Download 2 The Cell: An Overview

 2 The Cell: An Overview IF NOTHING ELSE, MY STUDENTS SHOULD LEARN…
1. All organisms are made up of cells.
2. All cells share some common structures/characteristics (unity), but there are some
differences between cells within and between different organisms (diversity).
LEARNING OBJECTIVES
Students should be able to:

Describe the cell theory. [Comprehension]

Identify how cell theory underlies topics in biology, including remaining chapters in
this textbook. [Synthesis]

Define: cell, nucleic acids, DNA, RNA. [Knowledge]

List the types of organisms that include unicellular forms. [Knowledge]

List the types of organisms that are typically multicellular. [Knowledge]

Describe the basic features of cell structure and function shared by all living cells.
[Knowledge, Comprehension]

Explain why grouping bacteria and archaeans into a single domain is no longer
considered to be accurate. [Comprehension]

Define: microscopy, illumination, magnification, resolution. [Knowledge]

Compare and contrast light microscopy and electron microscopy. [Comprehension]

Explain why most cells are very small. [Comprehension]

Define: plasma membrane, bilayer, hydrophobic, gene, cytosol, cytoplasm, organelle,
cytoskeleton. [Knowledge]
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THE CELL: AN OVERVIEW
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
Describe the basic structure and function of the plasma membrane. [Comprehension]

Describe what the structures and activities that typically occur in a cell’s cytoplasm.
[Comprehension]

Define: prokaryote, eukaryote, nucleus, nucleoid, messenger RNA (mRNA),
ribosomal RNA (rRNA), ribosome, ATP, flagellum, pilus. [Knowledge]

Describe what is meant by the term “organelle,” and the purpose and significance of
such structures in eukaryotic cells. [Comprehension]

Define: organelle, nucleus, nuclear envelope, lamins, nuclear pore, nucleoplasm,
chromosome, chromatin, nucleolus, rough endoplasmic reticulum, smooth
endoplasmic reticulum, Golgi complex, vesicle, endocytosis, exocytosis, lysosome,
mitochondrion, motor protein, cytoskeleton, cilium, eukaryotic flagellum,
chloroplast, central vacuole, tonoplast. [Knowledge]

Describe the basic structure of a ribosome. [Comprehension]

Describe the structure and functions of organelles discussed in this chapter
(including the nucleus; rough endoplasmic reticulum, smooth endoplasmic reticulum;
Golgi complex; lysosomes; mitochondria; chloroplasts) found in eukaryotic cells.
[Comprehension]

Describe how certain proteins are imported into the nucleus. [Comprehension]

Explain the relationship (and connections) between the plasma membrane,
endoplasmic reticulum, and Golgi complex in eukaryotic cells. [Comprehension]

List and describe the major eukaryotic cytoskeletal elements, where they are typically
found, and their roles in the cell. [Knowledge, Comprehension]

Explain why cytoskeletal elements associate with motor proteins for certain cellular
processes, providing examples of two different processes. [Knowledge, Comprehension]

Compare and contrast eukaryotic cilia and flagella [Comprehension, Analysis]

List different types of organisms that possess cell walls. [Knowledge]

Describe the extracellular structures (cell surface specializations) of animal and plant
cells (extracellular matrix and cell wall). [Comprehension]

List and describe the three types of cell junctions common in animal tissues.
[Knowledge, Comprehension]
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
Compare and contrast the organization of DNA in bacteria vs. archaeans vs.
eukaryotes. [Comprehension, Analysis]

Compare and contrast the bacterial flagellum and the eukaryotic flagellum.
[Comprehension, Analysis]

Compare and contrast cells of prokaryotes and those of eukaryotes, identifying
similarities and key differences between prokaryotic and eukaryotic cells. [Analysis,
Evaluation]
WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS?

Cell theory is one of the major themes underlying biology. As the cell is the
fundamental unit of life, what occurs in and around the cell is important in all
aspects of biology.

Similarities in different cell types allow the identification of fundamental cellular
processes despite gross morphological differences. For example, use of E. coli, yeast,
fruit flies, and Arabidopsis as model organisms allows observations into many
processes that cannot easily be studied in other organisms.

Understanding the structures and functions of cells (and cellular components) is vital
not only in understanding various aspects of biology but many aspects of health and
disease.
WHY SHOULD STUDENTS CARE?

Understanding cell theory is likely to be of value throughout the entire course, since
this is one of the major themes in biology. Subsequent topics rely heavily on students
understanding the basics of cellular structure and function.

Research in cell biology has clear implications in human health/disease as well as in
many other applied aspects of biological research.

Bacterial cells are different from archaeal cells (although both are prokaryotic), and
prokaryotes differ from eukaryotes. As students learn more about organisms,
systems, etc., they will need to be aware of the key differences as well as the
similarities of the different types of cells.

Understanding how bacteria differ from human cells has practical value when
considering treatment of infections (most antibiotics exhibit selective toxicity—they
kill/inhibit bacteria, while leaving the host unharmed).
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THE CELL: AN OVERVIEW
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WHAT ARE COMMON STUDENT
MISCONCEPTIONS/STUMBLING BLOCKS?
1. Many students will not have encountered the three domains of life (Bacteria, Archaea,
and Eukarya) and will be under the impression that bacteria and archaeans are
basically the same (or are very closely related). In discussion of prokaryotes and
eukaryotes, we recommend stressing that the Bacteria and Archaea domains reflect
the fact that they are evolutionarily distinct, and that although archaeans are
microscopic and lack a true nucleus, they share many characteristics with eukaryotes,
and are more closely related to eukaryotes than to bacteria.
2. Many students have the misconception that plants lack mitochondria (i.e., “Animal
cells have mitochondria, plants have chloroplasts”).
3. The different cell components (bacterial cell structures, eukaryotic organelles,
cytoskeletal elements, cell junctions, etc.) may prove overwhelming in terms of new
vocabulary, and students may focus on memorization rather than comprehending the
concepts (particularly structure and function). However, some understanding of the
structure of the cell is helpful in understanding the various processes that occur in
cells (and are discussed at greater length in Chapters 4–15).
4. Students often have trouble visualizing the dynamic, crowded living cell from text
descriptions and figures of cell structures. Similarly, as we often depict cells (through
figures) in isolation, it can be challenging to picture the arrangements of cells in
tissues.
5. Some terms, such as “flagellum” and “cell wall” are used to describe structures of
evolutionarily distant organisms (e.g., flagella of bacteria and animal cells; plant and
fungal cell walls). Students can get the impression that these structures are more
similar between the different groups than they actually are (which can conflict with
understanding of evolutionary relationships).
WHAT CAN I DO IN CLASS?
In addition to the theory of evolution by natural selection, cell theory is a major underlying
concept for biology. Highlight key similarities among different cells and organisms. This
chapter will help orient students when discussing later topics (e.g., cellular respiration in
mitochondria [Chapter 6], photosynthesis in chloroplasts [Chapter 7]).
At the beginning of class, students can be introduced to a news story about recent research
developments involving cell biology. The story could be medical (if teaching pre-medical
students, majors, non-majors), agricultural (majors, agriculture), or biotechnological (majors,
non-majors, engineers).
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If time is available, and you have obtained rights to show the video in class, you may want to
show Episode 1 “The Hidden Kingdom” from the BBC three-part series, The Cell. Host
Adam Rutherford highlights the key historical experiments that identified cells, and
development of cell theory, in an engaging and informative manner.
Ask students: How is the endomembrane system distinct from other membranes in a
eukaryotic cell?
The concept of an organelle is something instructors may want to bring up in class. While
this is typically presented matter-of-factly in introductory texts, there is considerable debate
as to what defines an organelle. The glossary of this textbook defines an organelle as: “The
nucleus and other specialized internal structures and compartments of eukaryotic cells.” This
is similar to definitions found in many other introductory biology textbooks, and provides a
simple way for students to distinguish eukaryotic cells from bacterial and archaeal cells.
However, if one considers an organelle to be a “structure that carries out a specialized
metabolic function inside a cell” (from Starr et al., Biology: The Unity & Diversity of Life,
12th ed., Nelson Publishing), or “any discrete, membrane-bound structure in the cytoplasm
of a cell (e.g., mitochondrion)” (Freeman, Biological Science, 3rd ed., Pearson Education), there
are many bacterial and archaeal examples that satisfy one or both definitions. In reality, the
scientific literature includes countless examples of “bacterial organelles” (e.g., Kerfeld et al.,
2005; Murat et al., 2010). It may be simplest for instructors to use the tautological definition:
an organelle is a eukaryotic organelle (specialized internal structures and compartments).
Nevertheless, we recommend letting students know that this is not a universally accepted
definition (it also gives students some insight into the conversations that occur in science—
i.e., experts do not always agree on everything, and science is a process, not a set of
established facts). Some biological researchers even consider specialized eukaryotic
structures that are not membrane-bound to be organelles (e.g., Andersen and Mann, 2006).
We have used the question “What is an organelle” in class discussions, showing different
definitions from major textbooks, having students identify common elements, and vote on
the definition we would use in class.
Students can be asked to create a table showing the components/organelles of cells,
considering bacteria vs. eukaryotes (and plants vs. animals). Ideally, they should highlight
common elements to all cells, and identify where different cell types vary. [Stumbling Blocks 2, 3]
There are some beautiful, informative animations available that model the cell. For example,
there is the David Bolinsky TEDtalk (see link below), and “The Inner Life of the Cell” series
from Harvard. [Stumbling Block 4]
In many processes, motor proteins must be associated with cytoskeletal elements.
Figure 2.20 shows the motor protein kinesin associating with microtubules to move a vesicle
or other cell structure. Additional examples that instructors can mention to students (and
that may come up in later topics) include movement of chromosomes (microtubules and
kinesins), muscle contraction (actin microfilaments and myosin) and movement of flagella/
cilia (microtubules and dynein). The Kinesin home page (http://www.cellbio.duke.edu
/kinesin/index.html) has some interesting information and visuals.
Copyright © 2013 by Nelson Education Ltd.
THE CELL: AN OVERVIEW
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In considering the bacterial flagellum and eukaryotic flagellum, you may wish to introduce
students to the idea of convergent evolution (homoplasy) as opposed to similarities that
arise from shared ancestry (homology) (see Chapter 18). In both cases, the “flagellum” is
long and thin (relative to the cell) and is used in liquid for propulsion (of the cell, or of liquid
moving across the cell). However, the structures themselves are constructed very differently.
The bacterial flagellum is a hollow tube composed of flagellin, with a rotary motor at the
base, embedded in the cell wall/membrane; the eukaryotic flagellum is a much larger
structure. The eukaryotic flagellum (and cilium) is an extension of the cell, within the plasma
membrane, primarily made up of microtubules and associated motor and structural proteins,
exhibiting sinuous movement by the action of dynein motor proteins and microtubule
sliding. The differences in structure also lead to different types of flagellar motion (i.e., rotary
vs. undulating). The term “prokaryotic flagellum” should be avoided, as the flagellum in
archaeans is actually more similar to the bacterial pilus than the bacterial flagellum. [Stumbling
Blocks 1, 5]
Like the term “flagellum,” “cell wall” refers to an extracellular structure present in many
different types of cells, and cells walls are not necessarily homologous. The cell walls of
bacteria, archaeans, plants, and fungi show considerable differences in composition/
structure. Ask students: Why do we use the same terms to describe structures that are
evolutionarily and biochemically distinct? [Stumbling Blocks 1, 5]
When discussing the extracellular matrix (ECM) of animal cells, you may want to discuss
Duchenne Muscular Dystrophy (DMD), a common form of muscular dystrophy
characterized by early deterioration of muscle tissues. Individuals with DMD do not produce
functional dystrophin, which normally links the cytoskeleton of the muscle cells and the
extracellular matrix. Without dystrophin, damage to the sarcolemma (plasma membrane of
muscle cells) occurs, leading to necrosis of muscle fibres. The gene for dystrophin has been
identified and is on the X chromosome (i.e., this is an example of an X-linked condition
which can be revisited when exploring Chapter 11 genetics topics). Ask students: As we
know what gene is involved in this condition, would it be possible to use this information to
treat/prevent DMD? If so, how?
Clicker questions:
1. What do cells of all living organisms have in common?
A.
B.
C.
D.
mitochondria, chloroplasts, plasma membrane
chromosome(s), plasma membrane, ribosome(s) *
chromosome(s), plasma membrane, cell wall
plasma membrane, mitochondria, chromosome(s)
This question can help students understand that there are structures present in all organisms,
despite the major differences between the different groups.
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2. Which of the following is present in both plant cells and animal cells?
A.
B.
C.
D.
chloroplasts
mitochondria *
Both chloroplasts and mitochondria are present in plant cells and animal cells.
None of the above are present in both plant cells and animal cells.
This question addresses Stumbling Block 2. Plants have chloroplasts, which are involved in
energy transformation reactions, but they still rely on mitochondria to carry out cellular
respiration reactions to break down energy sources and create ATP for physiological
activities.
3. Which of the following statements is true? Animal tissues are composed of cells
A. packed tightly together, with plasma membranes of adjacent cells in direct
contact with one another.
B. with cell walls linked by channels to allow passage of certain molecules (e.g.,
water, cell signals).
C. and intercellular space containing a complex matrix that may be liquid, solid,
semi-solid, or elastic. *
D. and cytoskeletons secreted by specialized cells elsewhere in the body transported
to appropriate types of tissue.
Prior to discussing extracellular surface specializations (ECM of animal cells, cell walls of
plant cells), this question prompts students to think about the nature of tissues composed of
animal cells. (Option B describes plant cell walls, which have plasmodesmata connections.)
[Stumbling Block 4]
4. Comparing the bacterial flagellum to the eukaryotic flagellum, which of the following
statements is true?
A. Bacterial flagella are similar in length and diameter to eukaryotic flagella.
B. A rotational motor (like a propeller) is present at the base of both types of
flagella.
C. Bacterial flagella are bound by the plasma membrane and contain microtubules
and motor proteins; eukaryotic flagella are NOT within a plasma membrane and
are hollow protein tubes. *
D. Bacterial flagella are smaller than eukaryotic flagella, but are composed of the
same types of proteins, are bound by the plasma membrane, and arose from a
common ancestor.
E. Both types of flagella are used to move the cell.
This question addresses Stumbling Block 5, and highlights structural features of the bacterial
and eukaryotic flagella.
Copyright © 2013 by Nelson Education Ltd.
THE CELL: AN OVERVIEW
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WHAT OTHER RESOURCES ARE AVAILABLE?

BBC The Cell. Ep. 1 “The Hidden Kingdom”:
http://www.bbc.co.uk/programmes/b00m425d

TEDtalk: David Bolinsky animates a cell:
http://www.ted.com/talks/david_bolinsky_animates_a_cell.html

The Inner Life of the Cell series (Harvard University):
http://multimedia.mcb.harvard.edu/innerlifeseries.html

Kerfeld, C.A., Sawaya, M.R., Tanaka, S., Nguyen, C.V., Phillips, M., Beeby, M., and
Yeates, T.O. 2005. Protein structures forming the shell of primitive bacterial
organelles. Science 309(5736): 936–938.

Murat, D., Byrne, M., and Komeili, A. 2010. Cell biology of prokaryotic organelles.
Cold Spring Harbor Perspectives in Biology 2(10): a000422.

Andersen, J.S., and Mann, M. 2006. Organellar proteomics: turning inventories into
insights. EMBO Reports 7(9): 874–879.

Kinesin home page (created by Liz Greene and Steve Henikoff):
http://www.cellbio.duke.edu/kinesin/index.html

Le Rumeur, E., Winder, S.J., and Hubert, J.F. 2010. Dystrophin: more than just the
sum of its parts. Biochimica et Biophysica Acta 1804(9): 1713–1722.
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