Problem Set 3
BILD1 SP16
1) Parts of the Cell
Answer the following questions pertaining to the parts of the cell listed below.
Nucleus, Mitochondria, Golgi, Endoplasmic Reticulum, Lysosome, Plasma Membrane, Chloroplast,
Ribosome, Vacuole, Peroxisome
(a)
(b)
(c)
(d)
(e)
(f)
(g)
(h)
(i)
(j)
(k)
(l)
Is it in both prokaryotes and eukaryotes? If not, which cell type contains it?
Is it enclosed by a lipid bi-layer? If so how many?
Does it contain DNA?
Is it involved in protein synthesis?
Does glycosylation occur here?
Does lipid biosynthesis occur here
Does it have a role in phagocytosis?
Is it required for detoxification?
Is it a water storage organelle?
Is it required to process energy?
Is it composed of or does it contain membrane stacks?
Is it involved in protein export? If so, how?
Nucleus
a) Eukaryotes have a nucleus while prokaryotes do not.
b) Yes, the nucleus is enclosed by a double membrane called the nuclear envelope.
c) Yes, the nucleus contains most of the cell’s (eukaryotes) DNA.
d) The nucleus is not directly involved in protein synthesis. However all genes are here and
genes encode proteins.
e-k) NO
Mitochondria
a)Eukaryotes have mitochondria while prokaryotes do not.
b) Yes, the mitochondria are enclosed by a double membrane, (Remember the inner and
outer membrane discussed in relation to the electron transport chain?).
c) Yes, mitochondria have their own circular DNA, this one of the components of the
Endosymbiosis Theory.
d) Yes, the mitochondria have their own ribosomes that synthesize some of their proteins.
e-i) NO
j) Yes, the mitochondria is often called the power plant of the cell, this is where most of
the cells energy is processed. Remember cellular respiration? Most of the ATP was made in
the mitochondria.
k-l NO
Golgi
a) Eukaryotes have the golgi while prokaryotes do not.
b) Yes, the golgi is enclosed by a single membrane.
c) NO
d) The golgi is not directly involved in protein synthesis, but it does play a role in the
modification of proteins and transport.
e) Yes, sugars are added to proteins here.
f-j) NO
k) Yes, the golgi appears as stacked disks; check out the text page 66 to see this.
l) Yes. The golgi receives proteins from the ER on its cis side then modifies and figures out
the final destination of the proteins and sends them on their way out through the trans
side.
Endoplasmic Reticulum
a) Eukaryotes have ER while prokaryotes do not.
b) Yes, the ER is enclosed by a single membrane.
c) No
d) Yes, The ribosomes on ROUGH ER are the sites for protein synthesis. These proteins
include all secreted proteins, all membrane proteins and proteins targeted to organelles.
RER is also is the site of all protein folding.
e) Yes, sugars are added to proteins here.
f) Yes, lipid biosynthesis occurs primarily in the SMOOTH ER (not coated by ribosomes),
but also in the RER.
g) No
h) Yes, the SMOOTH ER is the site of detoxification for drugs.
i) No
j) No
k) Yes, the ER appears to be composed of stacks of tubes, this can be seen on page 65 of
the text.
l) Yes, after synthesis and some modification of protein the ER sends them on their way to
the Golgi where more modification is done, and where the proteins are eventually sent to
their final destination.
Lysosome
a) Eukaryotes have lysosomes while prokaryotes do not.
b) Lysosomes are enclosed by a single membrane.
c-f No
g) Yes Lysosomes are what digest and break down the food and foreign objects brought into
the cell via phagocytosis.
h) Yes, Lysosomes help get rid of undigested materials.
i-l) No
Plasma Membrane
a) Yes, both eukaryotes and prokaryotes have a plasma membrane.
b) The plasma membrane is made of a single phospholipid bilayer in EUKARYOTES. In
prokaryotes, there can be ONE or TWO bilayers.
c-f) No
g) Yes, the plasma membrane plays a major role is phagocytosis, (bringing stuff into the
cell). The plasma membrane deepens and forms a pocket around things outside of the cell,
eventually enclosing these objects. This forms a vesicle which will now be on the interior of
the cell.
h,i) No
j) In prokaryotes, only, the plasma membrane can be invaginated to increase surface area
for respiration or photosynthesis to occur.
k) No
l) Yes, proteins destined for outside of the cell are sent from the golgi in a vesicle to the
plasma membrane, where the vesicle will fuse and eventually become part of the plasma
membrane, allowing the contents of the vesicle to now be outside of the cell.
Chloroplast
a) Prokaryotes do not have chloroplasts, only eukaryotic plant cells do.
b) Yes, the chloroplast is enclosed by a double membrane.
c) Yes, the chloroplast has its own DNA.
d) Yes, the chloroplast has its own ribosomes that are used to synthesize some of its
proteins.
e-i) No
j) Yes, the chloroplast is the site of photosynthesis, where light energy is turned into ATP.
k) Yes the chloroplast contains the thylakoids, which are flat stacked compartments.
l) No
Ribosome
a) Both eukaryotes and prokaryotes have ribosomes.
b) No, the ribosome is NOT membrane enclosed; this is why some texts tend to say
ribosomes are not considered organelles, which are characterized by having a membrane.
c)No
d) Yes!! The ribosome is the protein synthesis machinery! All protein synthesis comes from
ribosomes.
e-k) No
l) Yes, ribosomes are critical for protein export. The newly synthesized protein is docked
exiting the Ribosome is docked on the ER and then synthesized there before being
exported. (see notes Lecture 8)
Vacuole
a) Prokaryotes do not have vacuoles, only eukaryotic cells do, mainly plant cells.
b) Yes, the vacuole is enclosed by a single membrane.
c-h) No
i) Yes! The vacuole is a water storage organelle used to store not only water, but other
soluble components, including waste products.
j-l) No
Peroxisome
a) Peroxisomes are only found in eukaryotic cells.
b) Yes, peroxisomes are enclosed by a single membrane.
c-e) no.
f) Yes, some lipid synthesis occurs here via oxidation enzymes.
g) No
h) Yes, the peroxisome is where toxic byproducts are broken down and is important for
detoxification.
i-l) No
2) Endosymbiosis
a) Using the ideas proposed in the endosymbiosis model, explain this model for the origin of
chloroplasts. What features of chloroplasts are similar to prokaryotes in support of this
theory?
1. Chloroplast are bacteria sized, double membrane organelles that do similar processes that
carbon fixing bacteria do. 2. Chloroplast organelles have their own circular prokaryotic-like
genomes. 3. And lastly, their ribosomes and proteins resemble those of the prokaryotic
world.
3) The endomembrane system
(a) How many times do fission and fusion
events occur to yield a transmembrane
protein inserted in the plasma membrane?
To answer this question, design a
transmembrane protein that is
glycosylated (use a ) so that you can easily
tell the difference between the protein
parts that should be on the outside of the
cell vs. the inside of the cell. Draw your
way through the membrane trafficking
pathways, using the schematic parts shown
below and lecture notes about the
endomembrane system to help you.
Remember to show where/when fission or
fusion is taking place. Also show cis and
trans face of Golgi throughout diagram.
RER Lumen
Transmembrane protein leaves RER
by vesicle FISSION.
FISSION
FUSION
Transmembrane protein
transported in Vesicle to Golgi.
Enters the CIS face of the Golgi
And fuses with Cis-Golgi
Transmembrane protein now
inside Golgi network – note
glycosyl appendages inside
lumen of Golgi
FISSION
Starting at the RER, we have 2 fission events
and 2 fusion events.
FUSION
Transmembrane protein
leaves the Trans-Golgi face in
vesicle – FISSION –
transported to plasma
membrane
Vesicle fuses with plasma
membrane – depositing the
transmembrane protein.
Note Glycosyl appendages on
the outside of the cell.
Inside Cell
(b) How many times do fission and fusion
Outside Cell
Plasma
membrane
events occur for a secreted protein?
What are the differences between this pathway and the one you did in part (a)?
For a secreted protein, starting at the RER, we have 2 fission events, and 2 fusion events.
The difference between the two pathways is that a secretory protein would be fully
contained within the lumen of the ER while the transmembrane protein had portions
emerging the ER membrane. The protein trafficking pathways would be similar, except with
a secretory protein after it fuses with the plasma membrane is all free outside of the cell,
instead of physically becoming part of the plasma membrane, as a transmembrane protein
would do.
Apical
(c) Considering an epithelial cell in the stomach. It has
basal, lateral, and apical membrane regions. We
discussed tight junctions in class - how they separate
membrane regions by creating a barrier to movement.
As a transmembrane protein is trafficked from the ER
to the plasma membrane -describe the way in which
transmembrane proteins can be targeted to either the
basal or apical regions of the cell.
Tight
Junction
Lateral
Basal
As we discussed in class, the transmembrane protein would have to be transported in a
vesicle from the trans-golgi to the correct plasma membrane surface because movement
passed the tight junction is blocked. A way the cell accomplishes this is to tag proteins –
glycosylation – as zip codes for various destinations – in this case, the basal or apical PM
surfaces.
Besides modifications of the transmembrane protein – what other aspects of proper targeting
do we have to account for? (Thinking question!!)
You would need some sort of receptor protein and/or a motor protein that would transport
the vesicle containing the transmembrane protein (with specific plasma membrane surface
destination). Another way is to have a receptor protein at the membrane destination that
would recognize specific vesicles carrying specific transmembrane protein cargo.
4) Cytoskeleton and motor proteins
a) Describe the three major types of cytoskeleton elements we discussed in class.
b) How are cells anchored to the extracellular matrix (ECM)
c) Why are microtubules and microfilaments both needed to anchor cells to the ECM?
d) Remember the cartoon of a cell motility using extension (of lamellipodia) and retraction – why
would microtubules and microfilaments both be needed? Think about membrane dynamics.
e) How do motor proteins use ATP to produce movement (displacement)?
a) Microtubules are made of tubulin polymers – which are used as compression resisting
support for cells (Cell shape). They are also the “railway” system for intracellular movement
in the cell – chromosomes and vesicle movement. Motor proteins involved.
microfilament are made of actin polymers – which are use for tension-bearing support for
the cell (Cell shape). They also provide cell motility – through changes in cell shape.
Important for muscle contraction and cell division. Motor proteins involved.
intermediate filaments made of keratin polymers - which are use for tension-bearing
support for the cell (Cell shape). Important for organelle anchorage. No motor proteins
involved.
b) cells are anchored to the ECM through a network of secreted ECM proteins that are
linked to microfilaments by integrins (a transmembrane protein).
c) Microfilaments are needed for anchorage to the ECM – as stated in part B. Microtubules
are also needed to deliver the integrin (transmembrane protein) to the plasma membrane.
d) Cell motility is produced by extension of lamellipodia (produced by microfilaments - actin
polymerization) at the front of a cell and retraction at the back (microfilament
depolymerization. Microtubules are needed to deliver new membrane at the extension side
as well as to deliver transmembrane proteins that help sense the direction the cells wants
to travel.
e) Motor proteins bind ATP and produce movement through the hydrolysis of ATP. They
can take “another step” by releasing ADP and Pi, then bind another ATP molecule to begin
the “ratcheting cycle” again.
5) Transport through protein channels
(a) Why do cells need transport proteins? Why can’t components just diffuse through the membrane
bi-layer?
(b) Why do some forms of transport require ATP to drive transport whereas others do not?
(c) How does co-transport work? What is the energy source?
a) As we all know, the cell membrane is composed of a phospholipid bilayer which has a
hydrophilic exterior and a hydrophobic interior, not allowing the diffusion of polar items
through the membrane. This is why we have transport proteins, which are lined with polar
things allowing the polar items that couldn’t get through the plasma membrane, to cross
through the protein to the other side of the cell. This is called facilitated diffusion.
b) Sometimes the items that want to cross the membranes are going against their
concentration gradient; instead of diffusing from a region of high concentration to a region
of low concentration, they want to go from low concentration to high concentration. Since
this is going against the gradient, this type of transport, called active transport, requires
energy. On the other hand, when something is going down its gradient, it would not require
energy.
c) Cotransport, also called secondary active transport is the transport of something against
its gradient, but instead of directly using ATP like primary active transport, it uses the
gradient made by primary active transport system to get energy. For example, say we want
to take sucrose into the cell against its concentration gradient; we need to use a
cotransport system. First, ATP is used by a proton pump to pump H+ outside the cell –
against its concentration gradient. Now some H+ outside of the cell can then get together
with some sucrose, diffuse into the cell down the H+ conc. gradient through a cotransporter, based solely on the H+ gradient made by the pump. In doing this the H+
releases energy, and this energy helps the sugar travel against its gradient into the cell.
6) Diffusion
a) Diagram the rate diffusion versus concentration of substrate for: CO2, glucose, glucose with a
carrier protein.
b) What is the difference between active transport and facilitated diffusion?
a)
CO2
Glucose with
a carrier protein
Rate of
transport
b)
(ATP) to
Glucose w/out
a carrier protein
Conc. of
molecule
Active transport requires energy
transport a molecule across a
membrane against its
concentration gradient.
Facilitated diffusion – does not require energy. Molecules move across membranes down
their conc. Gradient through a channel or carrier protein.
7) Signal transduction
a) Give an example of long-distance and local signal transduction.
b) Explain how nerve cells provide examples of both local and long-distance signaling.
c) Describe the 3 stages of cell signaling.
d) What type of protein regulation is seen for all receptor proteins?
e) Why is cAMP called a second messenger?
f) In G-protein receptor signaling, why are inhibitors of G-proteins a better target to down-regulate
a signal transduction pathway than a protein kinase activated by cAMP?
g) Describe an electrochemical gradient using the terms ion, chemical gradient, and membrane
potential.
a) Hormonal signaling would be long-distance signal transduction because the hormone is
produced by a gland; it then travels in the blood – making its way to target cells that in many
cases is far from the hormone producing tissue.
Signaling between two adjacent cells would be an example of local signal transduction.
b) This was a thinking question – have to actually think about the nature of
neurotransmission (which I know you have not had to learn yet – but the questions helps you
think about the many ways of signaling). Nerve cells secrete molecules (neurotransmitters)
that act on the adjacent (cell) – LOCAL. But it can also activate other neurons that are not
directly connected because neurotransmission involves the propagation of an Action
potential (AP) that can travel between many many cells – by causing AP in the next
connected cell – and so on, etc.
c) Three stages of cell signaling Reception – a molecule (ligand) binds a receptor on a receptive (target) cell
Transduction – the signal is passed through the membrane into the cell – and amplified
Response – the signal elicits a specific response (e.g. transcription – turning on a gene to
eventually make a protein to do some action in the cell.)
d) Allosteric regulation
e) cAMP is a second messenger because it is made by Adenylyl cyclase that is activated by
a G-protein – which was activated by a G-protein coupled receptor. The first signal
(messenger) would be the ligand that bound the G-protien coupled receptor. And cAMP
would activate downstream proteins needed in the response. cAMP also is important for
amplification of a signal.
f) The G-protein coupled receptor would be a better target because you could abrogate the
signal at one step. Kinases are many times a part of a huge phosphorylation cascade that
that affects many downstream proteins. cAMP also is involved in amplification so you would
not want to try to block a step that potentially is activating many kinases.
g) The electrochemical gradient is produced by transporting cations outside the cell. This
produces a net negative ionic charge inside the cell. The difference between the ion charge
across the membrane ( positive outside and negative inside) produces a membrane potential
that can be used along with the chemical gradient established to drive certain actions in
cells – e.g. and action potential of a neuron.