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A Tour of the Cell
Cells are fundamental units of life
Overview: The Fundamental Units of Life
The Cell Theory
• One of the most important principles in biology
• Explains structure, function, reproduction,
evolution of living systems
• The Cell Theory: All organisms are made of
one or more cells
Overview: The Fundamental Units of Life
The Cell Theory: Comments and corollaries
• The cell is the simplest collection of matter
that can live and reproduce
• Cells are structural subunits of living systems
• Cell structure is correlated to cellular function
• All cells come from pre-existing cells through
some form of cell division
• All cells are related by their descent from
earlier cells
Overview: The Fundamental Units of Life
The Cell Theory
• In science a hypothesis becomes a theory
when supported by much data.
• Abundant data support the Cell Theory
• Microscopy
• Biochemistry
• Genetics
Concept 6.1: To study cells, biologists use microscopes
and the tools of biochemistry
Microscopic evidence
• Cells observed
in every
organism
• Cell to cell
similarities
• Better stains
better
microscopes
• Schleiden and
Schwann in
1830s
Biochemical evidence
Tissue
or cells
Homogenization
Homogenate
Centrifugation
Break down cells or tissues in a blender
Separate fractions with a centrifuge
Analyze components
They are similar or the same!
Genetic evidence
• All cells use
ribosomes to
make protein
• All ribosome
contain RNA
aka rRNA
• rRNA comes
from a gene
You can compare rRNA genes from different species
Carl Woese beginning in 1970s and 80s
Three Domains of Life
Universal Tree
Based on genetic relationships:ribosomal RNA
Prokaryotes and Eukaryotes
• Archaea and Bacteria have a prokaryotic form
of organization: no defined nucleus
• Eukaryota have a well-defined nucleus to
house DNA
• Eukaryotes probably evolved from prokaryotes
through multiple processes of gene and
organelle acquisition
Common features of all cells (prokaryotic and
eukaryotic)
– Plasma membrane aka cell membrane is
boundary
– Semifluid substance called cytosol or
cytoplasm
– DNA carries genetic material
– Ribosomes are protein factories
– Organelles- dedicated substructures in cell
• Terminology
• 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-domain Eucaryota
Concept 6.2: Eukaryotic cells have many internal
membranes that compartmentalize their
functions; prokaryotic cells have few
• Eukaryotic cells are generally considered larger
and more complex than prokaryotic cells
• Prokaryotic cells are generally considered to be
tougher than eukaryotic cells
• Prokaryotes as a group have more biochemical
diversity than eukaryotes as a group
• Prokaryotic cells (A+B) are characterized by
having
–
–
–
–
No true nucleus
DNA in an unbordered region called the nucleoid
Membrane-bound organelles: few to none
Cytoplasm bound by the plasma membrane
Pseudomonas
Methanobacterium
These cells are small!!!
See first page of Ch. 6 notes for scale
Diagram of a prokaryotic cell (Bacteria)
Fimbriae
Nucleoid
Ribosomes
Plasma membrane
Cell wall
Capsule
0.5 µm
(a) A typical
rod-shaped
bacterium
Flagella
(b) A thin section
through the
bacterium
Bacillus
coagulans (TEM)
• Eukaryotic cells are characterized by having
– DNA in a nucleus that is bounded by a
membranous nuclear envelope
– Membrane-bound organelles
– Cytoplasm in the region between the plasma
membrane and nucleus
• Eukaryotic cells are generally much larger than
prokaryotic cells
• The plasma membrane is a selective barrier
between cells and the outside world
• it allows sufficient passage of oxygen,
nutrients, and waste to service the entire
volume of every cell
• The general structure of a biological membrane
is a double layer of phospholipids-therefore
membranes in general have the properties of
lipids
• Surface area is a key feature for cells!
• The logistics of carrying out cellular metabolism
sets limits on the size of cells
• The surface area to volume ratio of a cell is
critical
• As the surface area increases by a factor of n2,
the volume increases by a factor of n3
• Small cells have a greater surface area relative
to volume
Surface area increases while
total volume remains constant
A large number of small cells
has a greater surface area
than one large cell of the
same total volume
The need for surface area
controls cell size
The need for surface area 1
Total surface area
[Sum of the surface areas
(height  width) of all boxes
sides  number of boxes]
Total volume
[height  width  length 
number of boxes]
Surface-to-volume
(S-to-V) ratio
[surface area ÷ volume]
5
1
6
150
750
1
125
125
6
1.2
6
Cells have to be pretty small in order to maintain
enough plasma membrane area to support the
cytoplasm and the rest of the cell. Surface
area/Volume Rule.
An Overview of the Eukaryotic Cell
• A eukaryotic cell is compartmentalized. It has
internal membranes that partition the cell into
organelles or regions for specialization
• All eukaryotic cells have most of the same
organelles-and they have the same basic
structure.
Concept 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 (chloroplasts and mitochondria
also contain some DNA)
• Nuclear DNA is organized into organelles
called chromosomes (made of chromatin)
• Ribosomes outside the nucleus use the
information from the DNA to make proteins
The Nucleus: Information Central
• The nucleus contains most of the cell’s genes
and is usually the most conspicuous organelle
• The nuclear envelope is a membrane that
encloses the nucleus, separating it from the
cytoplasm. It is backed up by the nuclear
lamina
• The nuclear membrane is a double membrane
(two unit membranes); each unit membrane
consists of a lipid bilayer
• Most nuclei contain a highly visible nucleolus
Illustration of a nucleus
1 µm
Nucleus
Nucleolus
Chromatin
Nuclear envelope:
Inner membrane
Outer membrane
Nuclear pore
Pore
complex
Surface of
nuclear envelope
Rough ER
Ribosome
1 µm
0.25 µm
Close-up of nuclear
envelope
Pore complexes (TEM)
Nuclear lamina (TEM)
Ribosomes: Protein Factories
• Ribosomes are particles (organelles without a
membrane) made of ribosomal RNA and
protein
• Ribosomes are made in the nucleus but they
function outside the nucleus
• Ribosomes carry out protein synthesis in two
locations:
– In the cytosol (free ribosomes)
– On the outside of the endoplasmic reticulum or
the nuclear envelope (bound ribosomes)
Cytosol
Endoplasmic reticulum (ER)
Free ribosomes
Bound ribosomes
Large
subunit
0.5 µm
TEM showing ER and ribosomes
Small
subunit
Diagram of a ribosome
Concept 6.4: The endomembrane system regulates
protein traffic and performs metabolic functions in
the cell
• Main components of the endomembrane
system:
–Nuclear envelope
–Endoplasmic reticulum
–Golgi apparatus
–Lysosomes
–Vacuoles
• These components are connected directly or
via transfer by vesicles (also part of system)
Nucleus
Rough ER
Smooth ER
cis Golgi
trans Golgi
Plasma
membrane
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
• There are two distinct regions of ER:
– Smooth ER, which lacks ribosomes
– Rough ER, with ribosomes studding its
surface
Functions of ER
• The smooth ER
– Biochemical factory for lipids and
carbohydrates, also metabolizes poisons
• The rough ER
– Has bound ribosomes, which secrete
glycoproteins (proteins covalently bonded to
carbohydrates)
– Distributes transport vesicles, proteins
surrounded by membranes
– Is a membrane factory for the cell
The Golgi Apparatus: Shipping and
Receiving Center (UPS Store of the eukaryotic cell)
• 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
Lysosomes: Digestive Compartments
• A lysosome is a membranous sac of hydrolytic enzymes
that can digest macromolecules
• Lysosomal enzymes can hydrolyze proteins, fats,
polysaccharides, and nucleic acids
• Lysosomal enzymes operate best at about pH 5.0
• Some types of cell can engulf another cell by
phagocytosis; this forms a food vacuole
• A lysosome fuses with the food vacuole and digests the
molecules
• Lysosomes also use enzymes to recycle the cell’s own
organelles and macromolecules, a process called
autophagy
Vacuoles: Diverse Maintenance Compartments
• Vacuole is a generic term for a container in a
cell with a lipid membrane
• Food vacuoles are formed by phagocytosis
• Contractile vacuoles, found in many
freshwater protists, pump excess water out of
cells
• Central vacuoles, found in many mature plant
cells, hold organic compounds and water
Nucleus
Rough ER
Smooth ER
cis Golgi
trans Golgi
Plasma
membrane
The orientation of the membrane is
topologically preserved:
Inside is always inside.
Outside is always outside.
Concept 6.5: Mitochondria and chloroplasts
change energy from one form to another
(transduce)
• Mitochondria (mt) are the sites of cellular
respiration, a metabolic process that harvests
chemical energy in the form of ATP
• Chloroplasts (ct), found in plants and algae,
are the sites of photosynthesis. They transduce
light energy to chemical energy
• Mt and ct are surprisingly similar
• Peroxisomes are very different but are also
involved in the metabolism of oxygen
• Mitochondria and chloroplasts
– Are not part of the endomembrane system
– Have a double membrane
– Contain their own DNA
– Have proteins made by free ribosomes
– Make some of their own proteins inside the
organelle, using their own special ribosomes
– Are evolutionary descendants of prokaryotic
cells (endosymbionts)
Possible mechanism of endosymbiosis?
• Lynn Margulis
• Modern day advocate of the
Endosymbiont Hypothesis
(Theory)
• Evolution through association
http://www.brandeis.edu/magazine/2015/winter/fea
tured-stories/crackpottery.html
See above for a desceiption of a “hereticheroine”.
Intermembrane space
Outer
membrane
Free
ribosomes
in the
mitochondrial
matrix
Inner
membrane
Cristae
Matrix
0.1 µm
Ribosomes
Stroma
Inner and outer
membranes
Granum
Thylakoid
1 µm
Peroxisomes: Oxidation
• Peroxisomes are specialized metabolic
compartments bounded by a single membrane
• Peroxisomes use oxygen to remove hydrogens
from various molecules
• This reaction produces hydrogen peroxide
• Peroxisomes break down hydrogen peroxide to
water and oxygen.
• No ribosomes or DNA
• Good example of compartmentalization
Compartmentalization in a plant cell
Chloroplast
Peroxisome
Mitochondrion
1 µm
Concept 6.6: The cytoskeleton is a network of fibers
that organizes structures and activities in the cell
• The cytoskeleton is a network of fibers
extending throughout the cytoplasm
• It organizes the cell’s structures and activities,
anchoring many organelles
• It helps cells move
• It is composed of three types of molecular
structures:
– Microtubules
– Microfilaments
– Intermediate filaments
Components of the Cytoskeleton
• Three main types of fibers make up the
cytoskeleton:
– Microtubules are the thickest of the three
components of the cytoskeleton (tubulin)
– Microfilaments, also called actin filaments,
are the thinnest components
– Intermediate filaments are fibers with
diameters in a middle range-variable
Some images
of the
cytoskeleton
0.25 µm
Microtubules
• Microtubules are hollow rods about 25 nm in
diameter and about 200 nm to 25 microns long
• Functions of microtubules:
– Shaping the cell
– Guiding movement of organelles
– Separating chromosomes during cell division
– Cell movement
(cilia and
flagella)
Internal structure-cilia and flagella
0.1 μm
Outer microtubule
doublet
Motor proteins
(dyneins)
Central
microtubule
Radial spoke
(b) Cross section of
motile cilium
“9+2” arrangement
Cross-linking
proteins between
outer doublets
Plasma
membrane
Guiding
movement
of
organelles
ATP
Vesicle
Receptor for
motor protein
Motor protein Microtubule
(ATP powered) of cytoskeleton
(a)
Microtubule
(b)
Vesicles
0.25 µm
Microfilaments (Actin Filaments)
• Microfilaments are solid rods about 7 nm in
diameter, built as a twisted double chain of
actin subunits
• The structural role of microfilaments is to bear
tension, resisting pulling forces within the cell
• They form a 3-D network called the cortex just
inside the plasma membrane to help support
the cell’s shape
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
they do not assemble and disassemble as
frequently
• Diverse protein components
Intermediate filaments
contain proteins such as
keratin, vimentin, desmin
Organization different from
microtubules and
microfilaments
Up to 70 types
Concept 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
Plant
Cell
Wall
Secondary
cell wall
Primary
cell wall
Middle
lamella
1 μm
Central vacuole
Cytosol
Plasma membrane
Plant cell walls
Plasmodesmata-intercellular junctions
The Extracellular Matrix (ECM) of Animal Cells
• Animal cells lack cell walls but are covered by
an elaborate extracellular matrix (ECM)
• The ECM is made up of glycoproteins such as
collagen, proteoglycans, and fibronectin
• ECM proteins bind to receptor proteins in the
plasma membrane called integrins
• Functions of the ECM:
–Support
–Adhesion
–Movement
–Regulation
Collagen
Proteoglycan
complex
EXTRACELLULAR FLUID
Polysaccharide
molecule
Carbohydrates
Fibronectin
Core
protein
Integrins
Proteoglycan
molecule
Plasma
membrane
Proteoglycan complex
Microfilaments
CYTOPLASM
Tight junctions prevent
fluid from moving
across a layer of cells.
Tight
junction
TEM
0.5 μm
Tight junction
Intermediate
filaments
Desmosome
Desmosome
1 μm
Gap
junction
Ions or small
molecules
Extracellular
matrix
Space
between cells
TEM
Plasma
membranes of
adjacent cells
Gap junctions
Intercellular connections
0.1 μm