Chapter 7
A Tour of the Cell
HOW WE STUDY CELLS
Microscopes
1. light microscope
 visible light is passed through the specimen and
through the glass lenses
 lenses refract/bend the light in such a way that the
image of the specimen is magnified as it is projected
 resolving power: size of a small bacterium
2. electron microscope
 focuses a beam of electrons through the specimen or
onto its surface
 cell ultrastructure  cell’s anatomy as revealed by
the EM
 reveals organelles
 disadvantage: methods used to prepare the cell kills it
or introduces structural features that do not exist in
the cell
a. transmission electron microscope
~ used to study internal ultrastructure of cells
~ uses electromagnets as lenses to focus and
magnify the image by bending the paths of the e-
~ very thin sections of preserved cells stained with
atoms of heavy metals are used
b. scanning electron microscope
~ useful for a detailed study of the surface of the
specimen
~ e- beam scans the surface, w/c is usually coated
with a thin film of gold
~ image appears to be 3D
resolving power
- measure of the clarity of the image
- minimum distance two points can be separated and still be
distinguished as two separate pts.
- Limited by the shortest wavelength of light used to
illuminate the specimen
- Inversely related to the wavelength of radiation a
microscope uses
Isolation of Organelles
Cell Fractionation
- take cells apart, separating major organelles in order to
study their functions
- instrument: centrifuge, ultracentrifuge
1. homogenization
 disruption of cells
 break cells apart without damaging organelles
 pellet  larger, heavier structures(nuclei, cellular
debris) found at the bottom of the test tube
 supernatant  light parts of cell suspended in liquid
found at the top of the test tube
2. supernatant from 1 is centrifuged again
 pellet  mitochondria and chloroplasts
 supernatant
3. supernatant from 2 is centrifuged
 pellet  microsomes  pieces of plasma membrane
and internal membranes
 supernatant
4. supernatant from 3 is centrifuged
 pellet  rich in ribosomes
A PANORAMIC VIEW OF THE CELL
Prokaryotic vs. Eurkaryotic Cells
Similarities
1. all have plasma membrane
 phospholipid bilayer
 semi-permeable
 allows sufficient passage of oxygen, nutrients, and wastes
to service the entire volume of the cell
 have proteins attached to/embedded on it
 carbohydrate side chains can be found on its outer surface
 hydrophilic region  phospholipid heads, exterior proteins,
parts of proteins, and carbohydrate side chains
 hydrophobic region  phospholipid tails
2. cytosol
 semifluid substance
 where organelles are suspended (eukaryotic)
3. all have chromosomes, DNA
4. all have ribosomes  protein synthesizers
Prokaryotic cells
- nucleoid
 region where DNA is concentrated
 not bound by a membrane
- cytoplasm  also known as the interior of the cell
- smaller in size
 mycoplasmas  bacteria, smallest cells
- plasma membrane
Eukaryotic cells
- have a nucleus
 contains the chromosomes
 membrane-enclosed (nuclear envelope) organelle
- cytoplasm
 region between plasma membrane and nucleus
 membrane-bound organelles of specialized form and fcn
are suspended in it
- bigger in size
 Size is a general aspect of cell structure that relates to
function.
 Metabolism depends on cell size
 The smaller the object, the greater the ration of SA to
Volume
 The need for a surface sufficiently large to accommodate
the volume helps explain the microscopic size of cells
 Larger organisms don’t have larger cells, they have more
cells
- Plasma membrane
Internal Membranes (Eukaryotic Cell)
- Partition the cell into compartments  organelles
- Participate directly in metabolism
- Many enzymes are built right into the membranes
- Allows Incompatible process to go on simultaneously  Cell
compartments provide diff. local environments that favor
specific metabolic fcns
- Generally consists of phospholipid bilayer and other lipids
- Diverse proteins are attached or embedded
- Each type has a unique composition of lipids and proteins
suited to that membrane’s fcns
THE NUCLEUS AND RIBOSOMES
The Nucleus  cells that specialize in protein secretion (pancreatic cells,
- genetic library of the cell digestive enzymes) frequently have a high proportion of
 some genes can be found in mitochondria and this type of ribosomes
chloroplasts) - both are structurally identical and can alternate between the
- enclosed by the nuclear envelope two roles
 double membrane - cell adjusts the nos of each as metabolism changes
 consists of lipid bilayer, proteins
- nuclear envelope is perforated by pores THE ENDOMEMBRANE SYSTEM
 in its lip the inner and outer membranes of the nuclear - related either through
envelope fuse together  direct physical continuity or
 lined by a pore complex  protein structure that  by transfer of membrane segments as tiny vesicles 
regulates the entry/exit of certain large sacs made of membrane
macromolecules and particles - various membranes making up this system are not identical in
- nuclear lamina form and fcn
 lines the nucleus side of the nuclear envelope - thickness, molecular composition and metabolic behavior are
 a netlike array of protein filaments/intermediate not fixed
filaments that maintains the shape of the nucleus
- nuclear matrix 1. nuclear envelope
 framework of fibers extending throughout the nuclear 2. ER
interior 3. Golgi apparatus
- chromatin 4. Lysosomes
 fibrous material  where DNA + proteins are 5. Various kinds of vacuoles
organized 6. Plasma membrane
 located inside the nucleus
Endoplasmic Reticulum (ER)
 coils up as cell prepares to divide  chromosomes
- An extensive membranous labyrinth
 each eukaryotic specie has a characteristic no of
- Consists of a network of membranous tubules and cisternae
chromosomes
 sacs
- nucleolus
- Separates the cisternal space (internal compartment of ER)
 structure found in a nondividing nucleus from cytosol
 granules and fibers adjoining part of the chromatin 1. Smooth ER
 where ribosomal RNA (rRNA) is synthesized and 2. Rough ER
assembled with proteins imported from the cytoplasm
into the main components of ribosomes (ribosomal Smooth ER
subunits) - cytoplasmic surface lacks ribosomes
 subunits pass through the pores to the cytoplasm  - functions
form ribosomes  synthesis of lipids
 its no. depends on species and stage in cell’s  metabolism of carbo  liver cells
reproductive cycle  detoxification of drugs and poison
 not enclosed by a membrane - enzymes of smooth ER are impt to the synthesis of lipids
- synthesizes proteins  oils
 synthesizes messenger RNA (mRNA)  made  phospholipids
according to instructions of DNA  steroids  sex hormones, steroid hormones of adrenal
 mRNA goes to cytoplasm via nuclear pores glands (cells that produce these are rich in SER)
 ribosomes translate its genetic message into the - ex. Muscle cells
primary structure of a specific polypeptide
Rough ER
Ribosomes - ribosomes stud the cytoplasmic surface
- particles made of rRNA and protein
- organelles that carry out protein synthesis Synthesis of Secretory Proteins
- composed of two subunits - ribosomes attached to it makes the proteins  cell secretes it
 large - ex. Pancreas  hormone insulin
 small - polypeptide chain grows from a bound ribosome
- not enclosed in membrane - the chain is threaded into the cisternal space through a pore
formed by a protein in the ER
1. free ribosomes - new protein folds into its native conformation
 suspended in cytosol - gylcoproteins
 proteins made by this type will function within the  many secretory proteins are of this type
cytosol  proteins that are covalently bonded to carbohydrates
 ex of protein: enzymes that catalyze first steps of  carbohydrate appendix  oligosaccharide
sugar breakdown - secretory proteins are formed  ER keeps them separate from
2. bound ribosomes proteins produced by free ribosomes
 attached to the outside of ER or nuclear envelope - sec. Proteins depart from ER wrapped in vesicles
 generally make proteins that are destined for insertion  membranes
into membranes, packaging within certain organelles  bud like bubbles from transitional ER
(ie lysosomes), export from cell (secretion)
- transport vesicles  transit from one part of the cell to docking sites on surface of specific organelles or plasma
another membrane

Membrane Production Lysosomes

- RER is a membrane factory  grows in place - membrane-bounded sac of hydrolytic enzymes that the cell
- Adds phospholipids and proteins uses to digest macromolecules
- Polypeptide produced by ribosomes  inserted into ER  - lysosomal enzymes
anchored by hydrophobic portions  hydrolyze proteins, polysaccharides, fats, and nucleic
- Can make its own membrane phospholipids acids
- Expands and can be transferred n the form of transport  work best at pH 5
vesicles to other components of the endomembrane sys. - lysosomal membrane maintains low pH by pumping H+ from
the cytosol (pH 7) into the lumen of the lysosome
Golgi Apparatus - excessive leakage from a large no. of lysosomes can kill a cell
- Usual destination of transport vesicles by autodigestion
- Center of - provides a space where the cell can digest macromolecules
 Manufacturing safely
 warehousing - hydrolytic enzymes and lysosomal enzymes are made by RER
 sorting and transferred to Golgi for further processing
 shipping - some lysosomes probably arise by budding from the trans face
- Products of the ER (proteins and phospholipids of of the Golgi
membranes) are modified and stored, then sent to other - proteins of inner surface of l. membrane and digestive
destinations enzymes themselves are probably spared from destruction by
- Extensive in cells specialized for secretion having 3D conformations that protect vulnerable bonds from
- Consists of the cisternae enzymatic attacks
 flattened membranous sacs - digestion products pass into cytosol and become nutrients for
 stacked up the cell
 its membrane separates its internal space from the - autophagy
cytosol  lysosomes also use their hydrolytic enzymes to recycle the
- vesicles concentrated in the vicinity of the Golgi are cell’s own oganic material
engaged in the transfer of material between Golgi and  happens when a lysosome engulfs another organelle or
other structures small amount of cytosol
- has a distinct polarity  membranes of cisternae at  organic monomers are returned to cytosol for reuse
opposite ends having different  ex. Human liver cell
 thickness  cell continually renews itself
 molecular composition - programmed destruction of cells by their own lysosomal
enzymes  impt for devt of multicellular organisms
2 poles - lysosomal storage diseases
1. cis face  a variety of inherited disorders
 receiving  affect lysosomal metabolism
 usually located near the ER  hydrolytic enzyme doesn’t function
 contains a team of enzymes different from trans face  lysosomes become so engorged with indigestible
2. trans face substances  begin to interfere with other cellular
 shipping activities
 gives rise to vesicles  pinch off and travel to other  Pompe’s disease  liver is damaged by accumulation of
site glycogen
 Tay-Sach’s  lipid-digesting enzyme is missing/inactive
Manufacturing  brain is impaired by an accumulation of lipids
- manufactures and refines its products in stages
- secreted polysaccharides (pectin, noncellulose polysac.), phagocytosis
macromolecules - engulfing smaller organisms or other food particles
- how amoebas and other protists eat
Procedure for Transport - food vacuole fuses with a lysosome  food is digested
- transport vesicles  ER to Golgi - macrophages
- vesicle that buds from ER will add its membrane and  human cells that carry out phagocytosis
lumen (cavity) to the cis face by fusing with the Golgi  destroys bacteria and other invaders
membrane
Vacuoles
Shipping - membrane-bounded sacs
- sorts the products - larger than vesicles
- targets the products for various parts of the cell - function in cell maintenance
- molecular identification tags
 have been added to the Golgi products 1. food vacuoles
 aid in sorting  formed by phagocytosis
- transport vesicles budded from the Golgi may have 2. contractile vacuoles
external molecules on their membranes that recognize  freshwater protists
 pumps excess water out of the cell
3. central vacuole
 found in mature plant cells
 enclosed by a membrane  tonoplast
 develops by the coalescence of smaller vacuoles 
derived from ER and Golgi
 contains cell sap
 versatile compartment
 hold reserves of impt organic compounds
 main repository of inorganic ions  K and Cl
 disposal sites for metabolic by-products
 some contain pigments that color the cell
 may also help in protection against predators 
containing cpds that are poisonous/unpalatable to
some animals
 role in plant growth  as it absorbs water, it
elongates the cell with min. investment in new
cytoplasm  greater ration of membrane surface to
cytosolic volume
 comprises > 80% of plant cell
tonoplast
- part of endomembrane system
- semi-permeable
- soln inside the vacuole is different from cytosol
OTHER MEMBRANOUS ORGANELLES
Mitochondria
- main energy transformers of cells
- sites of cellular respiration  generation of ATP by
extracting energy from sugars, fats, and other fuels with
the help of oxygen
- enclosed by membranes  made by free ribosomes and
ribosomes in the mitochondrion
- not part of endomembrane system
- also contains a small amount of DNA  programs the
synthesis of proteins made on its own ribosomes
- semi-autonomous organelles that grow and reproduce
within the cell
- found in nearly all eukaryotic cells
- its no in cell is correlated with cell’s level of metabolic
activity
- enclosed by 2 membranes  phospholipid bilayer with
embedded proteins
1. outer membrane
 smooth
2. inner membrane
 convoluted
 cristae  inner foldings
 divides the mit. Into 2 internal compartments:
intermembrane space and mitochondrial matrix
 enzyme that makes ATP is made into the inner
membrane
 large surface area due to cristae enhances
productivity of respiration
Intermembrane space
- narrow region between the inner and outer membranes
Mitochondrial matrix
- enclosed by the inner membrane
- contains different enzymes, mitochondrial DNA and
ribosomes
- -
Chloroplasts
- found only on green plants and algae
- sites of photosynthesis
- convert solar to chemical energy
 absorb sunlight
 synthesis of organic cpds from CO2 and H2O
- enclosed by membranes  made by free ribosomes and
ribosomes in chloroplasts
- not part of endomembrane system
- also contains a small amount of DNA  programs the
synthesis of proteins made on its own ribosomes
- semi-autonomous organelles that grow and reproduce within
the cell
- member of plastids
- contain chlorophyll  green pigment
- constains enzymes and other molecules  photosynthetic
production of sugar
- lens-shaped
- its contents are partitioned from cytosol by an envelope
consisting of 2 membranes separated by a very narrow
intermembrane space
- thylakoids
 another membranous system
 flattened sacs
 stacked like poker chips
 divides the interior of the chloroplast into the thylakoid
space and stroma
- granum/grana(pl.)  each stack of thylakoids
- stroma
 fluid outside thylakoid
 contains the chloroplast DNA, ribosomes, and enzymes
- shapes are plastic
plastids
- amyloplasts  colorless plastids that store amylose (starch) in
roots and tubers
- chromoplasts  have pigments that give fruits and flowers
their yellow and orange hues
- chloroplasts
PEROXISOMES
- generate and degrade hydrogen peroxide (H2O2)
- a specialized metabolic compartment bounded by a single
membrane
- contain enzymes that transfer hydrogen from various
substrates to oxygen  H2O2
- functions of reactions
 use oxygen to break fatty acids down to small molecules
 transported to mitochondria as fuel for respiration
 liver  detoxify alchohol
- H2O2 is toxic but the peroxisome contains an enzyme that
converts it to water
- Grow by incorporating proteins and lipids made in the cytosol
- Increase their no. by splitting in two when they reach a certain
size
- Glyoxysomes
 specialized peroxisomes
 found in fat-storing tissues of plant seeds
 contain enzyme that initiate conversion of fatty acids to
sugar  emerging seedling can use as energy and carbon
source until it is able to produce sugar for itself
THE CYTOSKELETON
network of fibers extending throughout the cytoplasm
- role  organizing structures and activities of the cell
Functions
- give mechanical support to the cell
- maintain cell shape
 impt for animal cells which don’t have cell walls
 it’s strength and resilience is based on its architecture
- provides anchorage for many organelles and cytosolic
enzyme molecules
- changing of cell shape  cytoskeleton can be quickly
dismantled in one place and reassembled in another
- manipulates plasma membrane to form food vacuoles
during phagocytosis
- cytoplasmic streaming  materials are circulated around
- regulation of biochemical activities within the cell
- cell motility
Cell motility
- changes in cell location
- limited movements of parts of the cell
- requires the interaction of the cytoskeleton with motor
molecules (proteins)
- motor molecules bring about the movements of cilia and
flagella, contraction of muscles
- monorails  path of the vesicles to their destinations
Types of Fibers Making up the Cytoskeleton
1. microtubules
2. microfilaments
3. intermediate filaments
Microtubules
- thickest of the 3 fibers
- found in cytoplasm of all eukaryotic cells
- hollow rods
- its wall is constructed from tubulin
 globular protein
 alpha and beta-tubulin
- grows in length by adding tubulin dimers to its ends
- can be disassembled
- can also serve as tracks along w/c organelles equipped
with motor molecules can move
- maintenance of cell shape  compression-resisting
“girders”
- cell motility (cilia and flagella)
- chromosome movements in cell division
- organelle movements
Centrosomes
- a region often located near the nucleus
- where microtubules grow out  compression-resisting
girders of the cytoskeleton
- centrosomes of most plants lack centrioles
Centrioles
- in animal cells  occurs in pairs within the centrosome
- each composed of 9 sets of triplet microtubules arranged
in a ring
- replicate before a cell divides
- may help organize microtubule assembly though not
essential in this function
Cilia
- locomotor appendages that protrude from some cells
- if cilia or flagella extend from cells that are held in place as
part of a tissue layer, they function to move fluid over the
tissue
- usually occur in large nos. on cell surface
- beating pattern  like oars  alternating power and recovery
strokes generating force in a direction perpendicular to the
cilium’s axis
Flagella
- locomotor appendages that protrude from some cells
- same diameter as cilia but longer
- usually limited to just one or a few per cell
- beating pattern  undulating motion that generates the same
force in the same direction as the flagellum’s axis
Cilia and Flagella
- utlrastructure  core of microtubules sheathed in an extension
of the plasma membrane
- microtubule assembly of a cilium/flagellum is anchored in the
cell by a basal body  structurally identical to a centriole
- dynein
 protein
 motor molecules extending from each microtubule doublet
to the next are made of this
 dynein arms are responsible for bending movements of
cilia and flagella
- walking
 dynein arms slide past another in opposite directions
 elongating the cilium/flagellum
- lateral movement
 sliding past one another  limited
 dynein must have something to pull against
 forces exterted by the d. arms causes the doublets to
curve thereby bending the cilium/flagellum
-
Microfilaments
- also called actin filaments
- thinnest in diameter
- two intertwined strands of actin  globular protein
- maintenance of cell shape  tension-bearing elements
 form a 3D network together with other proteins just inside
the plasma membrane
 gives the cortext (outer cytoplasmic layer) the semisolid
consistency of a gel
- bundles  core of microvilli  projections that increase the
surface area of the cell
- changes in cell shape
- muscle contraction
 actin filaments arranged // to one another
 actin filaments are interdigitated with myosin  acts as
motor molecule by means of projections that walk along
actin filaments
 results from actin and myosin fibers sliiding past one
another  shortening the muscle cell
 actin-myosin aggregates are responsible for localized
contractions of cells
- cytoplasmic streaming
 actin-myosin interactions and sol-gel transformations may
be involved in this process
 a circular flow of cytoplasm within cells
 common in large plant cells
 seppds distribution of materials within the cell
- cell motility (pseudopodia)
 amoeboid movement, white blood cells
 extend and contract through the reversible assembly of
actin subunits into microfilaments and of microfilaments
into networks that convert cytoplasm to gel
- cell division  cleavage furrow formation
Intermediate Filaments
- diameter of fiber is in the middle of the diameter of the 2
- fibrous proteins supercoiled into thicker cables
- protein subunit  from keratin family (kind of subunit
depends on cell type)
- permanent fixtures of cells
- maintenance of cell shape  tension-bearing elements
- anchorage of nucleus and certain other organelles (ie.
Nucleus)
- formation of nuclear lamina  lines interior of nuclear
envelope
CELL SURFACES AND JUNCTIONS
Cell Wall (Plant Cells)
- protects the plant cell
- maintains its shape
- prevents excessive uptake of water
- in specialized cells  hold the plant up against gravity
- thicker than plasma membrane
- chemical composition varies from
 species to species
 cell type
- basic design is consistent
- microfibrils made up of cellulose are embedded in a
matrix of other polysaccharides and protein
Layers of the Cell Wall
1. primary cell wall
 first secreted by a young plant cell
 thin and flexible
2. middle lamella
 between primary walls of adjacent cells
 thin layer rich in pectins  sticky polysaccharides
 glues the cells together
 strengthens the wall when the cell stops growing
3. secondary cell wall
 between plasma membrane and primary wall
 often deposited in several laminated layers
 protection and support
 wood consists mainly of this
EXTRACELLULAR MATRIX (ECM) OF ANIMAL CELLS
- equivalent of cell wall
- main ingredient  glycoproteins
 proteins with covalently bonded carbohydrate 
usually short chains of sugar
- collagen
 most abundant glycoprotein in ECM of most animal
cells
 forms strong fibers outside the cells
 accounts for half the total protein in the body
 embedded in a network of proteoglycans
- proteoglycans
 glycoproteins of another class
 rich in carbhohydrates
 can form large complexes
- fibronectins
 glycoproteins
 some cells are attached to ECM by this
 bind to receptor proteins (integrins)
- integrins
 built in the plasma membrane
 span the membrane
 bind on their cytoplasmic side to the microfilaments of the
cytoskeleton
 in a position to transmit changes in ECM to cytoskeleton
and vice versa
 integrate changes occurring outside and inside the cell
Intercellular Junctions
- help integrate cells into higher levels of structure and function
- neighboring cells often adhere, interact, and communicate
through special patches of direct physical contact
Plasmodesmata (Plants)
- plasmodesma (s.)
- channels that perforate the cell wall
- cytosol passes through this and connects the living contents of
adjacent cells
- water and small solutes can pass freely from cell to cell
- in certain circumstances, proteins and RNA can also do this
- macromolecules reach this by moving along cytoskeleton
Intercellular Junctions for Animals
- these are esp. common in epithelial tissue  lines internal
surfaces of the body
1. tight junctions
 membranes of adjoining cells are actually fused
 forms continuous belts around the cells
 prevent leakage of extracellular fluid across a layer of
epithelial cells
2. desmosomes
 also called anchoring junctions
 function like rivets  fastens cells together into strong
sheets
 intermediate filaments made of keratin reinforce this
3. gap junctions
 also called communicating junctions
 provide cytoplasmic channels between adjacent animal
cells
 special membrane proteins surround each pore  wide
enough for sugars, salt ions, amino acids, and other small
molecules to pass
 especially common in animal embryos