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NOTES: CH 6 –
A Tour of the Cell
Overview: The Importance of Cells
● All organisms are made of cells
● The cell is the simplest collection of matter
that can live
● Cell structure is correlated to cellular function
● All cells are related by their descent from
earlier cells
10 m
Human height
Length of some
nerve and
muscle cells
0.1 m
Chicken egg
Unaided eye
1m
1 cm
Frog egg
100 µm
Most plant and
animal cells
10 µm
Nucleus
Most bacteria
1 µm
100 nm
Mitochondrion
Smallest bacteria
Viruses
Ribosomes
10 nm
Proteins
Lipids
1 nm
Small molecules
0.1 nm
Atoms
Electron microscope
Measurements
1 centimeter (cm) = 10–2 meter (m) = 0.4 inch
1 millimeter (mm) = 10–3 m
1 micrometer (µm) = 10–3 mm = 10–6 m
1 nanometer (nm) = 10–3 µm = 10–9 m
Light microscope
1 mm
6.1 – Biologists use microscopes and the
tools of biochemistry to study cells
Brightfield (unstained
specimen)
50 µm
Brightfield (stained
specimen)
Phase-contrast
MICROSCOPES
1) Light Microscope
2) Electron Microscope (1950’s)
● Transmission Electron Microscope
● Scanning Electron Microscope
Light Microscope
● works by passing visible light
through a thin section of
specimen and then through
glass lenses
● resolving power = 0.2 µm (size
of small bacteria)
● max. magnification about 1000x
Electron Microscope (1950’s)
● uses electron beams which
have shorter wavelengths
of light
● resolving power = 0.2 nm
(most cell structures)
● magnification up to
40,000x
Electron Microscope
1) Transmission Electron Microscope
-electrons transmitted through
specimen are focused and image is
magnified using electromagnets
-used to study internal cell structure
2) Scanning Electron Microscope
-electron beam scans the surface of a
spec.
-useful for studying the surface of
specimen in 3-D.
Disadvantages to EM…
● can only view dead cells (elaborate
preparation)
● very expensive!
zooxanthellae cells
cultured from coral
Aiptasia pulchella in a
Scanning Electron
Microscope
WE CAN ALSO STUDY CELLS BY...
● Cell Fractionation =
disrupting cells to
separate out cell
organelles
● Centrifugation =
spinning mixtures of
cells and their parts at
very high speeds;
separates the
components
6.2 – Eukaryotic cells have internal
membranes that compartmentalize their
functions
Types of CELLS:
● The basic structural and functional unit of every
organism is one of two types of cells:
prokaryotic or eukaryotic
● Only organisms of the domains Bacteria and
Archaea consist of prokaryotic cells
● Protists, fungi, animals, and plants all consist of
eukaryotic cells (& are in the domain Eukarya)
ALL CELLS:
● have a cell membrane
● have cytoplasm / cytosol
● have ribosomes (make
proteins)
● can reproduce & contain
genetic material (DNA /
chromatin / chromosomes)
CELLS CAN BE CLASSIFIED AS:
1) PROKARYOTES
2) EUKARYOTES
1) PROKARYOTES
• oldest cells (3.5 billion years)
• single celled
• lack nucleus & membranebound organelles
• genetic material in a single,
circular molecule (PLASMID)
in region called NUCLEOID
• small (1-2 µm)
• Domains Bacteria and
Archaea
2) EUKARYOTES
• “newer” cells (1.5 billion
years)
• single or multicellular
• have a “true” nucleus &
membrane-bound organelles
• genetic material organized
into CHROMOSOMES in
NUCLEUS
• larger (2-1000 µm)
• Domain Eukarya, includes
Kingdoms Protista, Fungi,
Plantae, Animalia
Pili
Nucleoid
Ribosomes
Plasma
membrane
Bacterial
chromosome
Cell wall
Capsule
0.5 µm
Flagella
A typical
rod-shaped
bacterium
A thin section through the
bacterium Bacillus
coagulans (TEM)
● although eukaryotic cells are larger than
prokaryotes, there is a limit on cell size due to
the logistics of carrying out cellular metabolism
Surface area increases while
Total volume remains constant
5
1
1
Total surface area
(height x width x
number of sides x
number of boxes)
6
150
750
Total volume
(height x width x length
X number of boxes)
1
125
125
Surface-to-volume
ratio
(surface area  volume)
6
1.2
6
PLASMA MEMBRANE: the boundary
of every cell
● The plasma membrane is a selective barrier
that allows sufficient passage of oxygen,
nutrients, and waste to service the volume of
the cell
● The general structure of
a biological membrane is
a double layer of
phospholipids
Outside of cell
Carbohydrate side chain
Hydrophilic
region
Inside of cell 0.1 µm
Hydrophobic
region
Hydrophilic
region
TEM of a plasma membrane
Phospholipid
Proteins
Structure of the plasma membrane
A Panoramic View of the
Eukaryotic Cell:
● A eukaryotic cell has internal membranes
that partition the cell into organelles
● Plant and animal cells have most of the
same organelles
ENDOPLASMIC RETICULUM (ER
Nuclear envelope
Flagellum
Rough ER
Smooth ER
NUCLEUS
Nucleolus
Chromatin
Centrosome
Plasma membrane
CYTOSKELETON
Microfilaments
Intermediate filaments
Microtubules
Ribosomes:
Microvilli
Golgi apparatus
Peroxisome
Mitochondrion
Lysosome
In animal cells but not plant cells:
Lysosomes
Centrioles
Flagella (in some plant sperm)
Nuclear
envelope
NUCLEUS
Nucleolus
Chromatin
Centrosome
Rough
endoplasmic
reticulum
Smooth
endoplasmic
reticulum
Ribosomes
(small brown dots)
Central vacuole
Golgi
apparatus
Microfilaments
Intermediate
filaments
Microtubules
CYTOSKELETON
Mitochondrion
Peroxisome
Chloroplast
Plasma
membrane
Cell wall
Plasmodesmata
Wall of adjacent cell
In plant cells but not animal cells:
Chloroplasts
Central vacuole and tonoplast
Cell wall
Plasmodesmata
6.3 - The eukaryotic cell’s genetic
instructions are housed in the
NUCLEUS and carried out by the
ribosomes
● the nucleus contains most of the DNA in a
eukaryotic cell
● ribosomes use the information from the DNA
to make proteins
The Nucleus:
Genetic Library of the Cell
● the nucleus contains most of the cell’s genes
and is usually the most conspicuous organelle
● the nuclear envelope encloses the nucleus,
separating it from the cytoplasm
● houses the information / instructions for cell
functioning and maintenance …the “control
center” of the cell
● averages 5 µm in diameter
Nucleus
Nucleus
1 µm
Nucleolus
Chromatin
Nuclear envelope:
Inner membrane
Outer membrane
Nuclear pore
Pore
complex
Rough ER
Surface of nuclear envelope
Ribosome
1 µm
0.25 µm
Close-up of nuclear
envelope
Pore complexes (TEM)
Nuclear lamina (TEM)
NUCLEAR ENVELOPE
● double membrane which encloses
the nucleus
-each of the 2 membranes is a
phospholipid bilayer w/specific
proteins
-is perforated by pores which
regulate molecular traffic into and
out of the nucleus
-RNA and proteins enter or leave
the nucleus through these pores
-breaks down prior to cell division
CHROMATIN
● fibrous, threadlike
complex of DNA and
histone proteins
which make up
chromosomes in
eukaryotic cells
CHROMOSOMES
● compacted, coiled up
chromatin;
● visible under microscope;
● form just prior to cell division;
● human cells have 46
chromosomes (23 pairs)
NUCLEOLUS
● dense, spherical region in the nucleus
-visible in a nondividing cell
-may be 2 or more per cell
-packages ribosomal subunits from:
1) rRNA: transcribed in nucleolus
2) RNA produced elsewhere in nucleus
-ribosomal subunits pass through nuclear
pores to the cytoplasm where assembly into
ribosomes is completed
RIBOSOMES
● cytoplasmic organelle; site of
protein synthesis
-made of RNA and protein
-made in the nucleolus
-cells with high rates of protein
synthesis have large numbers of
nucleoli & ribosomes (e.g. human
liver cells have millions)
RIBOSOMES
● Ribosomes carry out
protein synthesis in two
locations:
-in the cytosol (free
ribosomes)
-attached to the outside of
the endoplasmic reticulum
(ER) or the nuclear
envelope (bound
ribosomes)
Ribosomes
ER
Cytosol
Endoplasmic
reticulum (ER)
Free ribosomes
Bound ribosomes
Large
subunit
Small
subunit
0.5 µm
TEM showing ER
and ribosomes
Diagram of
a ribosome
Cell Organelles (continued)
The Endomembrane System
**all structures are
essentially
compartments,
closed off by
their
membranes
from the
cytoplasm
6.4 - The endomembrane system regulates
protein traffic and performs metabolic
functions in the cell
● Components of the endomembrane system:
–
–
–
–
–
–
Nuclear envelope
Endoplasmic reticulum
Golgi apparatus
Lysosomes
Vacuoles
Plasma membrane
● These components are either continuous or
connected via transfer vesicles
The Endoplasmic Reticulum:
Biosynthetic Factory
● The endoplasmic reticulum (ER) accounts for
more than half of the total membrane in many
eukaryotic cells
● The ER membrane is continuous with the
nuclear envelope
ENDOPLASMIC RETICULUM (ER):
● extensive network of tubules and sacs
● used for transport and/or modification of
proteins;
● can be ROUGH (ribosomes) or SMOOTH
(no ribosomes)
Rough ER:
● manufactures secretory
proteins and membranes ;
● proteins made here may
be modified
(i.e. folded into their
tertiary structure)
● usually closer in to nucleus
than smooth ER
Smooth ER:
● synthesizes lipids, phospholipids, steroids
● participates in carbohydrate metabolism
● detoxifies drugs and poisons
● stores calcium ions (for muscle
contraction)
Smooth ER
Rough ER
Nuclear
envelope
ER lumen
Cisternae
Ribosomes
Transport vesicle
Smooth ER
Transitional ER
Rough ER
200 nm
The Golgi Apparatus: Shipping and
Receiving Center
● The Golgi apparatus consists
of flattened membranous sacs
called cisternae
● Functions of the Golgi
apparatus:
– Modifies products of the ER
– Manufactures certain
macromolecules
– Sorts and packages materials
into transport vesicles
GOLGI APPARATUS:
●
cis face (forming face; faces the rough ER) receives
products by accepting transport vesicles from the rough
ER
●
trans face (maturing face; faces the
cell membrane) pinches off vesicles
from the Golgi and transports
molecules to other sites
Golgi
apparatus
cis face
(“receiving” side of
Golgi apparatus)
Vesicles also
transport certain
proteins back to ER
Vesicles move
from ER to Golgi
Vesicles coalesce to
form new cis Golgi cisternae
0.1 µm
Cisternae
Cisternal
maturation:
Golgi cisternae
move in a cisto-trans
direction
Vesicles form and
leave Golgi, carrying
specific proteins to
other locations or to
the plasma membrane for secretion
Vesicles transport specific
proteins backward to newer
Golgi cisternae
trans face
(“shipping” side of
Golgi apparatus)
TEM of Golgi apparatus
Lysosomes: Digestive
Compartments
● A lysosome is a membranous sac of hydrolytic
enzymes
● Lysosomal enzymes can hydrolyze proteins,
fats, polysaccharides, and nucleic acids
● Lysosomes also use enzymes to recycle
organelles and macromolecules, a process
called autophagy
1 µm
Nucleus
Lysosome
Lysosome contains Food vacuole Hydrolytic
active hydrolytic
enzymes digest
fuses with
enzymes
food particles
lysosome
Digestive
enzymes
Plasma
membrane
Lysosome
Digestion
Food vacuole
Phagocytosis: lysosome digesting food
Lysosome containing
two damaged organelles
1 µm
Mitochondrion
fragment
Peroxisome
fragment
Lysosome fuses with
vesicle containing
damaged organelle
Hydrolytic enzymes
digest organelle
components
Lysosome
Digestion
Vesicle containing
damaged mitochondrion
Autophagy: lysosome breaking down
damaged organelle
LYSOSOMES
● probably pinch off from the trans face of Golgi;
● are responsible for intracellular digestion;
● recycle the cell’s own organic material;
● destroy cells
Other Membrane-Bound
Organelles:
1) Vacuoles
2) Peroxisomes
VESICLES /
VACUOLES:
● membrane-enclosed sac
used for storage and/or
transport animal cells,
vacuoles are small and
look like vesicles
**Vacuoles in plants have
special characteristics:
-plant cells have a LARGE
central vacuole that
stores water and watersoluble organic compounds
and inorganic ions (K+ and
Cl-);
PLANT VACUOLES…
● contain soluble pigments in some cells (red and blue
pigments in flowers);
● play a role in plant growth by absorbing water and
elongating the cell;
PLANT VACUOLES…
● help protect from predators by storing waste
products that may also be poisonous compounds
● Are surrounded by a membrane called the
TONOPLAST
● some fresh-water protists
have a contractile vacuole
that pumps excess water
from the cell
Central vacuole
Cytosol
Tonoplast
Nucleus
Central
vacuole
Cell wall
Chloroplast
5 µm
The Endomembrane System:
A Review
● The endomembrane system is a complex
and dynamic player in the cell’s
compartmental organization
Nucleus
Rough ER
Smooth ER
Nuclear envelope
Nucleus
Rough ER
Smooth ER
Nuclear envelope
cis Golgi
Transport vesicle
trans Golgi
Nucleus
Rough ER
Smooth ER
Nuclear envelope
cis Golgi
Transport vesicle
Plasma
membrane
trans Golgi
6.5 - Mitochondria and chloroplasts
change energy from one form to
another
● Mitochondria are the sites of cellular respiration
● Chloroplasts, found only in plants and algae,
are the sites of photosynthesis
● Mitochondria and chloroplasts are not part of
the endomembrane system
● Peroxisomes are oxidative organelles
MITOCHONDRIA:
● sites of cellular respiration
● found in nearly all eukaryotic cells
● the # in cells varies and is related to the
cell’s metabolic activity
● inner membrane is convoluted
and contains proteins/enzymes
involved in cellular respiration
● inner membranes many
infoldings are called CRISTAE;
they increase the surface area
for cellular respiration reactions
to occur
● region within inner membrane is
the MITOCHONDRIAL
MATRIX
Mitochondria in a human liver cell
Mitochondrion
Intermembrane space
Outer
membrane
Free
ribosomes
in the
mitochondrial
matrix
Inner
membrane
Cristae
Matrix
Mitochondrial
DNA
100 nm
CHLOROPLASTS: (“the
organelles that feed the world”)
● contain chlorophyll;
● site of photosynthesis
(convert light energy
into chemical energy;
● found in eukaryotic
algae, leaves and
other green plant
organs;
● can change shape,
move and divide
Chloroplasts: Capture of Light
Energy
● Chloroplast structure includes:
-Thylakoids, membranous sacs
-Stroma, the internal fluid
Chloroplast
Ribosomes
Stroma
Chloroplast
DNA
Inner and outer
membranes
Granum
1 µm
Thylakoid
PEROXISOMES:
● contain special
enzymes for specific
metabolic pathways
● found in nearly all
eukaryotic cells
● contain peroxide-producing enzymes
that transfer hydrogen ions to oxygen
producing hydrogen peroxide
● contain catalase enzyme which
converts / detoxifies hydrogen peroxide
to water
Chloroplast
Peroxisome
Mitochondrion
1 µm
6.6 - The cytoskeleton is a network of
fibers that organizes structures and
activities in the cell
● anchors and/or provides “tracks” for many
organelles
● It is composed of three types of molecular
structures:
– Microtubules
– Microfilaments
– Intermediate filaments
Microtubule
Microfilaments
0.25 µm
Components of the Cytoskeleton
● Microtubules are the thickest of the three
components of the cytoskeleton
● Microfilaments, also called actin filaments,
are the thinnest components
● Intermediate filaments are fibers with
diameters in a middle range
Roles of the Cytoskeleton: Support,
Motility, and Regulation
● the cytoskeleton helps to support the cell and
maintain its shape
● it interacts with motor proteins to produce
motility (movement)
● inside the cell, vesicles can travel along
“monorails” provided by the cytoskeleton
● recent evidence suggests that the
cytoskeleton may help regulate biochemical
activities
Vesicle
ATP
Receptor for
motor protein
Motor protein
(ATP powered)
Microtubule
of cytoskeleton
Microtubule
Vesicles
0.25 µm
Microtubules:
● straight, hollow rods made of protein called
TUBULIN;
● can serve as “tracks” to
guide organelle movement;
● involved in separation of chromosomes in cell
division; make up CENTRIOLES;
Cilia and Flagella
● Microtubules control the beating of cilia and
flagella, locomotor appendages of some cells
● Cilia and flagella differ in their beating patterns
FLAGELLA and CILIA:
● FLAGELLA: longer
than cilia; usually found
singly or in pairs; used
to propel a cell
● CILIA: shorter than
flagella; usually present
in great numbers;
wavelike motion used to
sweep extracellular
material over/away from
cell
Direction of swimming
Motion of flagella
5 µm
Direction of organism’s movement
Direction of
active stroke
Motion of cilia
Direction of
recovery stroke
15 µm
● Cilia and flagella share a common
ultrastructure:
-A core of microtubules sheathed by the
plasma membrane
-A basal body that anchors the cilium or
flagellum
-A motor protein called DYNEIN, which
drives the bending movements of a cilium or
flagellum
Outer microtubule
doublet
Dynein arms
Central
microtubule
0.1 µm
Cross-linking
proteins inside
outer doublets
Microtubules
Plasma
membrane
Basal body
0.5 µm
Radial
spoke
0.1 µm
Triplet
Cross section of basal body
Plasma
membrane
Microtubule
doublets
Dynein arm
Dynein “walking”
ATP
Cross-linking
proteins inside
outer doublets
Anchorage
in cell
Effect of cross-linking proteins
Wavelike motion
ATP
Microfilaments:
● can exist as single filaments or in bundles;
● formed from the protein ACTIN;
● help the cell (or parts of the cell) to contract;
● they stabilize cell shape;
● Involved in “pinching” contractions during cell
division;
● Involved in forming “pseudopodia” that enable some
cells to move.
Yellow: nucleus
Green: microfilaments throughout
cytoplasm
Cortex (outer cytoplasm):
gel with actin network
Inner cytoplasm: sol
with actin subunits
Extending
pseudopodium
Amoeboid movement
Muscle cell
Actin filament
Myosin filament
Myosin arm
Myosin motors in muscle cell contraction
Nonmoving
cytoplasm (gel)
Chloroplast
Streaming
cytoplasm
(sol)
Vacuole
Parallel actin
filaments
Cytoplasmic streaming in plant cells
Cell wall
Intermediate Filaments
● Intermediate filaments range in diameter from
8–12 nanometers, larger than microfilaments
but smaller than microtubules
● They support cell shape and fix organelles in
place
● Intermediate filaments are more permanent
cytoskeleton fixtures than the other two classes
6.7 - Extracellular components and
connections between cells help coordinate
cellular activities
● Most cells synthesize and secrete materials
that are external to the plasma membrane
● These extracellular structures include:
– Cell walls of plants
– The extracellular matrix (ECM) of animal cells
– Intercellular junctions
Extracellular Structures:
● CELL WALL:
-semirigid structure
outside of cell membrane
of PLANT CELLS;
-consists of CELLULOSE
fibers + complex
polysaccharides
& proteins
-provides support, limits cell’s volume, and protects
against fungi and/or microorganism infection.
Cell Walls of Plants
● Plant cell walls may have multiple layers:
– Primary cell wall: relatively thin and flexible
– Middle lamella: thin layer between primary walls
of adjacent cells
– Secondary cell wall (in some cells): added
between the plasma membrane and the primary
cell wall
● Plasmodesmata are channels between
adjacent plant cells
Central
vacuole
of cell
Plasma
membrane
Secondary
cell wall
Primary
cell wall
Central
vacuole
of cell
Middle
lamella
1 µm
Central vacuole
Cytosol
Plasma membrane
Plant cell walls
Plasmodesmata
The Extracellular Matrix (ECM) of
Animal Cells:
● Animal cells lack cell walls but are covered by
an elaborate extracellular matrix (ECM)
● Functions of the ECM:
– Support
– Adhesion
– Movement
– Regulation
Extracellular Structures:
● EXTRACELLULAR MATRIX:
– fibrous proteins such as COLLAGEN and
glycoproteins are secreted by and surround
cells;
– it holds cells together in tissues;
– helps filter materials passing between different
tissues;
– orients cell movement during
development;
– involved in cell-cell signalling.
Collagen
fiber
EXTRACELLULAR FLUID
Fibronectin
Plasma
membrane
Integrin
CYTOPLASM
Microfilaments
Proteoglycan
complex
Proteoglycan
complex
Polysaccharide
molecule
Carbohydrates
Core
protein
Proteoglycan
molecule
Intercellular Junctions
● Neighboring cells in tissues, organs, or organ
systems often adhere, interact, and
communicate through direct physical contact
● Intercellular junctions facilitate this contact
Plants: Plasmodesmata
● Plasmodesmata are channels that perforate
plant cell walls
● Through plasmodesmata, water and small
solutes (and sometimes proteins and RNA) can
pass from cell to cell
Cell walls
Interior
of cell
Interior
of cell
0.5 µm
Plasmodesmata
Plasma membranes
Animals: Tight Junctions,
Desmosomes, and Gap Junctions
● At tight junctions, membranes of neighboring
cells are pressed together, preventing leakage of
extracellular fluid
● Desmosomes (anchoring junctions) fasten cells
together into strong sheets
● Gap junctions (communicating junctions) provide
cytoplasmic channels between adjacent cells
Tight junctions prevent
fluid from moving
across a layer of cells
Tight junction
0.5 µm
Tight junction
Intermediate
filaments
Desmosome
1 µm
Space
between
cells
Gap
junctions
Plasma membranes
of adjacent cells
Gap junction
Extracellular
matrix
0.1 µm
The Cell: A Living Unit Greater
Than the Sum of Its Parts
● Cells rely on the integration of structures and
organelles in order to function
● For example, a macrophage’s ability to destroy
bacteria involves the whole cell, coordinating
components such as the cytoskeleton,
lysosomes, and plasma membrane
5 µm