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									                              Teacher Notes for Cells as Molecular Factories
                        Dr. Ingrid Waldron, Department of Biology, University of Pennsylvania, 20111

Cells can be thought of as molecular factories both because cells produce molecules and because
cells are made up of molecules. This discussion/worksheet activity develops these concepts for
eukaryotic cells. The questions also incorporate reviews of the functions of cell organelles and
biological molecules.

To maximize student participation and learning, you may want to have your students complete
the worksheet individually or in pairs and then have a class discussion of the questions.

The primary teaching points are:
    A cell has many parts that work together to accomplish the functions of life, such as
       protein secretion and recycling of damaged molecules and organelles.
    A cell consists of many many molecules that cooperate to accomplish needed functions.
       In eukaryotic cells, many of these molecules are organized in tiny organelles that perform
       specialized functions inside the cell.
    Inside a living cell there is constant activity.

Before beginning this activity students should have a basic understanding of
    biological molecules, especially proteins, mRNA and DNA (see "Understanding the
       Functions of Proteins and DNA", available at
       http://serendip.brynmawr.edu/exchange/bioactivities/proteins)
    eukaryotic cell organelles and their functions.



                                                                                                           (continued on the next page)




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  These teacher notes, the student handout for this activity, and multiple additional activities for teaching biology are available at
http://serendip.brynmawr.edu/exchange/bioactivities. Hands-on, minds-on activities for teaching biology are available at
http://serendip.brynmawr.edu/sci_edu/waldron/.
Suggestions for Discussion of Questions and Biology Background

1. This question provides a review of organelle functions and also emphasizes the important
point that the various organelles cooperate together to accomplish a function such as protein
secretion.
Factory              Which part of the cell accomplishes this function?
Function
Management           Nucleus
-- sends out
instructions
(DNA -- > RNA)
Workbench            Ribosome
-- makes
products
(proteins)
Processing and       Rough endoplasmic reticulum (rough ER) + Golgi apparatus (which consists
distribution         of multiple Golgi bodies)
-- prepares          (Many secreted proteins have carbohydrates attached; the carbohydrate is
products to leave often bonded to the protein in the rough ER and processed by removal,
factory/cell         substitution or modification of a sugar monomer in the Golgi apparatus.)
                     (A helpful figure that illustrates how the nucleus, ribosomes, rough ER and
                     Golgi work together is shown on the next page.)
Structure and        Cytoskeleton + Transport vesicles
Transport
-- moves proteins
around in
factory/cell
Security fence       Plasma or cell membrane
with gates           (Biologists generally prefer the term plasma membrane and use the term
-- controls what     cellular membranes to include the plasma membrane and the membranes
comes into and       inside a cell.)
leaves the
factory/cell
Powerhouse           Mitochondria
-- provides          (Note that mitochondria do not make energy; mitochondria transfer energy
energy in a form from organic molecules such as glucose to ATP; see "How Biological
the factory/cell     Organisms Use Energy", available at
can use (ATP)        http://serendip.brynmawr.edu/exchange/bioactivities/energy)
Cleanup crew         Lysosomes
-- disposes of old (Digestive enzymes break down damaged organelles and macromolecules
and worn out         into smaller molecules (e.g. amino acids, nucleotides or monosaccharides)
products and         that leave the lysosome and are reused by the cell.)
equipment;
prepares them
for recycling




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                        (from Krogh, Biology - A Guide to the Natural World, Fifth Edition)


2. This question continues to develop the theme that organelles work together to accomplish
needed cellular functions. This question also introduces the important concept that cells are
constantly replacing molecules and organelles, as illustrated by the following examples:
    studies in yeast cells show that many protein molecules only last a day or two
    a typical eukaryotic cell produces hundreds of new protein molecules each second
    studies of human lymphocytes show that messenger RNA molecules only last minutes to
       hours, transfer RNA molecules last hours to days, and ribosomal RNA molecules are
       replaced within about two weeks on average
    a typical human cell uses and replaces an average of 10 million ATP molecules per
       second
    each cell in our body replaces roughly 1000 ribosomes per minute
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      mitochondria in human cells are replaced on average every 10 days

These examples illustrate the general point that, although biological organisms appear stable,
their components are in constant flux. Our bodies are constantly breaking down and replacing
molecules, organelles and cells. In addition, ions, molecules, organelles and many types of cells
are in constant motion (as illustrated in question 3).

Removal and digestion of damaged proteins is accomplished in part by lysosomes and in part by
large protein complexes called proteasomes. Lysosomes also digest proteins under starvation
conditions to provide amino acids that can undergo cellular respiration to produce needed ATP.
Lysosomes digest and recycle the components of multiple types of molecules and organelles.
Defects in lysosome function can result in a variety of diseases (e.g. Tay-Sachs disease).

Questions 4 and 5 reinforce student understanding that all parts of the cell consists of molecules
and many of the molecules in a eukaryotic cell are organized in organelles. Protein locations and
functions include:
    protein enzymes are found in most parts of the cell (e.g. cytosol, endoplasmic reticulum,
       nucleus, plasma membrane)
    proteins in the nucleus contribute to chromosome structure and regulation of transcription
    proteins in the cytoskeleton contribute to structure and transport, e.g. of vesicles
    proteins in the plasma membrane contribute to transport of substances across the plasma
       membrane and recognition of hormonal and other signals

Questions 3-5 do not mention several important types of molecules found in cells, e.g.
phospholipids which are discussed in the following optional additional questions.

Optional Additional Question

To illustrate how molecules work together to accomplish important biological functions you may
want to discuss the selectively permeable (semipermeable) plasma membrane (cell membrane).
For this purpose, you could use the optional question shown below or the more detailed and
structured discussion/worksheet activity presented on the next two pages.

Each cell is surrounded by a selectively permeable membrane that regulates what gets into and
out of the cell. Explain how the arrangement of phospholipid and protein molecules shown in
the diagram results in the selective permeability of the membrane that surrounds the cell.




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The plasma membrane that surrounds a cell regulates what gets into and out of the cell and maintains the
internal environment needed for the cell to function. To understand the structure and function of the
plasma membrane, we need to begin by reviewing the difference between polar and nonpolar
molecules.

★ What does it mean to say that a molecule is a polar molecule?




★ Explain why H2O is a polar molecule.




★ How do you know that O2 is a nonpolar molecule?




A cell membrane (also called a plasma membrane) consists primarily of phospholipid and protein
molecules. Each phospholipid molecule has both a polar part and a nonpolar part. The polar head of a
phospholipid molecule is attracted to polar water molecules, and the nonpolar tails are not attracted to
water. There is lots of water on both sides of the cell membrane. (The extracellular fluid outside the cell
and the cytosol inside the cell both contain lots of water.) Since only the polar heads of the phospholipid
molecules are attracted to water, the polar heads of the phospholipid molecules face outward toward the
water on both sides of the cell membrane and the phospholipid molecules in the cell membrane are
organized in a phospholipid bilayer, as shown in the first figure.




                        (Figure from Krogh, Biology -- a Guide to the Natural World, Fourth Edition)

★ The first figure shows O2 diffusing into a cell. Label the outside of the cell, the phospholipid bilayer of
the cell membrane, and the cytosol inside the cell. Circle an individual phospholipid molecule and label
the polar head with a P and the nonpolar tails with an N.

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Nonpolar molecules like O2 can diffuse across the phospholipid bilayer of the cell membrane,
because nonpolar molecules can dissolve in the nonpolar tails (which make up the bulk of the
phospholipid bilayer).

In contrast, polar molecules like glucose or ions can not dissolve in the nonpolar tails of the phospholipid
bilayer, so polar molecules and ions can not diffuse across the phospholipid bilayer of the cell
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membrane.

Each type of polar molecule or ion requires the help of a different protein to cross the cell
membrane (second and third figures on the previous page). Thus, the proteins in the cell membrane
regulate which ions and polar molecules can get into or out of the cell. The combination of these
membrane proteins with the phospholipid bilayer results in the selective permeability of the cell
membrane.

★ For each type of molecule listed in the table, indicate whether this molecule can diffuse through the
phospholipid bilayer or requires a transport protein to cross the cell membrane.

      Type of molecule                Can diffuse through           Requires a transport protein
                                    the phospholipid bilayer        to cross the cell membrane
Amino acids (polar molecules)
CO2 (a nonpolar molecule)
Na+


★ The third figure on the previous page shows a process called active transport. Active transport uses
energy provided by ATP to pump an ion or molecule across the membrane. Why is active transport
needed for this substance to cross the membrane in the direction shown? Which way would the
substance move if it were moving by diffusion?




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  One exception is water, a very small polar molecule, which can diffuse through the phospholipid bilayer of the cell
membrane; however, rapid diffusion of water across the cell membrane requires a specialized protein, aquaporin. It
should also be noted that large nonpolar molecules require specialized processes to cross the plasma membrane (e.g.
receptor-mediated endocytosis is required for cholesterol uptake).
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