uses optical modifications to improve contrast in unstained specimens. Can be used to visualize the internal structures of cells and is commonly used to view whole cells or large cell structures such as nuclei.

Courtesy of Molecular Expressions

Figure 4.6b

b) Two different methods of fluorescence microscopy on the same sample

Standard (wide-field) fluorescence microscopy. Fluorescent molecules specifically label a particular type of cellular protein or organelle. A fluorescent molecule absorbs light at a particular wavelength and emits light at a longer wavelength. This microscope has filters that illuminate the sample with the wavelength of light that a fluorescent molecule absorbs, and then only the light that is emitted by the fluorescent molecules is allowed to reach the observer. To detect their cellular location, researchers often label specific cellular proteins using fluorescent antibodies that bind specifically to a particular protein.

Confocal fluorescence microscopy. Uses lasers that illuminate various points in the sample. These points are processed by a computer to give a very sharp focal plane. In this example, this microscope technique is used in conjunction with fluorescence microscopy to view fluorescent molecules within a cell.

Courtesy of Molecular Expressions

Electron microscope types

• Transmission electron microscopy (TEM)

Beam of electrons transmitted through sample Thin slices stained with heavy metals Some electrons are scattered while others pass through to form an image

• Scanning electron microscopy (SEM)

Sample coated with heavy metal Beam scans surface to make 3D image

Figure 4.7

a) Transmission electron micrograph (TEM)

b) Scanning electron micrograph (SEM)

a: ©Don W. Fawcett/Science Source; b: ©Eye of Science/Science Source

Overview of Cell Structure

Two categories of life:

• Prokaryotes Simple cell structure No nucleus

• Eukaryotes More complex cells DNA enclosed within membrane-bound nucleus Internal membranes form organelles

Prokaryotic cells

Two categories of prokaryotes:

• Bacteria Small cells, 1 micrometer to 10 micrometer in diameter Very abundant in environment and our bodies Vast majority are not harmful to humans Some species cause disease

• Archaea Also small cells, 1 micrometer to 10 micrometer in diameter Less common Often found in extreme environments

Typical bacterial cell

• Inside the plasma membrane: Cytoplasm – contained within plasma membrane

Nucleoid region – where DNA is located

Ribosomes – synthesize proteins

• Outside the plasma membrane: Cell wall – provides support and protection

Glycocalyx – traps water, gives protection, help evade immune system

Appendages – pilli (attachment), flagella (movement)

Figure 4.8

a) Diagram of a typical rod-shaped bacterium b) A colorized TEM of Escherichia coli

b: ©Dennis Kunkel Microscopy, Inc./Phototake

Eukaryotic cells

• DNA is housed inside membrane-bound nucleus

• Compartmentalized functions

• Organelles Membrane-bound compartments Each has a unique structure and function

• Variety Shape, size, and organization of cells vary considerably Differences between species Differences between specialized cell types

Animal cell

Access the text alternative for slide images.

Cell morphology

• Size and shape of eukaryotic cells show great variation

• Even cells that share the same genome can have very different morphologies

a: ©Ed Reschke/Getty Images; b: ©Eye of Science/Science Source

Plant cell

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The Proteome Largely Determines the Characteristics of a Cell 1

• How does a single organism produce different types of cells?

• The DNA is identical in each cell of an organism

• However, the cells have different proteomes

a: ©Ed Reschke/Getty Images; b: ©Eye of Science/Science Source

The Proteome Largely Determines the Characteristics of a Cell 2

The DNA in different cells is identical — but they have different proteomes

Structure determines function

Protein profile varies based on:

• Which proteins are expressed • Levels of expression • Which subtypes of proteins are expressed • post-translational modifications

Relevant to disease: proteomes of healthy cells are different from those of cancerous cells

Cell surface area and volume

As cells get larger, the surface area-to-volume ratio gets smaller. This affects cell function

Radius (micrometer): 1 10 100

Surface area  2micrometer  2A 4πr 

12.6 Approximately 1,260 Approximately 124,600

Volume  3micrometer  34V πr3 

4.2 Approximately 4,200 Approximately 4,200,000

Surface area/volume ratio: 3.0 : 1 0.3 : 1 0.03 : 1

The Cytosol

• Region of a eukaryotic cell that is outside the cell organelles but inside the plasma membrane

• Cytoplasm includes everything inside the plasma membrane

Cytosol

Endomembrane system

Semiautonomous organelles

Figure 4.13

Molecular synthesis and breakdown

• Sum of all chemical reactions by cells

• Catabolism

Breakdown of a molecule into smaller components

• Anabolism Synthesis of cellular molecules and macromolecules

• Cytosol is central coordinating region for metabolic activities of eukaryotic cells

Cytoskeleton

Network of three types of protein filaments

• Microtubules Long, hollow cylindrical structures Dynamic instability

• Intermediate filaments Intermediate in size Form twisted, ropelike structure

• Actin filaments Also known as microfilaments Long, thin fibers

Table 4.1

Table 4.1 Types of Cytoskeletal Filaments Found In Eukaryotic Cells

Characteristic Microtubules Intermediate filaments Actin filaments

Diameter 25 nanometer 10 nanometer 7 nanometer

Structure Hollow tubule Twisted filament Spiral filament

(left): ©Thomas Deerinck, NCMIR/Getty Images; (middle): ©Cultura Science/Alvin Telser, PhD/Getty Images; (right): ©Dr. Gopal Murti/SPL/Science Source

Protein composition Hollow tubule composed of the protein tubulin

Can be composed of different proteins including keratin, lamin, and others that form twisted filaments

Two intertwined strands composed of the protein actin

Common functions Cell shape; organization of cell organelles; chromosome sorting in cell division; intracellular movement of cargo; cell motility (cilia and flagella)

Cell shape; provide cells with mechanical strength; anchorage of cell and nuclear membranes

Cell shape; cell strength; muscle contraction; intracellular movement of cargo; cell movement (amoeboid movement); cytokinesis in animal cells

Motor Proteins

Use ATP as a source of energy for movement

Three domains— the head, hinge, and tail

Walking analogy • The ground is the cytoskeletal filament, your leg is the

head of the motor protein, and your hip is the hinge

Three kinds of movements • Motor protein carries cargo along the filament • Motor protein remains in place, the filament moves • Motor protein and filament both restrained – action of

the motor protein exerts a force that bends the filament

Figure 4.14

a) Three-domain structure of myosin, a motor protein

b) Movement of a motor protein along a cytoskeletal filament Access the text alternative for slide images.

Figure 4.15

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Flagella and cilia

• Flagella Usually longer than cilia Present singly or in pairs 9 + 2 microtubule array

• Cilia Often shorter than flagella Tend to cover all or part of the cell surface Also a 9 + 2 microtubule array

• Movement involves the propagation of a bend, beginning at the base and moving toward the tip

Figure 4.16

b: Courtesy of Dr. Barbara Surek, Culture Collection of Algae at the University of Cologne (CCAC); c: ©SPL/Science Source

Figure 4.17

(top left): ©Aaron J. Bell/Science Source; (top middle, bottom middle): ©Dr. William Dentler/University of Kansas

The Nucleus and Endomembrane System

• Network of membranes enclosing the nucleus, endoplasmic reticulum, Golgi apparatus, lysosomes, and vacuoles

• Also includes plasma membrane

• May be directly connected to each other or pass materials via vesicles

Figure 4.18

Nuclear envelope

• Double-membrane structure enclosing nucleus

• Outer membrane of the nuclear envelope is continuous with the ER membrane

• Nuclear pores provide passageways

• Materials within the nucleus are not part of the endomembrane system

Figure 4.19

(top right, middle right): ©Don W. Fawcett/Science Source

Nucleus

• Chromosomes Composed of DNA and proteins = chromatin

• Nuclear matrix Filamentous network Organizes chromosomes

• Ribosome assembly occurs in the nucleolus

Figure 4.20

Courtesy of Felix A. Habermann

Endoplasmic reticulum

• Network of membranes that form flattened, fluid-filled tubules or cisternae

• ER membrane encloses a single compartment called the ER lumen

• Rough endoplasmic reticulum (rough ER) Studded with ribosomes Involved in protein synthesis and sorting

• Smooth endoplasmic reticulum (smooth ER) Lacks ribosomes Detoxification, carbohydrate metabolism, calcium balance, synthesis, and modification of lipids

Figure 4.21

(right): ©Dennis Kunkel Microscopy, Inc./Phototake

Golgi apparatus

• Also called the Golgi body, Golgi complex, or simply Golgi

• Stack of flattened, membrane-bounded compartments

• Vesicles transport materials between stacks

• Three overlapping functions Secretion, processing, and protein sorting

Figure 4.22

Secreted Proteins Move Sequentially Through Organelles of the Endomembrane System

• George Palade used pulse-chase experiments to trace path of radioactive proteins

• Studied pancreatic cells – primary function is protein secretion

• Dark spots in TEM images revealed radioactive proteins

• First evidence that secreted proteins are synthesized into rough ER and move through a series of compartments before secretion

Figure 4.23 through Step 2

HYPOTHESIS Proteins that are to be secreted follow a particular intracellular pathway.

KEY MATERIALS Male guinea pigs.

1. Inject guinea pigs with a radioactive amino acid, 3 H – leucine   . After 3 minutes, inject them with nonlabeled leucine, which is called a chase.

2. At various times after the second injection, remove samples of pancreatic cells.

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Figure 4.23: Steps 3 to 5

3. Stain the sample with osmium tetroxide, which is a heavy metal that binds to membranes.

4. Cut thin sections of the samples, and place a thin layer of radiation-sensitive emulsion over the sample. Allow time for radioactive emission from radiolabeled proteins to precipitate silver atoms in the emulsion. Wash away unprecipitated silver atoms.

5. Observe the sample under a transmission electron microscope.

Figure 4.23 Steps 6 to 8

6. THE DATA

Schematic drawings of transmission electron micrographs

7. CONCLUSION To be secreted, proteins move from the ER to the Golgi to secretory vesicles and then to the plasma membrane, where they are released to the outside of the cell.

8. SOURCE Caro, L.G., and Palade, G.E. 1964. Protein synthesis, storage, and discharge in the pancreatic exocrine cell. An autoradiographic study. Journal of Cell Biology 20: 473 to 495.

Lysosomes

• Contain acid hydrolases that perform hydrolysis

• Many different types of acid hydrolases to break down proteins, carbohydrates, nucleic acids, and lipids

• Autophagy

Recycling of worn-out organelles through endocytosis

Vacuoles

• Functions are extremely varied, and they differ among cell types and environmental conditions

• Central vacuoles in plants for storage and support

• Contractile vacuoles in protists for expelling excess water

• Phagocytic vacuoles in protists and white blood cells for degradation

Figure 4.24

a: ©Biophoto Associates/Science Source; b: Courtesy of Dr. Peter Luykx, Biology, University of Miami; c: ©Dr. David Patterson/Science Source

Peroxisomes

• Catalyze certain reactions that break down molecules by removing hydrogen or adding oxygen

• Hydrogen peroxide (H2O2) is a byproduct

• Catalase breaks down dangerous H2O2 into water and oxygen

Figure 4.25

1. Vesicles bud from the ER and fuse with each other to form a premature peroxisome.

2. The import of additional proteins and lipids results in a mature peroxisome.

3. Mature peroxisomes may divide to produce more peroxisomes.

Plasma membrane

• Boundary between the cell and the extracellular environment

• Functions

Membrane transport in and out of cell, with selective permeability

Cell signaling using receptors

Cell adhesion

Figure 4.26

Cell adhesion: Proteins in the plasma membranes of adjacent cells hold the cells together.

Membrane transport: Proteins in the plasma membrane allow the transport of substances into and out of cells.

Cell signaling: An extracellular signal binds to a receptor in the plasma membrane that activates a signal transduction pathway, leading to a cellular response.

Semiautonomous organelles

• Mitochondria and chloroplasts

• Grow and divide to reproduce themselves

• They are not completely autonomous because they depend on the cell for synthesis of internal components

Figure 4.27

Mitochondria

• Primary role is to make ATP

• Outer and inner membrane

Intermembrane space and mitochondrial matrix

• Also involved in the synthesis, modification, and breakdown of several types of cellular molecules

Figure 4.28

Chloroplasts

• Photosynthesis

Capture light energy and use some of that energy to synthesize organic molecules such as glucose

• Found in nearly all species of plants and algae

• Outer and inner membrane Intermembrane space Thylakoid membrane

Figure 4.29

Chloroplasts and mitochondria

Contain their own DNA, divide by binary fission

a) Binary fission of mitochondria

b) Transmission electron micrograph of the process

1. Mitochondrial genome replicates.

2. Mitochondrion begins to divide by binary fission.

3. Binary fission is completed.

Endosymbiosis of chloroplast and mitochondrion

• Modern mitochondria were derived from purple bacteria, also called α proteobacteria‐

• Similarly, chloroplasts were derived from cyanobacteria (a photosynthetic blue- green bacteria)

Protein sorting

Eukaryotic proteins are sorted to the right destination

• Remain in cytosol

• Cotranslational sorting

• Post-translational sorting

Figure 4.32 Protein synthesis begins on ribosomes in the cytosol.

Cytosolic proteins complete their synthesis in the cytosol and remain there due to the lack of a sorting signal.

For proteins with an ER sorting signal, translation is paused, and the protein is then synthesized into the ER. Some of these proteins contain ER retention signals and remain in the ER. The others are sent to the Golgi via vesicles.

Some of these proteins contain Golgi retention signals and remain in the Golgi. The others are sent, via vesicles, to the lysosomes, plasma membrane, or outside the cell via secretory vesicles.

These proteins are completely synthesized in the cytosol. They contain sorting signals that send them to the nucleus, mitochondria, chloroplasts, or peroxisomes.

Cotranslational sorting

For ER, Golgi, lysosomes, vacuoles, plasma membrane, and secreted proteins

Begins in cytosol during translation

• ER signal sequence binds SRP and associates with ER channel

Second step in cotranslational sorting

• Vesicle buds from ER membrane and fuses with the target membrane and protein is delivered

Figure 4.33

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Post-translational sorting

• Most proteins for nucleus, mitochondria, chloroplasts, and peroxisomes

• Synthesized in cytosol and taken up by target organelle

• Short amino acid sequence directs the protein to its target where it is taken up from the cytosol

Figure 4.34

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Systems biology of cells

• Systems Biology – the study of how new properties of life arise from complex interactions of its components

• “Emergent properties”

• The cells is viewed in terms of functional connections (not just individual molecules)

• Eukaryotic cells have dynamic organization The nucleus, cytosol, endomembrane system and semiautonomous organelles work together

Table 4.2

Table 4.2 A Comparison of Cell Complexity Among Bacterial, Animal, and Plant Cells

Structures Bacteria Animal cells Plant cells

Extracellular structures

Cell wall* Present Absent Present

Flagella/cilia Flagella sometimes present Cilia or flagella present on certain cell types

Rarely presentϮ

Plasma membrane Present Present Present

Interior structures

Cytoplasm Usually a single compartment inside the plasma membrane

Composed of membrane-bound organelles that are surrounded by the cytosol

Ribosomes Present Present Present

Chromosomes Typically one circular chromosome per nucleoid; a nucleoid is not a membrane-bound compartment.

Multiple linear chromosomes in the nucleus, which is surrounded by a double membrane. Mitochondria also have chromosomes.

Multiple linear chromosomes in the nucleus, which is surrounded by a double membrane. Mitochondria and chloroplasts also have chromosomes.

Endomembrane system Absent Present Present

Mitochondria Absent Present Present

Chloroplasts Absent Absent Present

*Note that the biochemical composition of bacterial cell walls is very different from plant cell walls. ϮSome plant species produce sperm cells with flagella, but flowering plants produce sperm within pollen grains that lack flagella.

Figure 4.35

Nucleus • Location of most of the genome • Gene expression and regulation • Organization and protection of

chromosomes via the nuclear matrix • Site for ribosome subunit assembly

Endomembrane system 1. Nuclear envelope

• Double membrane that surrounds the nucleus 2. Endoplasmic reticulum Protein secretion and sorting

• Glycosylation • Lipid synthesis • Metabolic functions and accumulation of 2Ca 

3. Golgi apparatus • Protein secretion and sorting • Glycosylation

4. Lysosome/vacuoles • Degradation of organic molecules • Storage of organic molecules • Accumulation of water (plant vacuoles)

5. Peroxisomes • Breakdown of toxic molecules such as H2O2 • Breakdown and synthesis of organic molecules

6. Plasma membrane • Uptake and excretion of ions and molecules • Cell signaling • Cell adhesion

Semiautonomous organelles 1. Mitochondria

• Synthesis of ATP • Synthesis and modification of other

organic molecules • Production of heat

2. Chloroplasts (plants and algae) • Photosynthesis

Cytosol • Coordination of responses to the

environment • Coordination of metabolism • Synthesis of the proteome • Organization and movement via

cytoskeleton and motor proteins

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