A Tour of the

Cells

1
Microscopy
 Microscopes

•The discovery and early study of cells improved

with the invention of microscopes in the 17th
century.
•In a light microscope (LM) visible light passes
through the specimen and then through glass
lenses.
•The lenses refract light such that the image is
magnified into the eye
 Microscopes

•Magnification is the ratio of an object’s image to

its real size.
•Resolving power is a measure of image clarity.
•It is the minimum distance two points can be
separated by and still be viewed as two
separate points.
 Microscopes
•Light microscopes can
magnify effectively to
about 1,000 times the
size of the actual
specimen.
•At higher
magnifications, the
image blurs
 Microscopes

•While a light microscope can resolve

individual cells, it cannot resolve
organelles.
•To resolve smaller structures we use an
electron microscope (EM), which focuses a
beam of electrons through the specimen
or onto its surface.
 TEM
• Transmission electron microscopes (TEMs) are used
mainly to study the internal ultrastructure of cells.
• A TEM aims an electron beam through a thin section of the
specimen.
• The image is focused
and magnified by
electromagnets.
• To enhance contrast,
the thin sections are
stained with atoms
of heavy metals.
 SEM
• Scanning electron microscopes (SEMs) are useful for
studying surface structures.
• The sample surface is covered with a thin film of gold.
• The beam excites electrons on the surface.
• These secondary electrons are collected and focused on a
screen.
• The SEM has great
depth of field,
resulting in an
image that seems
three-dimensional.
 Electron Microscopes
• Electron microscopes reveal organelles, but they can only
be used on dead cells
• Light microscopes do not have as high a resolution, but
they can be used to study live cells.
• Microscopes are a major tool in cytology, the study of cell
structures.
• Cytology coupled with biochemistry, the study of molecules
and chemical processes in metabolism, developed into
modern cell biology.
 Isolating Cell Organelles

• The goal of cell fractionation is to separate the major

organelles of the cells so that their individual functions
can be studied.
 Cell Fractionation

• This process is driven by an ultracentrifuge, a machine

that can spin at up to 130,000 revolutions per minute
• Fractionation begins with homogenization, gently
disrupting the cell.
• Then, the homogenate is spun in a centrifuge to
separate heavier pieces into the pellet while lighter
particles remain in the supernatant.
• Repeating the process for longer & faster collects
smaller organelles in the pellet
Facts About Cells
 Cell Theory

•Cells are the basic living units of

organization and function
•All cells come from other cells
•Work of Schleiden, Schwann, and
Virchow contributed to this theory
•Each cell is a microcosm of life
Biological size and cell diversity
 Cell Size

•Cell surface area-to-volume ratio

•Plasma membrane must be large enough
relative to cell volume to regulate passage
of materials
•Volume increases faster than surface area
so cell must DIVIDE
•Cell size and shape related to function
 Prokaryotes & Eukaryotes

• All cells are surrounded by a plasma membrane.

• The semifluid substance within the membrane is the
cytosol, containing the organelles.
• All cells contain chromosomes which have genes in the
form of DNA.
• All cells also have ribosomes, tiny organelles that make
proteins using the instructions contained in genes.
 Prokaryotes & Eukaryotes

• A major difference between prokaryotic and

eukaryotic cells is the location of chromosomes.
• In a eukaryotic cell, chromosomes are contained in
a membrane-enclosed organelle, the nucleus.
• In a prokaryotic cell, the DNA is concentrated in the
nucleoid region without a membrane separating it
from the rest of the cell.
PROKARYOTE
 Prokaryotes & Eukaryotes

•In eukaryote cells, the chromosomes are contained

within a membranous nuclear envelope.
•The region between the nucleus and the plasma
membrane is the cytoplasm.
•All the material within the plasma membrane of a
prokaryotic cell is cytoplasm.
 Prokaryotes & Eukaryotes

•Within the cytoplasm of a eukaryotic cell

is a variety of membrane-bounded
organelles of specialized form and
function.
•These membrane-bounded organelles are
absent in prokaryotes.
 Prokaryotes & Eukaryotes
• Eukaryotic cells are bigger than prokaryotic cells
•Ability to carry on metabolism set limits on cell
size
•Approximate Cell Size:
• Smallest bacteria, mycoplasmas between 0.1 to 1.0
micron
• Most bacteria are 1-10 microns in diameter, while
Eukaryotic cells are typically 10-100 microns in
diameter
•The plasma membrane functions as a selective
barrier that allows passage of oxygen, nutrients,
and wastes for the whole volume of the cell.
 Importance of Surface Area
• The volume of cytoplasm determines the need for this
exchange.
• Rates of chemical exchange may be inadequate to
maintain a cell with a very large cytoplasm.
• The need for a surface sufficiently large to
accommodate the volume explains the microscopic size
of most cells.
• Larger organisms do not generally have larger cells than
smaller organisms - simply more cells.
 Internal Membranes

•A eukaryotic cell has extensive and elaborate

internal membranes
•Partition the cell into compartments
•Many enzymes are built into membranes
•Membrane compartments are involved in many
METABOLIC functions
 Membrane Structure

•The general structure of a biological membrane

is a double layer of phospholipids with other
lipids and diverse proteins.
•Each type of membrane has a unique
combination of lipids and proteins for its specific
functions.
• For example, those in the membranes of
mitochondria function in cellular respiration.
Nucleus & Ribosomes
 Nucleus

• Contains most of the genes in a eukaryotic cell.

• Some genes are located in mitochondria and
chloroplasts.
• Averages about 5 microns in diameter.
• Separated from the cytoplasm by a double membrane.
• These are separated by 20-40 nm.
• Where the double membranes are fused, a pore allows
large macromolecules and particles to pass through.
• The nuclear side of
the envelope is lined
by the nuclear
lamina, a network of
intermediate
filaments that
maintain the shape
of the nucleus.
• Within the nucleus, the DNA and associated proteins
are organized into fibrous material, chromatin.
• In a normal cell they appear as a diffuse mass.
• However when the cell prepares to divide, the
chromatin fibers coil up to be seen as separate
structures, chromosomes.
• Each eukaryotic species has a characteristic number of
chromosomes.
• A typical human cell has 46 chromosomes, but sex
cells (eggs and sperm) have only 23 chromosomes.
• In the nucleus is a region called
the nucleolus.
• In the nucleolus, ribosomal RNA
(rRNA) is synthesized and
assembled with proteins from the
cytoplasm to form ribosomal
subunits.
• The subunits pass from the
nuclear pores to the cytoplasm
where they combine to form
ribosomes.
• In the nucleus is a region called the nucleolus.
• In the nucleolus, ribosomal RNA (rRNA) is synthesized
and assembled with proteins from the cytoplasm to form
ribosomal subunits.
• The subunits pass from the nuclear pores to the
cytoplasm where they combine to form ribosomes.
• The nucleus directs protein synthesis by synthesizing
messenger RNA (mRNA).
• The mRNA travels to the cytoplasm and combines with
ribosomes to translate its genetic message into the
primary structure of a specific polypeptide.
 Ribosomes
• Ribosomes contain rRNA and protein.
• A ribosome is composed of two subunits that combine to carry out protein
synthesis.
• Cell types that synthesize large quantities of proteins
(e.g., pancreas) have large numbers of ribosomes and
prominent nuclei.
• Some ribosomes, free ribosomes, are suspended in the
cytosol and synthesize proteins that function within the
cytosol.
• Other ribosomes, bound ribosomes, are attached to
the outside of the endoplasmic reticulum.
• These synthesize proteins that are either included
into membranes or for export from the cell.
• Ribosomes can shift between roles depending on the
polypeptides they are synthesizing.
Endomembrane System
•Many of the internal membranes in a eukaryotic
cell are part of the endomembrane system.
•These membranes are either in direct contact or
connected via transfer of vesicles, sacs of
membrane.
•In spite of these links, these membranes have
diverse functions and structures.
•The endomembrane system includes the nuclear
envelope, endoplasmic reticulum, Golgi
apparatus, lysosomes, vacuoles, and the plasma
membrane.
 Endoplasmic Reticulum

• The endoplasmic reticulum (ER) accounts for half the

membranes in a eukaryotic cell.
• The ER includes membranous tubules and internal, fluid-
filled spaces, the cisternae.
•The ER membrane is continuous with the nuclear
envelope and the cisternal space of the ER is
continuous with the space between the two
membranes of the nuclear envelope.
• There are two connected
regions of ER that differ in
structure and function.
• Smooth ER looks smooth
because it lacks ribosomes.
• Rough ER looks rough
because ribosomes (bound
ribosomes) are attached to
the outside, including the
outside of the nuclear
envelope.
•The smooth ER is rich in enzymes and plays a
role in a variety of metabolic processes.
•Enzymes of smooth ER synthesize lipids,
including oils, phospholipids, and steroids.
•These includes the sex hormones of
vertebrates and adrenal steroids.
•The smooth ER also catalyzes a key step in the
mobilization of glucose from stored glycogen in
the liver.
•Other enzymes in the smooth ER of the liver
help detoxify drugs and poisons.
•Also detoxifies alcohol and barbiturates.
•Frequent exposure leads to the proliferation of
smooth ER, increasing tolerance to the target
and other drugs.
•Rough ER is especially abundant in
those cells that secrete proteins.
•As a polypeptide is synthesized by
the ribosome, it is threaded into
the cisternal space through a pore
in the ER membrane.
•Many of these polypeptides are
glycoproteins, polypeptides to
which an oligosaccharide is
attached.
• Rough ER is especially abundant in those cells that
secrete proteins.
• As a polypeptide is synthesized by the ribosome, it
is threaded into the cisternal space through a pore
formed by a protein in the ER membrane.
• Many of these polypeptides are glycoproteins,
polypeptides to which an oligosaccharide is
attached.
• These secretory proteins are packaged in
transport vesicles that carry them to their next
stage.
•Rough ER is also a membrane factory.
•Membrane bound proteins are synthesized
directly into the membrane.
•Enzymes in the rough ER also synthesize
phospholipids
•As the ER membrane expands, parts can be
transferred as transport vesicles to other
components of the endomembrane system.
 Golgi Apparatus

•Many transport vesicles from the ER travel to the

Golgi apparatus for modification of their contents.
•The Golgi is a center of manufacturing,
warehousing, sorting, and shipping.
•The Golgi apparatus is especially extensive in cells
specialized for secretion.
•The Golgi apparatus consists of flattened
membranous sacs – cisternae (looks like a stack
of pita bread)
•The membrane of each cisterna separates its
internal space from the cytosol
•One side of the Golgi, the cis side, receives
material by fusing with vesicles, while the other
side, the trans side, buds off vesicles that travel
to other sites.
• During their transit from the cis to the trans pole,
products from the ER are modified to reach their final
state.
• This includes modifications of the oligosaccharide
portion of glycoproteins.
• The Golgi can also manufacture its own
macromolecules, including pectin and other
noncellulose polysaccharides.
• During processing material is moved from cisterna to
cisterna, each with its own set of enzymes.
• Finally, the Golgi tags, sorts, and packages materials into
transport vesicles.
 Lysosomes
• The lysosome is a membrane-bounded sac of hydrolytic
enzymes that digests macromolecules.
• Lysosomal enzymes can hydrolyze proteins, fats,
polysaccharides, and nucleic acids.
• These enzymes work best at pH 5.
• Proteins in the lysosomal membrane pump hydrogen ions
from the cytosol to the lumen of the lysosomes.
• While rupturing one or a few lysosomes has little impact
on a cell, massive leakage from lysosomes can destroy an
cell by autodigestion
• Used to destroy old cells; called “CELL DEATH”
• The lysosomal
enzymes and
membrane are
synthesized by rough
ER and then
transferred to the
Golgi.
• At least some
lysosomes
bud from
the trans
face of
the Golgi.
• Lysosomes can fuse with food
vacuoles, formed when a food
item is brought into the cell by
phagocytosis.
• As the polymers are digested,
their monomers pass out to the
cytosol to become nutrients of
the cell.
• Lysosomes can also
fuse with another
organelle or part
of the cytosol.
• This recycling,
or
autophagy,
renews the cell.
• The lysosomes play a critical role in the programmed destruction of cells
in multicellular organisms.
• This process allows reconstruction during the developmental process.
• Several inherited diseases affect lysosomal metabolism.
• These individuals lack a functioning version of a normal hydrolytic enzyme.
• Lysosomes are engorged with indigestable substrates.
• These diseases include Pompe’s disease in the liver and Tay-Sachs disease in the
brain.
Vacuoles have Diverse Functions in Cell Maintenance

• Vesicles and vacuoles (larger versions) are membrane-

bound sacs with varied functions.
• Food vacuoles, from phagocytosis, fuse with
lysosomes.
• Contractile vacuoles, found in freshwater protists,
pump excess water out of the cell.
• Central vacuoles are found in many mature plant cells.
 Central Vacuole
• The membrane surrounding the central vacuole, the tonoplast, is selective
in its transport of solutes into the central vacuole.
• The functions of the central vacuole include stockpiling proteins or
inorganic ions, depositing metabolic byproducts, storing pigments, and
storing defensive compounds against herbivores.
• It also increases surface to volume ratio for the whole cell.
 Endomembrane System

• The endomembrane system plays a key role in the synthesis (and

hydrolysis) of macromolecules in the cell.
• The various
components
modify
macromolecules
for their various
functions.
Mitochondria, Chloroplasts,
and Peroxisomes
 Other Membranous Organelles

• Mitochondria and chloroplasts are the

main energy transformers of cells
• Peroxisomes generate and degrade H2O2
in performing various metabolic functions
 Mitochondria and Chloroplasts

• Mitochondria and chloroplasts are the organelles that convert energy to

forms that cells can use for work.
• Mitochondria are the sites of cellular respiration,
generating ATP from the catabolism of sugars, fats, and
other fuels in the presence of oxygen .
• Chloroplasts, found in plants and eukaryotic algae, are
the sites of photosynthesis.
• They convert solar energy to chemical energy and synthesize
new organic compounds from CO2 and H2O.
• Mitochondria and chloroplasts are NOT part of the
endomembrane system.
• Their proteins come primarily from free ribosomes in
the cytosol and a few from their own ribosomes.
• Both organelles have small quantities of DNA that
direct the synthesis of the polypeptides produced by
these internal ribosomes.
• Mitochondria and chloroplasts grow and reproduce as
semiautonomous organelles.
• Almost all eukaryotic cells have mitochondria.
• There may be one very large mitochondrion or hundreds to
thousands of individual mitochondria.
• The number of mitochondria is correlated with aerobic
metabolic activity.
• A typical mitochondrion is 1-10 microns long.
• Mitochondria are quite dynamic: moving, changing shape,
and dividing.
• Mitochondria have a smooth outer membrane and a
highly folded inner membrane, the cristae.
• This creates a fluid-filled space between them.
• The cristae (folds) present ample surface area for the
enzymes that synthesize ATP.
• The inner membrane encloses the mitochondrial
matrix, a fluid-filled space with DNA, ribosomes, and
enzymes.
• The chloroplast is one of several members of a generalized class of plant
structures called plastids.
• Amyloplasts store starch in roots and tubers.
• Chromoplasts store pigments for fruits and flowers.
• The chloroplast produces sugar via photosynthesis.
• Chloroplasts gain their color from high levels of the green
pigment chlorophyll.
• Chloroplasts measure about 2 microns x 5 microns and are found in leaves
and other green structures of plants and in eukaryotic algae.
• The processes in the chloroplast are separated from the cytosol by two
membranes.
• Inside the innermost membrane is a fluid-filled space, the stroma, in
which float membranous sacs, the thylakoids.
• The stroma contains DNA, ribosomes, and enzymes for part of
photosynthesis.
• The thylakoids, flattened sacs, are stacked into grana and are
critical for converting light to chemical energy .
•Like mitochondria, chloroplasts are dynamic
structures.
•Their shape is plastic and they can reproduce
themselves by pinching in two.
•Mitochondria and chloroplasts are mobile and
move around the cell along tracks in the
cytoskeleton.
 Peroxisomes

• Peroxisomes contain enzymes that transfer hydrogen

from various substrates to oxygen
• An intermediate product of this process is hydrogen peroxide
(H2O2), a poison, but the peroxisome has another enzyme that
converts H2O2 to water.
• Some peroxisomes break fatty acids down to smaller molecules that
are transported to mitochondria for fuel.
• Others detoxify alcohol and other harmful compounds.
• Specialized peroxisomes, glyoxysomes, convert the fatty acids in seeds
to sugars, an easier energy and carbon source to transport.
• Peroxisomes are bounded by a single membrane.
• They form NOT from the endomembrane system, but by incorporation of
proteins and lipids from the cytosol.
• They split in two
when they reach
a certain size.
The Cytoskeleton
 Introduction
• The cytoskeleton is a network of fibers extending
throughout the cytoplasm.
• The cytoskeleton
organizes the
structures and
activities of
the cell.
 Other Cytoskeleton Functions

• The cytoskeleton provides mechanical support and

maintains shape of the cell.
• The fibers act like a geodesic dome to stabilize a balance
between opposing forces.
• The cytoskeleton provides anchorage for many organelles
and cytosolic enzymes.
• The cytoskeleton is dynamic, dismantling in one part and
reassembling in another to change cell shape.
• The cytoskeleton also plays a major role in cell motility.
• This involves both changes in cell location and limited movements of parts of the
cell.
• The cytoskeleton interacts with motor proteins.
• In cilia and flagella motor proteins pull components
of the cytoskeleton past each other.
• This is also true
in muscle cells.
• Motor molecules also carry vesicles or organelles to various destinations
along “monorails’ provided by the cytoskeleton.
• Interactions of motor proteins and the cytoskeleton circulate materials
within a cell via streaming.
• Recently, evidence is accumulating that the cytoskeleton may
transmit mechanical
signals that rearrange
the nucleoli and
other structures.
• There are three main types of fibers in the cytoskeleton:
• Microtubules
• Microfilaments
• intermediate filaments
• Microtubules, the thickest fibers, are hollow rods about 25 microns in
diameter.
• Microtubule fibers are constructed of the globular protein, tubulin, and they
grow or shrink as more tubulin molecules are added or removed.
• They move chromosomes during cell division.
• Another function is
as tracks that guide
motor proteins
carrying organelles
to their destination.
•In many cells, microtubules grow out from a
centrosome near the nucleus.
•These microtubules resist compression to the
cell.
In animal cells, the centrosome has a pair of centrioles,
each with nine triplets of microtubules arranged in a
ring.

During cell division, the centrioles replicate.

• Microtubules are the central structural supports in cilia and flagella.
• Both can move unicellular and small multicellular organisms by propelling water
past the organism.
• If cilia and flagella are anchored in a large structure, they move fluid over a
surface.
• For example, cilia sweep mucus carrying trapped debris from the lungs.
• Cilia usually occur in large numbers on the cell surface.
• They are about 0.25 microns in diameter and 2-20
microns long.
• There are usually just one or a few flagella per cell.
• Flagella are the same width as cilia, but 10-200
microns long.
• A flagellum has an undulatory movement.
• Force is generated parallel to the flagellum’s axis.
• Cilia move more like oars with alternating power and
recovery strokes.
• They generate force perpendicular to the cilia’s axis.
• In spite of their differences, both cilia and flagella have the same ultrastructure.
• Both have a core of microtubules sheathed by the plasma membrane.
• Nine doublets of microtubules arranged around a pair at the center, the “9 + 2” pattern.
• Flexible “wheels” of proteins connect outer doublets to each other and to the core.
• The outer doublets are also connected by motor proteins.
• The cilium or flagellum is anchored in the cell by a basal body, whose structure is identical to a
centriole.
• The bending of cilia and flagella is driven by the arms of a motor protein,
dynein.
• Addition to dynein of a phosphate group from ATP and its removal causes
conformation changes in the protein.
• Dynein arms alternately
grab, move, and release
the outer microtubules.
• Protein cross-links limit
sliding and the force is
expressed as bending.
• Microfilaments, the thinnest class of the cytoskeletal
fibers, are solid rods of the globular protein actin.
• An actin microfilament consists of a twisted double
chain of actin subunits.
• Microfilaments are designed to resist tension.
• With other proteins, they form a three-dimensional
network just inside the plasma membrane.
The shape of the
microvilli in this
intestinal cell are
supported by
microfilaments,
anchored to a
network of
intermediate
filaments.
• In muscle cells, thousands of actin filaments are arranged parallel to one
another.
• Thicker filaments composed of a motor protein, myosin, interdigitate with
the thinner actin fibers.
• Myosin molecules walk along the actin filament, pulling stacks of actin fibers
together and shortening
the cell.
• In other cells, these actin-myosin aggregates are less organized but still
cause localized contraction.
• A contracting belt of microfilaments divides the cytoplasm of animal cells during cell
division.
• Localized contraction also drives amoeboid movement .
• Pseudopodia, cellular extensions, extend and contract through the
reversible assembly and contraction of actin subunits into
microfilaments.
• In plant cells (and others), actin-myosin interactions and sol-gel
transformations drive cytoplasmic streaming.
• This creates a circular flow of cytoplasm in the cell.
• This speeds the distribution of materials within the cell.
• Intermediate filaments, intermediate in
size at 8 - 12 nanometers, are specialized
for bearing tension.
• Intermediate filaments are built
from a diverse class of subunits
from a family of proteins called
keratins.
• Intermediate filaments are more
permanent fixtures of the cytoskeleton
than are the other two classes.
• They reinforce cell shape and fix
organelle location.
Cell Surfaces and Junctions
 Cell Walls

• The cell wall, found in prokaryotes, fungi, and some

protists, has multiple functions.
• In plants, the cell wall protects the cell, maintains its
shape, and prevents excessive uptake of water.
• It also supports the plant against the force of gravity.
• The thickness and chemical composition of cell walls
differs from species to species and among cell types.
• The basic design consists of microfibrils of cellulose embedded in a matrix
of proteins and other polysaccharides.
• This is like steel-reinforced concrete or fiberglass.
• A mature cell wall consists of a primary cell wall, a middle lamella with
sticky polysaccharides that holds cell together, and layers of secondary cell
wall.
 Extracellular Matrix (ECM)

• Lacking cell walls, animals cells do have an elaborate extracellular matrix

(ECM).
• The primary constituents of the extracellular matrix are glycoproteins,
especially collagen fibers, embedded in a network of proteoglycans.
• In many cells, fibronectins in the ECM connect to integrins, intrinsic
membrane proteins.
• The integrins connect the ECM to the cytoskeleton.
• The interconnections from the ECM to the cytoskeleton
via the fibronectin-integrin link permit the interaction
of changes inside and outside the cell.
• The ECM can regulate cell behavior.
• Embryonic cells migrate along specific pathways by matching
the orientation of their microfilaments to the “grain” of fibers
in the extracellular matrix.
• The extracellular matrix can influence the activity of genes in
the nucleus via a combination of chemical and mechanical
signaling pathways.
• This may coordinate all the cells within a tissue.
 Intercellular Junctions

• Neighboring cells in tissues, organs, or organ systems

often adhere, interact, and communicate through direct
physical contact.
• Plant cells are perforated with plasmodesmata, channels
allowing cysotol to pass between cells.
• Animal have 3 main types of intercellular links: tight junctions,
desmosomes, and gap junctions .
• In tight junctions, membranes of adjacent cells are fused, forming
continuous belts around cells.
• This prevents leakage of extracellular fluid.
• Desmosomes (or anchoring junctions) fasten cells together into strong
sheets, much like rivets.
• Intermediate filaments of keratin reinforce desmosomes.
• Gap junctions (or communicating junctions) provide cytoplasmic channels
between adjacent cells.
• Special membrane proteins surround these pores.
• Salt ions, sugar, amino acids, and other small molecules can
pass.
• In embryos, gap junctions facilitate chemical communication
during development.
• While the cell has many structures that have specific
functions, they must work together.
• For example, macrophages use actin filaments to move
and extend pseudopodia, capturing their prey,
bacteria.
• Food vacuoles are digested by lysosomes, a product of
the endomembrane system of ER and Golgi.
• The enzymes of the lysosomes and proteins of
the cytoskeleton are synthesized at the
ribosomes.
• The information for these proteins comes from
genetic messages sent by DNA in the nucleus.
• All of these processes require energy in the form
of ATP, supplied by the mitochondria.
• A cell is a living unit greater
than the sum of its parts.