BIO353: Exam 2 Short Answers
Module 11: Actin Filaments
1. Draw an actin monomer and an actin filament and label all the parts, molecular weights,
etc..
2. Explain the geography of actin filaments. Explain the geography of stress cable, filapodia
and lamelliapodia in a cell, and locomoting in a culture plate.
a. Actin filaments are located under the plasma membrane on the inside of the cell. Stress
cables as well as filopodia and lamellipodia are located near the plasma membrane.
3. Focusing on actin monomers and actin filaments: explain what occurs when a cell reverses
its direction by 180 degrees.
a. When a cell reverses its direction by 180 degrees, there is a reverse displacement for the
actin and myosin filament. There is an increase in the movement and contraction of the
filaments in direction towards each other. Due to the complete 180 degree reversal and
the presence of the extended N-terminus in the myosin, it will tend to block the complete
180 degree swing of other myosin and hence it might lead to interruption in the function
of the muscles. Due to the reversal, the actin monomer tends to fall in the same direction
and tends to make the muscle more polar.
4. Explain how the binding of ATP affects cytoskeletal monomers. Explain how the function of
cytoskeletal networks can change depending on reversible binding of cytoskeleton
associated proteins
a. Hydrolysis of ATP to ADP helps identify the assembly vs disassembly end with an ATP
“cap” on the assembly end and an ADP “cap” on the disassembly end. With ATP present,
the monomer changes shape and promotes self-assembly into the actin filament. When
ATP is hydrolyzed to ADP, it changes the conformation of the monomer making it less
, suited to fit into an actin filament. Position of ATP gives the monomer a polarity that
steps up the polarity of the actin filament.
5. Describe how myosin II can be made into a tool to analyze the different polarities of actin
filaments in the cell.
a. Myosin II can be made into a tool by scientists using biotechnology to determine the
orientation of an actin filament in stress cables by the winding of the heavy and light
chains.
6. Draw the structure of a myosin II molecule when its light chains are not phosphorylated.
7. Explain the geography of actin filaments as it relates to a living cell.
8. Explain how myosin II can be made into a tool by scientists using biotechnology. And
explain how this can be used to determine the orientation of an actin filament in:
a. stress cables - anti-parallel bundles of actin filaments, hence the myosin barbs will point
in opposite directions along the two filaments.
b. Filopodia - the barbs will all be directed at the tip as that is the positive end of the actin
(polymerizing/growing end)
9. Explain what cell permeabilization is.
a. Making holes in the cell to let aqueous solutions of cleaved myosin heads in. Done with a
non-ionic detergent and isotonic buffer.
Module 13: Microtubules
1. Describe the physical and chemical properties of the monomer and polymer of
microtubules.
a. The microtubule singlet is a “tube” and has an outer diameter of 25 nm and an inner
diameter of 15 nm, and can be various lengths in the cell. The functional monomer of
microtubules is composed of two proteins that are slightly different in amino acid
sequence, referred to as a heterodimer. The heterodimer is composed of two different
proteins: alpha-tubulin, beta-tubulin.
b. Alpha- and beta-tubulin are each composed of 450 amino acids and have a molecular
weight of 55 kD each; the monomer’s molecular weight is 110 kD.
, 2. Explain how microtubules assemble and disassemble.
a. In vitro, there is the rate-limiting step called nucleation that must occur first. This is
followed by elongation of the microtubule; this is not rate-limiting if the monomer
concentration is above the threshold level. In vivo, the cell circumvents the rate-limiting
step of nucleation by having associated proteins form a pre-assembled nucleation site
near the nucleus. This site is termed the centrosome, and is sometimes also referred to as
the microtubule organizing center.
b. Several microtubule-associated proteins prevent treadmilling from happening in vivo. The
most significant are the proteins associated with the centrosome that cap the disassembly
end of the microtubules; these prevent addition or subtraction of tubulin monomers from
the disassembly end.
c. the growing ends of a microtubule will have monomers with GTP resembling a GTP
“cap.” Closer to the centrosome, the microtubule will have monomers with GDP
resembling a GDP “cap.” The GTP cap stabilizes the microtubule and can permit further
growth; however, as the GTP cap shortens, the microtubule will be destroyed (i.e.,
catastrophic disassembly).
d. Catastrophic disassembly begins from the plus end.
3. Explain what molecules in a living cell are necessary to nucleate microtubules.
a. In vivo the nucleation step is avoided by having associated proteins form a pre-nucleation
site in the Centrosome. The specific molecules needed to form the pre-nucleation sites in
the nuclear envelope are gamma tubulins which are considered to be enriched at the
nucleation site for microtubules in living cells.
4. Explain the geography of microtubules.
a. Position of pre-assembled nucleation sites creates a location where microtubule singlets
can elongate (centrosome, MTOC).
b. Centrosome is positioned on one side of the nucleus, and the nucleus is near the center.
5. Explain how the geography of the cytoskeleton integrates with the transport of membrane
vesicles that are part of the endomembrane system.
a. The microtubules and actin filaments work with the endomembrane system. There are
three systems involved in the cytoskeletal system. Those systems include the actin
filament system, microtubule system, as well as the intermediate filament system.
Although there are only two out of the three systems that integrate with the transport of
membrane systems. Microtubules are present in the cell interior filling the area around
the nucleus and near the center of the cells. The centrosomal area can be detected as there
is an increased intensity in actin filaments. The actin filaments occupy the periphery of
the cell. There is little overlap between these areas but they all work together with the
transport of membrane vesicles that are part of the endomembrane system.
6. Explain how the structure of the microtubule singlet is altered when associated with a
cilium or flagellum, or in an animal cell, the centrosome. Can you draw the cross section of
the 9+2 configuration of microtubules?
a. -Microtubule singlet is composed of 13 protofilaments - considered a building block for
cilia, flagella, and centrioles.
b. -When a cilium/flagellum is viewed
in cross section, there are two
Module 11: Actin Filaments
1. Draw an actin monomer and an actin filament and label all the parts, molecular weights,
etc..
2. Explain the geography of actin filaments. Explain the geography of stress cable, filapodia
and lamelliapodia in a cell, and locomoting in a culture plate.
a. Actin filaments are located under the plasma membrane on the inside of the cell. Stress
cables as well as filopodia and lamellipodia are located near the plasma membrane.
3. Focusing on actin monomers and actin filaments: explain what occurs when a cell reverses
its direction by 180 degrees.
a. When a cell reverses its direction by 180 degrees, there is a reverse displacement for the
actin and myosin filament. There is an increase in the movement and contraction of the
filaments in direction towards each other. Due to the complete 180 degree reversal and
the presence of the extended N-terminus in the myosin, it will tend to block the complete
180 degree swing of other myosin and hence it might lead to interruption in the function
of the muscles. Due to the reversal, the actin monomer tends to fall in the same direction
and tends to make the muscle more polar.
4. Explain how the binding of ATP affects cytoskeletal monomers. Explain how the function of
cytoskeletal networks can change depending on reversible binding of cytoskeleton
associated proteins
a. Hydrolysis of ATP to ADP helps identify the assembly vs disassembly end with an ATP
“cap” on the assembly end and an ADP “cap” on the disassembly end. With ATP present,
the monomer changes shape and promotes self-assembly into the actin filament. When
ATP is hydrolyzed to ADP, it changes the conformation of the monomer making it less
, suited to fit into an actin filament. Position of ATP gives the monomer a polarity that
steps up the polarity of the actin filament.
5. Describe how myosin II can be made into a tool to analyze the different polarities of actin
filaments in the cell.
a. Myosin II can be made into a tool by scientists using biotechnology to determine the
orientation of an actin filament in stress cables by the winding of the heavy and light
chains.
6. Draw the structure of a myosin II molecule when its light chains are not phosphorylated.
7. Explain the geography of actin filaments as it relates to a living cell.
8. Explain how myosin II can be made into a tool by scientists using biotechnology. And
explain how this can be used to determine the orientation of an actin filament in:
a. stress cables - anti-parallel bundles of actin filaments, hence the myosin barbs will point
in opposite directions along the two filaments.
b. Filopodia - the barbs will all be directed at the tip as that is the positive end of the actin
(polymerizing/growing end)
9. Explain what cell permeabilization is.
a. Making holes in the cell to let aqueous solutions of cleaved myosin heads in. Done with a
non-ionic detergent and isotonic buffer.
Module 13: Microtubules
1. Describe the physical and chemical properties of the monomer and polymer of
microtubules.
a. The microtubule singlet is a “tube” and has an outer diameter of 25 nm and an inner
diameter of 15 nm, and can be various lengths in the cell. The functional monomer of
microtubules is composed of two proteins that are slightly different in amino acid
sequence, referred to as a heterodimer. The heterodimer is composed of two different
proteins: alpha-tubulin, beta-tubulin.
b. Alpha- and beta-tubulin are each composed of 450 amino acids and have a molecular
weight of 55 kD each; the monomer’s molecular weight is 110 kD.
, 2. Explain how microtubules assemble and disassemble.
a. In vitro, there is the rate-limiting step called nucleation that must occur first. This is
followed by elongation of the microtubule; this is not rate-limiting if the monomer
concentration is above the threshold level. In vivo, the cell circumvents the rate-limiting
step of nucleation by having associated proteins form a pre-assembled nucleation site
near the nucleus. This site is termed the centrosome, and is sometimes also referred to as
the microtubule organizing center.
b. Several microtubule-associated proteins prevent treadmilling from happening in vivo. The
most significant are the proteins associated with the centrosome that cap the disassembly
end of the microtubules; these prevent addition or subtraction of tubulin monomers from
the disassembly end.
c. the growing ends of a microtubule will have monomers with GTP resembling a GTP
“cap.” Closer to the centrosome, the microtubule will have monomers with GDP
resembling a GDP “cap.” The GTP cap stabilizes the microtubule and can permit further
growth; however, as the GTP cap shortens, the microtubule will be destroyed (i.e.,
catastrophic disassembly).
d. Catastrophic disassembly begins from the plus end.
3. Explain what molecules in a living cell are necessary to nucleate microtubules.
a. In vivo the nucleation step is avoided by having associated proteins form a pre-nucleation
site in the Centrosome. The specific molecules needed to form the pre-nucleation sites in
the nuclear envelope are gamma tubulins which are considered to be enriched at the
nucleation site for microtubules in living cells.
4. Explain the geography of microtubules.
a. Position of pre-assembled nucleation sites creates a location where microtubule singlets
can elongate (centrosome, MTOC).
b. Centrosome is positioned on one side of the nucleus, and the nucleus is near the center.
5. Explain how the geography of the cytoskeleton integrates with the transport of membrane
vesicles that are part of the endomembrane system.
a. The microtubules and actin filaments work with the endomembrane system. There are
three systems involved in the cytoskeletal system. Those systems include the actin
filament system, microtubule system, as well as the intermediate filament system.
Although there are only two out of the three systems that integrate with the transport of
membrane systems. Microtubules are present in the cell interior filling the area around
the nucleus and near the center of the cells. The centrosomal area can be detected as there
is an increased intensity in actin filaments. The actin filaments occupy the periphery of
the cell. There is little overlap between these areas but they all work together with the
transport of membrane vesicles that are part of the endomembrane system.
6. Explain how the structure of the microtubule singlet is altered when associated with a
cilium or flagellum, or in an animal cell, the centrosome. Can you draw the cross section of
the 9+2 configuration of microtubules?
a. -Microtubule singlet is composed of 13 protofilaments - considered a building block for
cilia, flagella, and centrioles.
b. -When a cilium/flagellum is viewed
in cross section, there are two
