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 The Organization of Cells
overview

The preceding chapters in Life dealt with the fundamental chemical processes and molecules in biology. Chapter 4 provides an overview of the internal and external structures of prokaryotic and eukaryotic cells. We can leave chemistry alone for a bit and concentrate on the structure of the smallest living units. This chapter represents a huge step forward in complexity from simple molecules to the accumulation of molecules referred to as cells. This may be the first time your students have been exposed to the structure of a prokaryote. Prokaryotes may be simple, but represent the oldest type of cell, so they must be doing something right! The eukaryotic cell is then examined in detail with the major subcellular structures discussed. The chapter finishes with an introduction to extracellular components of plant and animal cells.
chapter outline

CHAPTER 4 INFORMATION:
COMMENTS:
Read the chapter, not just the summary.
We will cover some of the material in later lectures.
CHAPTER 4: 64-90
SELF-QUIZ: all
APPLYING CONCEPTS: 1-3
LECTURE NOTES:
The cell theory states that cells are the
fundamental, smallest unit of life
What cells do:
Keep biomolecules from drifting away
Maintain concentration of molecules
Keep unwanted things out
Let or get desirable substances in
Let or get undesirable substances out
Obtain and process energy
Synthesize necessary products
Cells are small of necessity
Intracellular molecules move by
diffusion
Volume increases faster than surface
area (Fig. 4.2)
------------
All cells are like tiny water balloons
whose phoshoplipid bilayer skins
called a plasma membrane
Enclose the cellular contents
Regulate movement of substances
into and out of the cell
Help give the cell shape
Can be used in intercellular
communication
(Some cellular components DO lie
outside the plasma membrane)
All cells contain
cellular fluid called the cytosol
protein-synthesizing ribosomes
------------
Most organisms are prokaryotes - single
cells that do not have a nucleus (4.3)
Their DNA exists as a nucleoid
Cells with nuclei are eukaryotic
Prokaryotic cells tend to be smaller
than eukaryotic cells
In a few, certain cellular reactions occur in
plasma membrane infoldings (Fig. 4.4)
e.g. photosynthesis in stacks
Structures can occur outside the plasma
membrane
Bacteria can have a peptidoglycan wall
Or a polysaccharide slime capsule
Flagella provide motion (Fig. 4.5)
Pili provide intercellular adhesion
------------
Eukaryotic cells are generally larger than
prokaryotic cells
They mitigate the size problem by:
Altered cell shape
Sequestering molecules and
processes in internal compartments
These enclosed internal compartments
are termed organelles (Fig. 4.7)
All such organelles are enclosed by
phospholipid bilayers
Some organelles have single bilayers:
endoplasmic reticulum, Golgi
bodies, lysosomes, vesicles
Three organelles have two bilayers:
nucleus, plastid, mitochondrion
Organelles are suspended in a liquid
matrix called the cytosol
--------------
Protist, fungal, plant and animal cells have
many similarities
But also many differences
A nucleus is present in all eukaryotes (4.8):
About 5 µm in diameter
Nuclear envelope is a balloon-within-
a-balloon phospholipid bilayer pair
Nuclear pores are gates in and out
Stabilized by nuclear lamina
Inside of the nucleus is nucleoplasm,
Location of chromosomal DNA,
and thus of cellular regulation
Everything outside the nucleus but
inside the cell is the cytoplasm
---------------
Mitochondria are present in the cells of
most eukaryotes (Fig. 4.11)
Involved in cellular respiration (Ch. 7)
i.e., making ATP using the energy in
glucose
Can be 1000 per cell; 2-8 µm
Organization:
outer membrane
intermembrane space
inner membrane with cristae
matrix
--------------
Plastids are found in plants and algae
Proplastids can become:
amyloplastsófood storage (starch)
chromoplastsópigments (carotenoids)
chloroplastsóphotosynthesis (Chap. 8)
Chloroplasts make the cell green (Fig 4.13)
1-100 per cell; 5-20 µm long
Organization:
outer membrane
intermembrane space
inner membrane
stroma
thylakoid membrane
thylakoid space
Thylakoids are stacked in grana
Chlorophyll is in the thylakoid membrane
------------
Mitochondria and plastids are the result
of endosymbiosis
"Cells-within-a-cell"
Mitochondria are derived from
a proteobacteria and have their
own a proteobacterial-type DNA
Plastids are derived from cyanobacteria
and have their own cyanobacterial-like
DNA
Both also have their own bacterial-type
ribosomes and inner membranes (4.15)
-------------
Endoplasmic reticulum is of two types
rough
smooth
Rough ER is where secreted proteins are
made and integral proteins modified
(Fig. 4.16)
Flattened sacs with a single lipid bilayer
Inside of ER is called the lumen
ER sacs are interconnected, and also
connected to nuclear membrane
Look rough because they are studded
with ribosomes
ER proteins are injected into the bilayer
and/or lumen
Thus the lumen is unlike the cytosol
The inner surface of the lipid bilayer
is unlike the outer surface
Sections of the ER bilayer can bud off to
form vesicles for molecular transport
-------------
Other organelles you should read about:
Smooth ER
Golgi apparatus
Lysosomes
Vacuoles
Peroxisomes
Glyoxisomes
-------------
The cytoskeleton is a dynamic scaffolding
for the cytoplasm (Fig. 4.21)
Microfilaments consist of two intertwined
actin polymers
Continuous assembly and disassembly
in most cell types
Facilitate cytoplasmic streaming and
amoeboid motion
Actin plus myosin forms muscle fibers
Microtubules
Strings of tubulin heterodimers (a & b)
Polymerized at one end of the string
and degraded from the other end
Cellular components move along
microtubule filaments (4.26)
Sets of microtubules are what make
cilia and flagella move (see text)
key terms

Cell theory The encompassing theory that all living organisms are made up of cells that are themselves derived from other cells. Here is where you can point out the differences between viruses, which require cells for their replicating, and bacteria, which are self-replicating cells.
Prokaryotic cell Eubacteria and Archaebacteria. Cells without membrane-bound compartments. The most ancient type of cell.
Eukaryotic cell All other cell types. Contain membrane-bound organelles.
Plasma membrane A common feature of all cells; encloses the entire cell. Students may think that the plasma membrane is simply a bag enclosing the cell, but it is so much more. This is the interface between the cell and its surroundings; it regulates what enters or exits the cell and how the cell reacts to changes in its environment.
Nucleoid DNA in a prokaryote.
Cytoplasm, cytosol These two terms are often mistakenly used interchangeably. The cytoplasm is the nonorganelle component of the cell and includes insoluble macromolecules and macromolecular complexes. The cytosol is the fluid (water, ions, soluble molecules) inside the cell.
Ribosomes The role of ribosomes will be dealt with in later chapters, but here is the first example of a multisubunit structure found in cells. The students are familiar with the quaternary structure of proteins, so you can extend that concept to a structure that contains many proteins and nucleic acids. If a single protein is a marble, a ribosome would be a basketball (or larger) in size.
Cell wall A polymer of sugars, such as peptidoglycan, that encloses bacteria and provides for structural support. Outside of and separate from the plasma membrane. The functional similarity to plant and fungal cell walls is rather compelling.
Outer membrane
Capsule
Mesosomes A general term for membrane-bound areas in prokaryotes. Confusion can reign here since this is a prokaryotic feature! However, these structures are always contiguous with the plasma membrane and not separate organelles.
Flagella, pili Projections from bacterial cells that are used for transport (flagella) or adhesion (pili). The flagella in bacteria are distinct structurally from those in eukaryotes, even though the names are the same. Another potential area of confusion for students.
Resolution A concept students routinely confuse with magnification. Resolution is the smallest distance in which a single object can be distinguished as actually composed of two separate points. The increased resolving power of the electron microscope versus the light microscope is a function of the shorter wavelength of electrons versus visible light.
Transmission electron microscopy
Scanning electron microscopy
Organelles A general term for the independent functional components of cells. Most commonly thought of as membrane bound and, for the most part, organelles are membrane bound, but large cellular structures such as ribosomes are also organelles.
Nucleus Repository for DNA in eukaryotic cells. A complex structure enclosed by a double membrane nuclear envelope. The double membrane structure is why we refer to it as an envelope, not a membrane. There exist a large number of nuclear pores that tightly regulate the movement of materials into and out of the nucleus.
Chromatin An important concept for students to learn now. Often they feel that DNA in cells is organized into chromosomes, but this is only during division. Throughout most of the life of the cell, DNA is found in chromatin, a dispersed, fibrous mesh of DNA and proteins. The chromatin is not free to float around the nucleus since it is attached to the nuclear lamina present on the inner side of the nuclear envelope.
Nucleoplasm
Nucleoli An often overlooked feature of nuclei. Site of ribosomal RNA synthesis and ribosome formation. An excellent example of subcompartmentalization of an organelle.
Mitochondria Site of energy synthesis in cells. Another organelle that has two membranes, an outer and inner membrane. The outer membrane simply delineates the organelle and is essentially completely porous. The inner membrane is folded into structures referred to as cristae. Cristae enclose the mitochondrial matrix, a mixture of proteins, DNA, and ribosomes. The energy-producing machinery is found in the inner membrane and matrix. The structure (two membranes) and components (independent DNA and ribosomes) have led to the suggestion that mitochondria (and choloroplasts) were once autonomous prokaryotes that were engulfed and took up residence in the ancestors to eukaryotic cells. This is referred as the endosymbiosis theory.
ATP
Plastids Another potentially new term. This is a general term for a group of organelles found almost exclusively in plants, with functions including light harvesting (chloroplasts), pigment production (chromoplasts), and starch storage (leucoplasts).
Chloroplast The most commonly known plastid. Students seem to have a continual problem remembering the internal structure of chloroplasts. One reason for this may be due to the subtle difference between the chloroplast and the mitochondrion. The inner membrane of the mature chloroplast does not fold into the internal structures as it does in the mitochondrion. Instead, there are separate stacks of circular membranes called thylakoids. The thylakoids associate into stacks called grana. However, there is a functional analogy to mitochondria since the light-harvesting pigments are found in the thylakoids. Chloroplasts also have a matrix, which contains proteins, DNA, and ribosomes and is enclosed by the inner membrane. However, it is referred to as the stroma rather than the choloroplast matrix.
Endosymbiosis theory
Endomembrane system
Endoplasmic reticulum A huge, interconnected series of membrane-bound areas in the cell. Enclosed by a single membrane, there are regions that are specialized for different functions. The rough endoplasmic reticulum is the site of protein synthesis and folding into the tertiary structure. In the smooth endoplasmic reticulum, protein modification continues, and other important molecules such as lipids are synthesized.
Golgi apparatus A series of flattened sacs where proteins are modified and targeted for their final destination. One of the features of the cell your students will probably recognize.
Lysosomes Potentially a new organelle for your students. Lysosomes carry out the degradative functions in the cell in a structure enclosed by a single membrane. They may not be as glamorous as the nucleus or mitochondria, but ask the class what they think would be the effect of protein-degrading enzymes floating free in the cytoplasm.
Phagocytosis
Phagosome
Secondary lysosome
Microbodies A general term for small, single membrane-bound organelles found in plants and animals. Functions include destruction of toxic peroxides (peroxisomes) or carbohydrate production in plants (glyoxysome).
Vacuoles When students are looking at cells in the microscope and are asked to name the structures, they most often refer to anything other than the nucleus or chloroplasts as a vacuole. While abundant, there are many other organelles in a cell! In animal cells, vacuoles serve as transport or storage areas for ingested materials or wastes. In plants, a central vacuole represents the majority of the cell volume and serves a number of important roles. In protists, there is a specialized vacuole, the contractile vacuole, which actively pumps water out of the cell.
Cytoskeleton A group of three proteinaceous filament structures and accessory proteins that serve structural and locomotory roles in the cell. The name cytoskeleton may cause some confusion since a skeleton is thought to be immobile and rigid, whereas the cytoskeleton is a dynamic group of different components.
Microfilaments Polymers of the protein actin. Involved in cell shape and movement. A primary component of muscle fibers.
Intermediate filaments Polymers of one or several different proteins. Involved in mechanical strength. Enriched in tissues such as epidermis.
Microtubules Polymers of tubulin. Appear as hollow tubes as opposed to filaments. Multiple roles including cell shape, vesicle movement, and chromosome movement during mitosis.
Flagella, cilia Eukaryotic structures that project from the cell and are used for locomotion. The core is formed by microtubules. Completely different from flagella or pili in prokaryotes.
Doublets
Kinesin, dynein Proteins that act as molecular motors. Attach to microtubules and use the energy in ATP to move things along the microtubule.
Basal body, centrioles Specialized internal structures that organize the formation of microtubule-based structures.
Extracellular
Cell wall In plants, this outer layer is formed from cellulose. Encloses and supports the cell.
Plasmodesmata Specialized areas of the plasma membrane in plants that extend through the cell wall.
Extracellular matrix A variable mixture of proteins and carbohydrates that surrounds cells in various tissues. Provides an attachment and support function. Bone and cartilage are good examples of extracellular matrices.
Basal lamina
Proteoglycan
Cell fractionation Techniques used to rupture cells and then separate specific components using various forms of centrifugation. Development of this technique was critical to our investigations into subcellular structure and function.
Centrifuge
Differential centrifugation
Equilibrium centrifugation
Density gradient
chapter cross–references

A number of other chapters are referred to in Chapter 4. Below are the chapters referred to and the corresponding page number(s) where the reference is found in Chapter 4.
Chapter Page(s)
3 Macromolecules: Their Chemistry and Biology 75, 79, 81, 90
5 Cellular Membranes 74, 88, 94
6 Energy, Enzymes, and Metabolism 77
7 Cellular Pathways That Harvest Chemical Energy 78
9 Chromosomes, the Cell Cycle, and Cell Division 75, 89
12 From DNA to Protein: Genotype to Phenotype 75, 77, 81
13 The Genetics of Viruses and Prokaryotes 92
14 The Eukaryotic Genome and Its Expression 92
15 Development: Differential Gene Expression 75
18 Natural Defenses against Disease 75, 81
25 Bacteria and Archaea: The Prokaryotic Domains 66
26 Protists and the Dawn of the Eukarya 81, 85
31 The Flowering Plant Body 90
44 Effectors 88, 89
47 Animal Nutrition 81
Thought Questions
1. If cells need to be small, then why is a bird’s egg so large? Is the entire egg actually a cell?
2. Consider the anti-cancer drug Taxol, which acts to keep microtubules rigid. How does this fight cancer?
3. If each cell is an individual, then is one of your own cells an individual by itself? What if you used this cell to make a copy of yourself?