Chapter 04

Lecture Outline

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 Chapter 4
General Features of Cells

Key Concepts:
◼ Microscopy
◼ Overview of Cell Structure
◼ The Cytosol
◼ The Nucleus and Endomembrane System
◼ Semiautonomous Organelles
◼ Protein Sorting to Organelles
◼ Systems Biology of Cells: A Summary
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Cell theory

1. All living organisms are composed of one or

more cells
2. Cells are the smallest units of life
3. New cells come only from pre-existing cells by
cell division

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 Overview of Cell Structure

Two categories of life:

◼ Prokaryotes
❑ Simple cell structure
❑ No nucleus

◼ Eukaryotes
❑ More complex cells
❑ DNA enclosed within membrane-bound nucleus
❑ Internal membranes form organelles

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Prokaryotic cells
Two categories of prokaryotes:
◼ Bacteria
❑ Small cells, 1 μm – 10 μm in diameter
❑ Very abundant in environment and our bodies
❑ Vast majority are not harmful to humans
❑ Some species cause disease

◼ Archaea
❑ Also small cells, 1 μm – 10 μm in diameter
❑ Less common
❑ Often found in extreme environments
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Typical bacterial cell
◼ Inside the plasma membrane:
❑ Cytoplasm – contained within plasma membrane
❑ Nucleoid region – where DNA is located
❑ Ribosomes – synthesize proteins

◼ Outside the plasma membrane:

❑ Cell wall – provides support and protection
❑ Glycocalyx – traps water, gives protection, help evade
immune system
❑ Appendages – pilli (attachment), flagella (movement)

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Nucleoid region:
Site where the
DNA is found.

Ribosomes:
Synthesize Plasma
polypeptides. membrane:
Encloses the
cytoplasm.

Cytoplasm:
Site of metabolism. Cell wall:
Provides support
and protection.

Pili:
Allow bacteria to Glycocalyx:
attach to surfaces Outer gelatinous
and to each other. covering.

Flagella:
Allow certain 0.5 µm
bacteria to swim.

(a) Diagram of a typical rod-shaped bacterium (b) A colorized TEM of Escherichia coli
b: © Dr. Dennis Kunkel Microscopy/Visuals Unlimited

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Eukaryotic cells
◼ DNA is housed inside membrane-bound nucleus
◼ Compartmentalized functions
◼ Organelles
❑ Membrane-bound compartments
❑ Each has a unique structure and function

◼ Variety
❑ Shape, size, and organization of cells vary considerably
❑ Differences between species
❑ Differences between specialized cell types
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Animal cell Nuclear pore:

Nucleus:
Area where most of
the genetic material
is organized and
Passageway for
Centrosome: molecules into and expressed.
Site where out of the nucleus. Nuclear envelope: Nucleolus:
microtubules grow Double membrane Site for ribosome
and centrioles are that encloses the subunit assembly.
found. nucleus.

Lysosome:
Site where
Rough ER: macromolecules
Site of protein are degraded.
sorting and
secretion.

Ribosome:
Smooth ER: Site of polypeptide
Site of detoxification synthesis.
and lipid synthesis.

Chromatin:
A complex of
protein and DNA.
Mitochondrion:
Site of ATP synthesis. Plasma membrane:
Membrane that controls
movement of substances
into and out of the cell;
site of cell signaling.
Cytoskeleton:
Protein filaments that
provide shape and aid Cytosol:
in movement. Site of many metabolic
Peroxisome: pathways.
Site where hydrogen peroxide
and other harmful molecules Golgi apparatus:
are broken down. Site of modification,
sorting, and secretion
of lipids and proteins.

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10 μm 46 μm

(a) Human skin cell (b) Human nerve cell

a: © Ed Reschke/Getty Images; b: © Eye of Science/Photo Researchers, Inc.

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Plant cell Nucleus:

Area where most of
the genetic material
is organized and Nuclear pore:
expressed. Passageway for
Nucleolus: Nuclear envelope: molecules into and
Site for ribosome Double membrane out of the nucleus.
that encloses the Ribosome:
subunit assembly.
nucleus. Site of polypeptide
synthesis.

Central vacuole:
Site that provides
storage; regulation of Smooth ER:
cell volume. Site of detoxification
and lipid synthesis.

Rough ER:
Cytosol:
Site of protein
Site of many metabolic
sorting and
pathways.
secretion.

Chromatin:
A complex of Plasma membrane:
protein and DNA. Membrane that controls
movement of substances
into and out of the cell;
site of cell signaling.

Mitochondrion:
Site of ATP synthesis.

Cell wall:
Structure that
provides cell
Chloroplast:
Site of photosynthesis.
Peroxisome:
Site where hydrogen
peroxide and other
Cytoskeleton: harmful molecules are
Protein filaments that Golgi apparatus: broken down.
provide shape and aid Site of modification,
in movement. sorting, and secretion
of lipids and proteins.

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Video: PLANT VS ANIMAL CELLS

https://www.youtube.com/watch?v=ApvxVtBJxd0
 The Cytosol

◼ Region of a eukaryotic cell that is outside the cell

organelles but inside the plasma membrane
◼ Cytoplasm includes everything inside the
plasma membrane
❑ Cytosol
❑ Endomembrane system
❑ Semiautonomous organelles

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(a) Animal cell

(b) Plant cell

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Molecular synthesis and breakdown

◼ Sum of all chemical reactions by cells

◼ Catabolism
❑ Breakdown of a molecule into smaller components
◼ Anabolism
❑ Synthesis of cellular molecules and macromolecules
◼ Cytosol is central coordinating region for
metabolic activities of eukaryotic cells

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Cytoskeleton
Network of three types of protein filaments
◼ Microtubules
❑ Long,hollow cylindrical structures
❑ Dynamic instability

◼ Intermediate filaments
❑ Intermediatein size
❑ Form twisted, ropelike structure

◼ Actin filaments
❑ Alsoknown as microfilaments
❑ Long, thin fibers

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Table 4.1 Types of Cytoskeletal Filaments Found in Eukaryotic Cells

Characteristic Microtubules Intermediate filaments Actin filaments
Diameter 25 nm 10 nm 7 nm

Structure Hollow tubule Twisted filament Spiral filament

Plus end
α-Tubulin
Plus end
Actin protein
β-Tubulin

Lumen

1 0 nm

Minus end
(may be anchored Staggered alignment
in the centrosome of intermediate
of animal cells) filament proteins 7 nm
Minus end
25 nm

Protein composition Hollow tubule composed of the protein Can be composed of different proteins Two intertwined strands composed of the
tubulin including keratin, lamin, and others that protein actin
form twisted filaments

Centrosome

Common functions Cell shape; organization of cell Cell shape; provide cells with mechanical Cell shape; cell strength; muscle
organelles; chromosome sorting in strength; anchorage of cell and nuclear contraction; intracellular movement of
cell division; intracellular movement membranes cargo; cell movement (amoeboid
of cargo; cell motility (cilia and flagella) movement); cytokinesis in animal cells

(1): © Thomas Deerinck/Visuals Unlimited; (2–3): © Dr. Gopal Murti/Visuals Unlimited

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 Motor Proteins
such as myosins and kinesins, move along cytoskeletal filaments via a
force-dependent mechanism driven by the hydrolysis of ATP

◼ Use ATP as a source of energy for movement

◼ Three domains— the head, hinge, and tail
◼ Walking analogy
❑ The ground is the cytoskeletal filament, your leg is the
head of the motor protein, and your hip is the hinge

◼ Three kinds of movements

1. Motor protein carries cargo along the filament
2. Motor protein remains in place, the filament moves
3. Motor protein and filament both restrained – action of
the motor protein exerts a force that bends the filament
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Tail — binds to Hinge — region

other components that bends

Head — binds to cytoskeletal

filament; site of ATP binding
and hydrolysis

(a) Three-domain structure of myosin, a motor protein

Actin filament
Minus end

1 Head is released from

cytoskeletal filament.

2 Head cocks forward

and binds to filament.

3 Head cocks backward

(this moves the tail
from left to right).

(b) Movement of a motor protein along a cytoskeletal filament 19

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Cargo

Motor
protein
(kinesin)

– +
Microtubule

(a) Motor protein moves

Motor
proteins
in a fixed
position
– +

Actin
filament
– + moves to
the left

(b) Filament moves + + +

+
Motor
protein
(dynein)
Linking
protein

– – –
–
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(c) Filaments bend
 The Nucleus and
Endomembrane System

◼ Network of membranes enclosing the nucleus,

endoplasmic reticulum, Golgi apparatus,
lysosomes, and vacuoles
◼ Also includes plasma membrane
◼ May be directly connected to each other or
pass materials via vesicles

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Nucleus

Animal cell Plant cell

Nuclear envelope

Lysosome

Peroxisome
Vacuole
Endoplasmic
reticulum

Golgi
apparatus
Plasma
membrane
Peroxisome:
Site where hydrogen peroxide and other
harmful molecules are broken down.
Lysosome:
Site where macromolecules are degraded.
Golgi apparatus:
Site of modification, sorting, and secretion
of lipids and proteins.
Ribosome:
Site of polypeptide synthesis.
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Nuclear envelope
◼ Double-membrane structure enclosing nucleus
◼ Outer membrane of the nuclear envelope is
continuous with the ER membrane
◼ Nuclear pores provide passageways
◼ Materials within the nucleus are not part of the
endomembrane system

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Pore Nucleus
Nucleolus

Chromatin Chromatin

Nucleolus Nuclear lamina

Nuclear envelope
Pore in nuclear
envelope
5.4 µm

Pore complexes
Two
membranes
of nuclear
envelope

Nucleus:
Area where most of the genetic 0.4 µm
material is organized and expressed.

Nuclear envelope: Chromatin in nucleus

Double membrane that encloses the
nucleus. Nucleus Internal nuclear matrix
Nucleolus: Inner membrane
Site for ribosome subunit assembly. Nuclear envelope
Nuclear Outer membrane
Chromatin:
A complex of protein and DNA. pore
Nuclear lamin proteins
complex
Nuclear pore:
Passageway for molecules into and Cytosol
out of the nucleus.
(top right): © Dr. Donald Fawcett/Visuals Unlimited; (middle right): © Dr. Richard Kessel & Dr. Gene Shih/Visuals Unlimited

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Nucleus

◼ Chromosomes
❑ Composed of DNA and proteins = chromatin

◼ Nuclear matrix
❑ Filamentous network
❑ Organizes chromosomes

◼ Ribosome assembly occurs in the nucleolus

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Endoplasmic reticulum
◼ Network of membranes that form flattened,
fluid-filled tubules or cisternae
◼ ER membrane encloses a single compartment
called the ER lumen
◼ Rough endoplasmic reticulum (rough ER)
❑ Studded with ribosomes
❑ Involved in protein synthesis and sorting

◼ Smooth endoplasmic reticulum (smooth ER)

❑ Lacks ribosomes
❑ Detoxification, carbohydrate
metabolism, calcium
balance, synthesis, and modification of lipids
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Nuclear
Nucleolus Nucleus envelope Rough ER Smooth ER Nucleus

0.1
0.1 µm
µm

Ribosomes ER lumen Cisternae Ribosomes Rough ER Smooth ER Mitochondrion

© Dennis Kunkel Microscopy, Inc/Phototake

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Golgi apparatus
◼ Also called the Golgi body, Golgi complex, or
simply Golgi
◼ Stack of flattened, membrane-bounded
compartments
◼ Vesicles transport materials between stacks
◼ Three overlapping functions
❑ Secretion, processing, and protein sorting

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Secretory pathway

Cargo in vesicle

Cargo for secretion

Cargo released
outside cell

Lumen of
endoplasmic
reticulum

Lumen of Golgi
apparatus

Vesicles
Plasma
Cis Medial Trans
membrane

Rough endoplasmic reticulum Golgi apparatus

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Lysosomes
◼ Contain acid hydrolases that perform
hydrolysis
◼ Many different types of acid hydrolases to
break down proteins, carbohydrates, nucleic
acids, and lipids
◼ Autophagy
❑ Recycling of worn-out organelles through endocytosis

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Vacuoles
◼ Functions are extremely varied, and they differ
among cell types and environmental conditions
◼ Central vacuoles in plants for storage and
support
◼ Contractile vacuoles in protists for expelling
excess water
◼ Phagocytic vacuoles in protists and white
blood cells for degradation
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Contractile
vacuole

Central
vacuole
Food vacuole
0.25 μm

(a) Central vacuole in a plant cell (b) Contractile vacuoles in an algal cell (c) Food vacuoles in a paramecium
a: © E.H. Newcomb & S.E. Frederick/Biological Photo Service; b: Courtesy Dr. Peter Luykx, Biology, University of Miami;
c: © Dr. David Patterson/Photo Researchers, Inc.

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Peroxisomes

◼ Catalyze certain reactions that break down

molecules by removing hydrogen or adding
oxygen
◼ Hydrogen peroxide (H2O2) is a byproduct
◼ Catalase breaks down dangerous H2O2 into
water and oxygen

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1 Vesicles bud from the ER and 2 The import of additional

fuse with each other to form proteins and lipids results
a premature peroxisome. in a mature peroxisome.

Premature peroxisome Mature peroxisome

Division

3 Mature peroxisomes
may divide to produce
more peroxisomes.

ER

0.25 μm

(inset): © The McGraw-Hill Companies, Inc./Al Telser, photographer

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Plasma membrane

◼ Boundary between the cell and the extracellular

environment
◼ Functions
❑ Membrane transport in and out of cell, with selective
permeability
❑ Cell signaling using receptors
❑ Cell adhesion

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Cell 1
Cell adhesion:
Proteins in the plasma
membrane of adjacent cells
hold the cells together.

Membrane transport:
Proteins in the plasma Glucose
membrane allow the
transport of substances
into and out of cells.

Cell 2
Extracellular
signal

Cell signaling:
An extracellular signal
Cellular
binds to a receptor in
Signal response
the plasma membrane
that activates a signal transduction
transduction pathway, pathway
leading to a cellular
response.
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 Semiautonomous Organelles

◼ Mitochondria and chloroplasts

◼ Grow and divide to reproduce themselves
◼ They are not completely autonomous because
they depend on the cell for synthesis of internal
components

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Animal cell

Mitochondrion

Chloroplast

Plant cell 38
Mitochondria

◼ Primary role is to make ATP

◼ Outer and inner membrane
❑ Intermembrane space and mitochondrial matrix

◼ Also involved in the synthesis, modification, and

breakdown of several types of cellular molecules
◼ Contain their own DNA, divide by binary fission

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Outer
membrane
Intermembrane
space
Inner
membrane

Mitochondrial
matrix

Cristae

Cytosol

0.3 μm
© Dr. Donald Fawcett/Visuals Unlimited 40
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Mitochondrial chromosome
located in nucleoid

1 Mitochondrial
genome replicates.

2 Mitochondrion
begins to divide
by binary fission.

3 Binary fission is
completed.

(b) Transmission electron

micrographs of the
(a) Binary fission of process
mitochondria 41
© T. Kanaseki and Dr. Donald Fawcett/Visuals Unlimited
Chloroplasts
◼ Photosynthesis
❑ Capture light energy and use some of that energy to
synthesize organic molecules such as glucose

◼ Found in nearly all species of plants and algae

◼ Outer and inner membrane
❑ Intermembrane space
❑ Thylakoid membrane

◼ Contain their own DNA, divide by binary fission

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Outer
membrane
Inner
membrane
Thylakoid
membrane
Thylakoid
lumen

Granum
(stack of
thylakoids)
Stroma
Cytosol

0.7 µm
© Dr. Jeremy Burgess/Photo Researchers, Inc. 43
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Plants and algae
Animals, fungi, and protists (contain mitochondria
(contain mitochondria) and chloroplasts)

Billions of years ago (bya)

Evolution Evolution
Primordial
eukaryotic
cells
1

Cyanobacterium
Purple
bacterium

2
(a) Mitochondria originated (b) Chloroplasts originated
from endosymbiotic from endosymbiotic
purple bacteria. cyanobacteria.
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 Protein Sorting to Organelles

Eukaryotic proteins are sorted to the right destination

◼ Cotranslational sorting
❑ For ER, Golgi, lysosomes, vacuoles, plasma membrane,
and secreted proteins
❑ Begins in cytosol during translation
❑ Involves sorting signals and vesicle transport

◼ Post-translational sorting
❑ Most proteins for nucleus, mitochondria, chloroplasts,
and peroxisomes
❑ Synthesized in cytosol and sorted later
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Protein synthesis begins on

Ribosome ribosomes in the cytosol.

mRNA

Emerging polypeptide

Post-translational sorting to the nucleus,

Remain in cytosol
NH3+ mitochondria, chloroplasts, or peroxisomes

Cotranslational
COO– sorting to ER

NH3+
Completed polypeptide in cytosol
COO–
Cytosolic proteins complete
their synthesis in the cytosol NH3+
and remain there due to the Completed
NH3+ lack of a sorting signal. Completed polypeptide
COO– NH3+ in cytosol
polypeptide
ER in the ER
sorting These proteins are completely
signal NH3+ synthesized in the cytosol.
They contain sorting signals
For proteins with an ER sorting NH3+ ER lumen
that send them to the nucleus,
signal, translation is paused, and the mitochondria, chloroplasts, or
protein is then synthesized into the peroxisomes.
ER. Some of these proteins contain Endoplasmic
ER retention signals and remain in reticulum (ER)
the ER. The others are sent to the Vesicle transport
Golgi via vesicles. to Golgi

Some of these proteins contain

Golgi retention signals and
remain in the Golgi. The others
are sent, via vesicles, to the
Nucleus Peroxisome
lysosomes, plasma membrane,
or outside the cell via secretory
vesicles.

Golgi

Mitochondrion Chloroplast

Secretory
vesicle
Lysosome
or vacuole

Plasma
membrane

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1 SRP binds to 2 SRP binds to 3 SRP is released, and Signal

ER signal receptor in ER translation resumes. The peptidase
Ribosome sequence membrane. growing polypeptide is
and pauses threaded into a channel.
translation.
5′
mRNA

ER signal
sequence NH3+
NH3+ SRP
COO–
Cleaved
signal
Cytosol
sequence

SRP
ER membrane Channel The ER signal The polypeptide
receptor 4 5
protein sequence is cleaved is completely
by signal peptidase. synthesized and
ER lumen
released into the
ER lumen.

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1 In this example, a cargo of proteins binds to Golgi

T-snare
receptors in the ER membrane. The binding of membrane
coat proteins helps a vesicle bud from the
membrane, and V-snares are incorporated into
vesicle.

Coat
proteins

Protein cargo

Cargo receptor
3 After the vesicle 4 The vesicle 5 The vesicle fuses
V-snare is released, the binds to the with the target
coat is shed. target membrane membrane to
2 The vesicle pinches by a V-snare/ deliver the protein
off the membrane and T-snare cargo to its target
is released. interaction. destination.
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ER
membrane
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1 Chaperone 2 Matrix-targeting 3 Chaperones are 4 Protein is

proteins keep sequence binds released as protein transferred to a
protein unfolded. to receptor. is transferred to a channel in the
channel in the inner membrane. Contact site
outer membrane.
Active protein

Mitochondrial matrix
Chaperone Channel
Matrix-targeting proteins
sequence

Cytosol
Receptor
Outer 5 Chaperones 8 Chaperones are
protein
membrane bind to protein 6 Matrix-targeting released, and protein
as it enters the sequence is 7 Protein is folds into its
Intermembrane cleaved by an three-dimensional
matrix. completely
space enzyme in the structure.
threaded into
Inner matrix. the matrix.
membrane

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