revised notes for Topic 2.1-2.3

2.1.1-2.1.5, 2.7-2.10, 2.2 , 2.3
A. What It Says
1. All living things are made of one or more cells
2. The cell is the basic unit of life/the smallest unit that shows all the
characteristics of life
3. All cells come from pre-existing cells
B. History of Cell Discovery and Evidence for the Cell Theory
1. History of Cell Discovery
Table 1. Some significant events in the development of the cell theory.
and Hans
Anton(y) van
Schleiden and
Robert Brown
Invention of microscope
Invented compound microscope and iris diaphragm
Observed plant tissues, specifically cork, and found repeated
units he called cells described in Micrographia, published in
Also accomplished in a number of other areas including
physics (Hooke’s Law)
First observed unicellular organisms (protists) in pond water
Discovered bacteria
Improved the microscope
Found cells in all plants
Found cells in all animals
Proposed the cell theory (they were incorrect in stating that
cells form spontaneously)
Discovered the nucleus
“Cells come from pre-existing cells.”
Louis Pasteur
Disproved the “spontaneous generation” hypothesis
His experiment is described here:
*Were contemporaries and aware of each other’s work. Van Leeuwenhoek may have
read Hooke’s Micrographia and Hooke was given the job of confirming
Leeuwenhoek’s discovery of “little animals” or “animalcules” by the Royal Society of
2. Evidence For Each Part of the Cell Theory
a. All living things are made of one or more cells.
i. Schleiden and Schwann: plants and animals are made of cells
ii. observations of living things continue to support that they are made
of one (unicellular organisms such as Monerans and Protists) or
more (multicellular organisms such as Fungi, Plants and Animals)
smaller units called cells
a. Debatable: Viruses…are they alive? They are not cells!
b. The cell is the basic unit of life/smallest unit that shows all the
characteristics of living things.
i. structures within cells cannot survive on their own
ii. cells isolated from tissues can survive in culture
c. All cells come from pre-existing cells.
i. binary fission, mitosis and meiosis are the processes used for one
cell to produce more cells
a. Debatable: Where did the first cell come from? The first cell(s)
provide an exception to this part of the cell theory. Scientists
have yet to produce cells from non-living precursors in the
A discussion of “The Evolution of the Cell” can be found here:
II. Relative Sizes of Things
Figure 1: The relative sizes of chemical and biological structures.
III. Unicellular or Multicellular?
A. Emergent Properties: multicellular organisms are able to carry out certain
functions because they are multicellular and their cells interact with each
other; these properties make the whole more than “the sum of its parts”
B. each cell in a multicellular organism has the same set of genes
a. cells differentiate and become specialized by expressing some genes but
not others
C. Limits to Cell Size-will be discussed in the Membrane Section
IV. Types of Cells
A. Prokaryotic: cells that do not have a nucleus
B. Eukaryotic: cell that do have a nucleus
V. Structures Found in All Cells
A. Cell or Plasma Membrane
Figure 2: Diagram of the cell/plasma membrane.
Integral protein
Figure 3. Diagram of the cell/plasma membrane.
1. Structure:
a. most common model is called the “fluid mosaic model”
i. “fluid” because the component parts can move past each other much
like the molecules in a fluid
ii. mosaic because there are many different components to the cell
b. components:
i. phospholipids: the main component, have a phosphate “head” region
(hydrophilic or polar)* and 2 fatty acid “tails” (hydrophobic or polar)*
*more on the definitions of these terms when we study Topic 3 The Chemistry
of Life
Figure 4. The structure of phospholipids.
Non-polar region
ii. proteins: these are embedded amongst the phospholipid molecules
and may be found more on the internal surface (peripheral),
external surface (peripheral) or spanning the membrane (integral)
iii. glycoproteins: these are proteins with carbohydrate chains attached
to them, found only on extracellular surface
iv. glycolipids: these are fatty acids with carbohydrate chains attached to
them rather than phosphate groups, found only on
extracellular surface
v. cholesterol: a steroid (a class of lipid) that is found amongst the lipid
tails and helps to stabilize the membrane and maintain
its flexibility
2. Function(s):
a. holds all the internal components of the cell together and separates
them from the external environment thus allowing the internal
environment to be different from the external environment
b. actively selects some materials to enter and exit the cell because it is
selectively permeable
i. selectively permeable: describes a membrane that is semi-permeable
and also actively changes in order to control which substances can
pass through it (and thus enter or exit the cell)
c. communicates with other cells and senses the external environment
d. sticks to or joins with adjacent cells
e. anchors enzymes in prokaryotes
Here is a basic review of cell membrane structure with a review activity at the end:
B. Cytoplasm: the material inside the cell membrane and outside of other
membranes within the cell, other structures can be found in this
1. Structure
a. gel-like, mostly water, dissolved particles (small covalently bonded
molecules such as glucose) or dissociated particles (ions such as Na+,
Cl-, K+, H+, etc.) and some water-soluble larger molecules (e.g. certain
*often used as if synonymous with the term cytosol but cytosol refers
specifically to the water of the cytoplasm
2. Function
a. site of many chemical reactions
b. helps to give cell its shape
C. Ribosomes
1. Structure
a. made of ribonucleic acid (RNA) and many proteins
b. each ribosome is made of a smaller subunit and a larger subunit
c. size, measured in Svedberg units (based on rate of sedimentation in a
centrifuge), is different in prokaryotes and eukaryotes
i. in prokaryotes, smaller, 70S
ii. in eukaryotes, larger, 80S
2. Site of protein synthesis (more detail to come)
D. Deoxyribonucleic Acid (DNA)
1. Structure (more detail later)
a. made of smaller units called nucleotides
b. each nucleotide is made of the elements carbon, hydrogen, oxygen,
phosphorus and nitrogen
c. in prokaryotes, forms a ring-shaped chromosome and possibly one or
more ring-shaped plasmids
d. in eukaryotes, forms linear chromosomes
2. Function (more detail later)
a. often said to contain the “blueprint of life”
b. is the molecule that contains the genetic information of the cell
c. directs all of the chemical reactions that occur in the cell
3. Location
a. in the cytoplasm of prokaryotes, in a region often referred to as the
nucleoid region
b. in the nucleus of eukaryotes, separated from the cytoplasm by the
nuclear membrane
VI. Structure of Prokaryotic Cells
Figure 5. Shapes of Prokaryotic Cells
A. Overall Shape
1. Spherical (singular: coccus, plural: cocci)
2. Rod-shaped (singular: bacillus, plural: bacilli)
3. Spiral (singular: spirillum, plural: spirilla)
Figure 6. E. coli bacterium.
Figure 7. E. coli showing flagella (F) and pili (P).
Figure 8. Electron micrograph of E. coli.
Figure 9. Electron micrograph of E. coli.
B. Plasmid: extra-chromosomal genetic material
1. Structure
a. DNA in the shape of a ring
2. Function
a. extra genetic material
b. can be transferred between individuals
C. Cell Wall
1. Structure
A. made of peptidoglycan, a molecule that is a glycoprotein
1. if Gram+: more peptidoglycan and less lipopolysaccharide and
appear more purple after the Gram staining process
2. if Gram-: less peptidoglycan and more lipopolysaccharide and
appear pink after the Gram staining process
2. Function
a. gives the cell shape
b. protects the cell from external environment
c. anchors pili and flagella
d. prevents the cell from bursting in hypotonic environments
D. Flagella: long, whip-like structures, usually few in number
1. Structure
a. made of a protein called flagellin
2. Function
a. locomotion
Here is a movie of E. coli bacteria moving:
E. Pili
1. Structure
a. made of protein
b. short, straight structure that sticks out from the cell
2. Function
a. attach bacteria to each other and transfer DNA during a process called
b. attachment to surfaces
c. protection from phagocytosis
F. Fimbriae: another name for pili
G. Glycocalyx
1. Slime Layer
a. Structure
i. glycoproteins loosely associated with cell wall
b. Function
i. adhere to solid surfaces
ii. prevent drying out
2. Capsule
a. Structure
i. polysaccharides firmly attached to the cell wall
b. function
i. adhere to solid surfaces
ii. protects cell from phagocytosis by host immune system
H. Cytoskeleton
1. Structure
a. made of proteins, thought to be the evolutionary precursors of the
cytoskeleton proteins in eukaryotic cells
2. Function
a. contribute to cell shape
I. Endospores
1. Structure
a. protective covering enclosing cell wall, cell membrane, cytoplasm and
2. Function
a. maintain cell during stressful environmental conditions
i. resistant to radiation, drying out, extreme temperatures, starvation,
chemicals and lysozyme
Here is a basic summary and an interactive labelling exercise:
Another one:
VII. Eukaryotic Cells (have a nucleus)
A. Nucleus
1. Structure
a. large, membrane-bound (enclosed) structure containing unwound
chromosomes (chromatin) during most stages of the cell’s life cycle
2. Function
a. separates the chromosomes from the rest of the cell
i. the chromosomes control all of the chemical reactions (metabolism)
of the cell
A. Nuclear Membrane
1. Structure
a. phospholipid bilayer similar to the cell membrane
2. Function
a. controls the movement of material between the nucleus and thy
C. Nucleolus
1. Structure
a. darkly stained area of the nucleus
b. there may be more than one
2. Function
a. site of ribosome synthesis
D. Endoplasmic Reticulum (Smooth) (SER)
1. Structure
a. a system of tubules with a double membrane similar in structure to the
cell membrane
2. Function
a. site of lipid/fat synthesis
b. Involved in the detoxification of drugs or harmful chemicals
c. transports materials throughout the cell
E. Endoplasmic Reticulum (Rough) (RER)
1. Structure
a. smooth endoplasmic reticulum with ribosomes attached to it
2. Function
a. modifies and packages the proteins made by the attached ribosomes
b. transports the proteins to the Golgi apparatus
F. Golgi Apparatus
1. Structure
a. resembles a stack of pancakes
b. connected to the ER
2. Function
a. modifies and packages the proteins from the RER
i. packaged into small sacs called vesicles
b. synthesizes complex polysaccharides
G. Vesicle
1. Structure
a. small bag or sac with a double-membrane
2. Function
a. transport proteins from the Golgi apparatus to the cell membrane
H. Vacuole
1. Structure
a. large bag or sac
2. Function
a. storage of food, water, waste or proteins
b. in plants, water in the large central vacuole helps to put pressure on
the cell wall to maintain the cell’s shape and rigidity
c. in some protists, a contractile vacuole functions to store excess water
and pump it out of the cell so the cell doesn’t burst
I. Lysosome
1. Structure
a. sac or bag containing digestive enzymes
2. Function
a. fuse with food vacuoles so that the enzymes can break down large food
molecules into their building blocks so that they can be used by the cell
i. fused structure is known as a digestive vacuole
b. involved in the recycling of dead cells
i. burst and the enzymes digest the contents of the whole cell
ii. called a “suicide bag”
J. Mitochondrion (plural=mitochondria)
1. Structure (more detail later)
a. composed of an inner folded membrane and an outer membrane
b. has its own DNA and is capable of synthesizing some or its own
2. Function
a. site of the aerobic reactions of cellular respiration
K. Microtubules
1. Structure
a. proteins called tubulin
2. Function
a. shape and support the cell
b. serve as tracks that organelles can move along
c. anchor organelles such as nucleus
L. Microfilaments
1. Structure
a. rods made of proteins called actin
2. Function
a. involved in dividing of cytoplasm (cytokinesis) during cell division
b. involved in the projection of pseudopodia
c. involved in cytoplasmic streaming (the movement of cytoplasm seen in
M. Cytoskeleton
1. Structure
a. microtubules, microfilaments and intermediate filaments
2. Function
a. See microtubules and microfilaments
N. Intermediate Filaments
1. Structure
a. Rope-like fibrous proteins
2. Function
a. structural reinforcement
b. anchor organelles such as nucleus
O. Cilia
Figure 10. Structure of cilia and flagella.
1. Structure (the same as flagella)
a. many, short, “hair-like” structures
b. made of microtubules arranged in so that a pair of microtubules is
surrounded by a ring of 9 more microtubule pairs (doublets).
2. Function
a. movement of the cell
b. movement of materials outside the cell
P. Flagella
1. Structure (the same as cilia)
a. few, usually only 1 or 2, long, “whip-like” structures
b. made of microtubules arranged in so that a pair of microtubules is
surrounded by a ring of 9 more microtubule pairs (doublets).
2. Function
a. movement of the cell
Q. Structures found in Animal Cells (but not Plant Cells)
Figure 10 . A representative diagram of an animal cell.
1. Centrioles
Figure 12. Structure of centrioles.
a. Structure
i. microtubules, a pair of centrioles is found in each cell
b. Function
i. microtubules radiate from the centrioles during cell division to form
the spindle
R. The liver cell as an example of a typical animal cell
* IB specifically lists the following cell structures: free ribosomes, rough endoplasmic
reticulum (rER/RER), lysosome, Golgi apparatus, mitochondrion and nucleus and
expects that you can draw and label them on a diagram of a liver cell and be able to
label them on an electron micrograph of a liver cell.
1. From the click4biology website:
Ultrastructure of a liver cell.
1:Nucleolus; 2:Chromatin; 3:Dense Chromatin; 4:Nuclear Pores;
6:Rough Endoplasmic Reticulum; 7:Ribosomes; 8:Golgi Apparatus;
9:Smooth Endoplasmic Reticulum;
10:Peroxisomes; 11:Lysosomes; 12:Bile Capillary; 13:Desmosomes;
5. Kupffer cell of liver:
Ec = euchromatin; Grg = glycogen granules; Hc = heterochromatin; Hec =
Hepatocytus (hepatocyte = liver cell);
L = lumen of the sinusoid (which is a special capillary); Mi = mitochondrion (of the
crista-type); Mn = Membrana nuclearis (nuclear membrane);
Mpl = Macrophagocytus stellatus (Kupffer cell; belongs to the macrophages); Mt =
Mv = microvilli (immobile processes of liver cells); N = Nucleus (nucleus); P =
Plasmalemma (cell membrane);
Ph = phagolysosome; Pin = pinocytosis; Ps = Pseudopodia (pseudopods = mobile
cell processes); RER = rough endoplasmic reticulum;
Sp = Spatium perisinusoideum (Disse's space); V = Clathrin-coated vesicle
(endocytotic vesicle); Va = vacuole (belongs to L).
S. Structures found in Plant Cells (but not Animal Cells)
Figure 11. A representative diagram of a plant cell.
1. Central vacuole- plant cells tend to have one, large, central vacuole
a. Structure
i. membrane-bound
ii. filled with water, salts, minerals, nutrients, proteins, possibly
pigments or bitter-tasting chemicals
b. Function
i. storage of the above-mentioned materials
ii. produces turgor pressure when the vacuoles are filled with water
and exert pressure by pushing the cytoplasm against the cell wall
2. Chloroplasts
a. Structure
i. outer membrane and inner membrane organized into interconnected
b. Function
i. Site of photosynthesis
3. Plastids
a. Structure
i. membrane-bound
b. Function-varied
i. chloroplasts carry out photosynthesis
ii. amyloplasts/leucoplasts store starch
iii. chromoplasts store pigments
4. Cell Walls
a. Structure
i. mostly made of a polysaccharide called cellulose
b. Function
i. support the cell/provide a rigid layer
ii. recall the central vacuole pushes the cytoplasm against the cell wall
to produce turgor pressure
VIII. Prokaryotic vs. Eukaryotic Cells
Here is a table to compare prokaryotic and eukaryotic cells:
IX. Stem Cells
*First discovered by a pair of Canadian scientists (James Till and Ernest McCulloch)!
A talk with Dr. James Till is available here:
**Canada has a Stem Cell Network (
that is headquartered at the Sprott Centre for Stem Cell Research and the University
of Ottawa.
A. stem cell: cells that “retain the capacity to divide and have the ability to
differentiate along different pathways”
1. Different from other cells because
a. are unspecialized
b. can divide infinitely, even after long periods of inactivity
c. has potential to produce either more stem cells or specialized cells
1. 3 types
a. Embryonic (ES): from embryos
i. from embryos (mouse, 1981 and human 1998)
ii. embryos are from in vitro fertilization
a. in order to isolate the ES, the embryo is destroyed (ethics)
b. Adult/somatic: from adults
c. Induced pluripotent stem cells (iPSC/iPS): specialized adult cells
“reprogrammed” to become like stem cells
i. first produced in 2006
B. What is their normal role?
1. in the embryo they differentiate into all the different types of cells and
tissues required
2. in many tissues, serve as a reservoir of cells to replenish other cells in
order to repair the tissue
a. in gut, muscle, brain and bone marrow divide regularly to repair and
replace cells lost through wear and tear, injury or disease
b. in pancreas and heart only divide under particular circumstances
C. Research on Stem Cells
1. to learn more about how a single cell (embryo) develops into a
multicellular individual
a. what are the signals (both internal and external) that control
b. do different sets of signals promote differentiation into different cell
i. can we then control the signals to produce specific cell types for
research or therapeutical use
2. To learn how healthy cells replace damaged cells
D. Therapeutic Use of Stem Cells
1. bone marrow transplants to treat leukemia
a. chemotherapy and radiation treatments are used to kill
abnormal/cancerous leukocytes (white blood cells)
b. donor bone marrow is introduced into the patient’s bloodstream
c. stem cells migrate to patient’s bone marrow and begin to produce
healthy leukocytes
2. cell-based therapies to replace cells and tissues that are damaged/lost in
Alzheimer’s disease, spinal cord injury, stroke, burns, heart disease,
diabetes, osteoarthritis, Parkinson’s disease, multiple sclerosis and
rheumatoid arthritis
3. human epithelial stem cells used to replace damaged corneal tissue
4. “repair of a damaged left bronchus using a section of a donated trachea
that was first cleansed of all donor cells and then seeded with the
recipient's epithelial cells and cartilage-forming cells grown from stem
cells in her bone marrow. So far the patient is doing well and needs no
drugs to suppress her immune system.”
This site was updated Sept. 3, 2011 and accessed Oct. 26, 2011.
5. “Phase I clinical trials are underway to assess the safety of
injecting retinal cells derived from ES cells
o into the eyes of young people with an inherited form of juvenile
o into the eyes of adults with age-related macular degeneration.
injecting glial cells derived from ES cells into patients paralyzed by spinal cord
This site was updated Sept. 3, 2011 and accessed Oct. 26, 2011.
E. Immunological Issues
1. risk of rejection of the stem cells if from a donor that is genetically
different from the recipient (just as in all transplants)
a. 1 solution is to create embryonic stem cell by cloning the patient’s cells
Figure 12. Creating embryonic stem cells by cloning.
b. 1 solution is to use iPSC’s from the patient
i. but: iPSC’s have mutations and epigenetic markings not found in
embryonic stem cells and there are possible negative ramifications
because of this
F. Ethical Issues
1. harvesting stem cells from embryos means that a potential human life is
a. potential ways of getting around this include:
i. designing embryos that do not have the ability to implant in the
ii. getting oocytes to divide without fully maturing and then harvesting
stem cells from them
a. would only help females
iii. getting pluripotent stem cells from spermatogonia (stem cells that
produce sperm)
a. would only help males
iv. deriving pluripotent cells from cells present in amniotic fluid
XII. Here are some fascinating animations:
1. From Harvard: The Inner Life of the Cell
2. From John Kyrk:
XIII. Review
1. Here is a basic summary and an interactive labelling exercise:
2. Some multiple choice questions, short answer quesions and diagrams :
VIV. References1234566780]p[]\llllllllmkhgds
1. Sadava, Heller, Orians, Purves and Hilllis: Life: The Study of Biology (8th
2. A pretty complete history of cell theory:
3. More on the cell theory:
4. The Microbial World (only three chapters are available online):
5. About Robert Hooke:
7. About Anton Van Leeuwenhoek:
8. Bacterial cell:
9. Prokaryotic cell structure:
Plant cell:
Animal Cell:
Labelled rat liver cell (but more detail than is really needed):
Plant Cell “Tour”:
14. Ribosomes:
16. Gram staining information:
17. Prokaryotes:
18. Prokaryotic cytoskeleton:
20. Endospore:
22. Plant cell:
25. Cells and organelles in general:
23. Stem cells:
24. Stem cells:
25. More than you need to know but super interesting about stem cells:
Videos about the cell:
The Cell from BBC (3 part series):
Part One: The Hidden Kingdom (It seems as though as soon as you begin from this
link, the rest of the series just goes automatically.)
Part Two: The Chemistry of Life
Part Three: The Spark of LIfe
Another link to the same thing:
The Active Learner:
Random Sampling simulation: