Lecture 1

Cell Structure and Function

The Fundamental Units of Life--Cells

• All organisms are made of cells

• The cell is the simplest collection of matter that
can be alive (virus?)
• Cell structure is correlated to cellular function
 Microscopy

• In a light microscope (LM), visible light is passed through

a specimen and then through glass lenses
• Lenses refract (bend) the light, so that the image is
magnified
• Three important parameters of microscopy
– Magnification, the ratio of an object’s image size to
its real size (LM max 1000X vs. EM 100,000X )
– Resolution, the measure of the clarity of the image,
or the minimum distance of two distinguishable
points (LM 200nm vs. EM 2nm )
– Contrast, visible differences in parts of the sample
*Resolution is limited by the shortest wavelength of the radiation
used for imaging
 10 m

Human height
1m
Length of some
nerve and The size range of cells

Unaided eye
muscle cells
0.1 m
Chicken egg

1 cm

Frog egg
1 mm

Light microscopy
Human egg
100 m
Most plant and
animal cells
10 m
Nucleus
most cells: 1-100 µm
Most bacteria

Electron microscopy
Mitochondrion
1 m

Smallest bacteria Super-

100 nm
Viruses resolution
microscopy
Ribosomes
10 nm
Proteins
Lipids
1 nm
Small molecules

0.1 nm Atoms
Label the molecules with fluorescent dyes, which
absorb ultraviolet radiation and emit visible light
 GFP (Green Fluorescent Protein)

• Exhibits bright green fluorescence when exposed to light in

the blue to ultraviolet range
• Makes for an excellent tool in biology due to its ability to
form internal chromophore without requiring any cofactors
or enzymes/substrates
• Can be used in living cells or organisms
 Electron Microscopes (EMs)

• Two basic types of EMs are used to

study subcellular structures
• Scanning electron microscopes
(SEMs) focus a beam of electrons onto
the surface of a specimen, providing
images that look 3-D
• Transmission electron microscopes
(TEMs) focus a beam of electrons
through a specimen, and are used
mainly to study the internal structure of
cells
 Three Domains of Life & Two types of cells

• Two types of cells:

prokaryotic or eukaryotic
• Organisms of the
domains Bacteria and
Archaea consist of
prokaryotic cells
• Protists, fungi, animals,
and plants all consist of
eukaryotic cells
Comparing Prokaryotic and Eukaryotic Cells

• Basic features of all cells

– Plasma membrane
– Semifluid substance called cytosol
– Chromosomes (carry genes in form of DNA)
– Ribosomes (make proteins)
• Prokaryotic cells are
characterized by having
– No nucleus
– DNA in an unbound
region called the
nucleoid
– No membrane-bound
organelles
– Most have cell wall
• Eukaryotic cells are
characterized by having
– DNA in a nucleus that is
bounded by a membranous
nuclear envelope
– Membrane-bound
organelles
cytosol
 Plasma Membrane

• The plasma membrane

is a selective barrier that
allows sufficient passage
of oxygen, nutrients, and
waste
• The general structure of
a biological membrane is
a double layer of
phospholipids
Fluid Mosaic Model

• Phospholipids are
amphipathic molecules,
containing hydrophobic
and hydrophilic regions
• A membrane is a fluid
structure with a
“mosaic” of various
proteins embedded in it
 Surface area to volume ratio (SA/V)

• Metabolic requirements set upper limits

on the size of cells
• The surface area to volume ratio of a
cell is critical (sufficient material
exchange)
• As a cell increases in size, its volume
increases much faster than its surface
area
• Small cells have a greater surface area
relative to volume
 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 (what are the differences?)
Animal Cell
ENDOPLASMIC RETICULUM (ER)
Nuclear
Rough Smooth envelope
Flagellum ER ER NUCLEUS
Nucleolus
Chromatin
Centrosome
Plasma
membrane
CYTOSKELETON:
Microfilaments
Intermediate filaments
Microtubules
Ribosomes

Microvilli
Golgi apparatus
Peroxisome

Mitochondrion Lysosome
 Nuclear Rough Plant Cell
envelope endoplasmic
NUCLEUS reticulum Smooth
Nucleolus endoplasmic
reticulum
Chromatin

Ribosomes

Central vacuole
Golgi
apparatus Microfilaments
Intermediate CYTOSKELETON
filaments
Microtubules

Mitochondrion
Peroxisome
Plasma membrane Chloroplast

Cell wall Plasmodesmata

Wall of adjacent cell
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 (where

is the rest?)
• Ribosomes use the information from the DNA to make proteins
• The nuclear envelop encloses the nucleus, separating it from the
cytoplasm
• The nuclear envelop is a double membrane; each membrane
consists of a lipid bilayer
• Pores regulate the entry and exit of molecules from the nucleus
• The shape of the nucleus is maintained by the nuclear lamina, a
network of protein filaments that maintains the shape of the
nucleus
 1 m Nucleus and its envelope
Nucleus
Nucleolus

Chromatin

Nuclear envelope:
Inner membrane
Outer membrane
Nuclear pore

Rough ER
Pore
complex
Surface of nuclear
envelope Ribosome

Close-up
0.25 m

of nuclear Chromatin
envelope
1 m

Pore complexes (TEM)

Nuclear lamina (TEM)

• In the nucleus, DNA is organized into discrete units
called chromosomes
• Each chromosome is composed of a single DNA
molecule associated with proteins (histones)
• The DNA and proteins of chromosomes are together
called chromatin
• Chromatin condenses to form discrete
chromosomes as a cell prepares to divide
• The nucleolus is a densely stained region located
within the nucleus and is the site of ribosomal RNA
(rRNA) synthesis and ribosome assembly
 Ribosomes: Protein Factories

• Ribosomes are particles made of

ribosomal RNA (rRNA) and protein
• 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)
 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
by vesicles
 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, surface is studded with
ribosomes
Functions of Smooth ER
– Synthesizes lipids
– Detoxifies drugs and poisons
– Stores calcium ions

Functions of Rough ER
– Has bound ribosomes, the new
polypeptide chains enter the ER
lumen and are modified, like
covalently attached to carbohydrates.
These proteins are usually secretory
or membrane proteins
– Package proteins in transport
vesicles, which go to Golgi Apparatus
 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
– Sorts and packages
materials into transport
vesicles, and send them
to their final destinations
• Various Golgi enzymes modify the carbohydrate portions of
glycoproteins.
-- Carbohydrates are first added to proteins in rough ER.
-- The carbohydrate on the resulting glycoprotein is modified as it
passes through the rest of the ER and the Golgi.
-- The Golgi removes some sugar monomers and substitutes others,
producing a large variety of carbohydrates.

（just one example）

ABO blood type system
 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 work best in the acidic environment inside
the lysosome
• 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
Lysosomes
A “road-map” of the secretory and endocytic pathways
ER signal sequences direct ribosomes to the ER membrane
 Vacuoles: Diverse Maintenance Compartments

• A plant cell or fungal cell may have one or

several vacuoles, derived from endoplasmic
reticulum and Golgi apparatus
• 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
 Mitochondria and chloroplasts change
energy from one form to another

• Mitochondria are the sites of cellular respiration, a

metabolic process that uses oxygen to generate ATP
• Chloroplasts are the sites of photosynthesis
The Evolutionary Origins of Mitochondria and Chloroplasts

• Mitochondria and chloroplasts have similarities with

bacteria
– Enveloped by a double membrane, like engulfed
bacteria
– Contain free ribosomes and circular DNA
molecules
– Grow and reproduce somewhat independently in
cells
 Endosymbiont Theory

– An early ancestor of eukaryotic

cells engulfed a nonphotosynthetic
prokaryotic cell, which formed an
endosymbiont relationship with its
host
– The host cell and endosymbiont
merged into a single organism, a
eukaryotic cell with a
mitochondrion
– At least one of these cells may
have taken up a photosynthetic
prokaryote, becoming the
ancestor of cells that contain
chloroplasts
 Mitochondria: Chemical Energy Conversion

• Mitochondria have a smooth outer

membrane and an inner membrane
folded into cristae
• The inner membrane creates two
compartments: intermembrane space
and mitochondrial matrix (the fluid-filled
inner space)
• Some metabolic steps of cellular
respiration are catalyzed in the matrix
• Cristae present a large surface area for
enzymes that synthesize ATP
 Chloroplasts: Capture of Light Energy

• Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other
molecules that function in photosynthesis
• Chloroplasts are found in leaves and other green organs of plants and in algae
• Chloroplast structure includes
– Thylakoids, membranous sacs, stacked to form a granum
– Stroma, the internal fluid-filled space
 Peroxisomes: Oxidation

• Peroxisomes are specialized metabolic compartments bounded

by a single membrane
• Peroxisomes contain enzymes that transfer hydrogen from
various substrates to oxygen
• Peroxisomes produce hydrogen peroxide (toxic) and convert it to
water
• Peroxisomes perform reactions with many different functions
• How peroxisomes are related to other organelles is still unknown
 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
• Three main types of fibers make up the
cytoskeleton
– Microtubules are the thickest of the
three components
– Microfilaments, also called actin
filaments, are the thinnest
components
– Intermediate filaments are fibers Red: microfilaments (actins) Green: microtubules
with diameters in a middle range
 10 m

Column of tubulin dimers

25 nm

  Tubulin dimer
 10 m

Actin subunit

7 nm
 5 m

Keratin proteins
Fibrous subunit (keratins
coiled together)
812 nm
 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
– Locomotion of the cell (cilia and flagella)
 Vesicle Microtubule
ATP
Receptor for interacts with motor
motor protein proteins to produce
motility
Motor protein Microtubule
(ATP powered) of cytoskeleton
(a)

Microtubule Vesicles 0.25 m

(b)
 Centrosomes and Centrioles
• In many cells, microtubules grow out
from a centrosome near the nucleus
• The centrosome is a “microtubule-
organizing center”
• In animal cells, the centrosome has a
pair of centrioles, each with nine
triplets of microtubules arranged in a
ring
Microtubules separate chromosomes during cell division
Cilia and Flagella

• Microtubules control the beating of cilia and flagella,

locomotor appendages of some cells
• Cilia and flagella share a common
structure
– A core of microtubules sheathed
by the plasma membrane
– A basal body that anchors the
9+2
cilium or flagellum
– A motor protein called dynein,
which drives the bending
movements of a cilium or
flagellum

9+0
Microfilaments (Actin Filaments)

• Microfilaments are solid rods about 7nm

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
• Bundles of microfilaments make up the
core of microvilli of intestinal cells
• Actin functions in muscle contraction together with the
protein myosin
• In muscle cells, thousands of actin filaments are arranged
parallel to one another
• Thicker filaments composed of myosin interdigitate with the
thinner actin fibers
• Localized contraction brought about by actin and myosin
also drives amoeboid movement
• Pseudopodia (cellular extensions) extend and contract
through the reversible assembly and contraction of actin
subunits into microfilaments
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
 Cell Walls of Plants

• The cell wall is an extracellular structure that

distinguishes plant cells from animal cells
• Prokaryotes, fungi, and some protists also have cell
walls
• The cell wall protects the plant cell, maintains its shape,
and prevents excessive uptake of water
• Plant cell walls are made of cellulose fibers embedded
in other polysaccharides and protein
• Plant cell walls may have multiple
layers
– Primary cell wall: relatively thin
and flexible
– Secondary cell wall (in some
cells): added between the plasma
membrane and the primary cell
wall
• Plasmodesmata are channels
between adjacent plant cells
 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
 Cell Junctions

• Neighboring cells in tissues, organs, or organ

systems often adhere, interact, and communicate
through direct physical contact
• Intercellular junctions facilitate this contact
• There are several types of intercellular junctions
– Plasmodesmata
– Tight junctions
– Desmosomes
– Gap junctions
 Plasmodesmata in Plant Cells

• 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
Tight Junctions, Desmosomes, and
Gap Junctions in Animal Cells

• 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