BILD1_Problem Set 3

Plasma membrane

- Both eukaryotes and prokaryotes have a plasma membrane. - The plasma membrane is made of a single phospholipid bilayer in EUKARYOTES. In PROKARYOTES, there can be ONE or TWO bilayers. - The plasma membrane plays a major role in phagocytosis (bringing stuff inside 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. - In prokaryotes only, the plasma membrane can be invaginated to increase surface area for respiration or photosynthesis to occur. - 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 (proteins) to now be outside of the cell.

Golgi Apparatus

- Eukaryotes have the golgi while prokaryotes do not. - The golgi is enclosed by a single membrane. - The golgi is not directly involved in protein synthesis, but it does play a role in the modification of proteins and transport. - Glycosylation of proteins occurs here. - The golgi appears as stacked disks of membranes - The golgi receives proteins from the ER on its cis side then modifies and figures out the final destination of the proteins and send them on their way out through the trans side

Peroxisome

- Only found in eukaryotic cells - Peroxisomes are enclosed by a single membrane - Some lipid synthesis occurs here via oxidation enzymes - The peroxisome is where toxic byproducts are broken down and is important for detoxification.

Chloroplast

- Prokaryotes do not have chloroplasts, only eukaryotic plant cells do. - The chloroplast is enclosed by a double membrane. - The chloroplast has its own DNA - The chloroplast has its own ribosomes that are used to synthesize some of its proteins. - The chloroplasts is the site of photosynthesis, where light energy is turned into ATP. - The chloroplast contains the thylakoids, which are flat stacked membrane compartments.

Vacuole

- Prokaryotes do not have vacuoles, only eukaryotic plant cells do. - The vacuole is enclosed by a single membrane. - The vacuole is a water storage organelle used to store water and other soluble components, such as waste products.

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) Chloroplasts 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) Their ribosomes and proteins resemble those of the prokaryotic world.

Describe the three major types of cytoskeleton elements we discussed in class.

1) 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. 2) 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. 3) 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.

What is the difference between active transport and facilitated diffusion?

Active transport requires energy (ATP) to 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.

What type of protein regulation is seen for all receptor proteins?

Allosteric regulation

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.

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.

How does co-transport work? What is the energy source?

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 co- transporter, 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.

Give an example of long-distance and local signal transduction.

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.

Why are microtubules and microfilaments both needed to anchor cells to the ECM?

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.

How do motor proteins use ATP to produce movement (displacement)?

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.

Why do some forms of transport require ATP to drive transport whereas others do not?

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.

Describe an electrochemical gradient using the terms ion, chemical gradient, and membrane potential.

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.

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.

Why is cAMP called a second messenger?

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.

How are cells anchored to the extracellular matrix (ECM)?

cells are anchored to the ECM through a network of secreted ECM proteins that are linked to microfilaments by integrins (a transmembrane protein)

Ribosome

- Both eukaryotes and prokaryotes have ribosomes - 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. - The ribosome is the protein synthesis machine! All protein synthesis comes from ribosomes. - Ribosomes are critical for protein export. The newly synthesized proteins is docked exiting the ribosome and docked on the ER before being exported.

Endoplasmic Reticulum

- Eukaryotes have ER while prokaryotes do not. - The ER is enclosed by a single membrane. - 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 the site of all protein folding. - Sugars are added to proteins here - Lipid biosynthesis occurs primarily in the SMOOTH ER (not coated by ribosomes), but also in the RER. - The smooth ER is the site of detoxification for drugs. - The ER appears to be composed of stacks of membrane tubes. - After synthesis and some modification of proteins, the ER sends proteins on their way to the Golgi where more modification is done, and where proteins are eventually sent to their final destination.

Nucleus

- Eukaryotes have a nucleus while prokaryotes do not. - The nucleus is enclosed by a double membrane called the nuclear envelope. - The nucleus contains most of the cell's (eukaryotes) DNA. - The nucleus is not directly involved in protein synthesis. However all genes are here and genes encode proteins.

Lysosome

- Eukaryotes have lysosomes while prokaryotes do not. - Lysosomes are enclosed by a single membrane. - Lysosomes are what digest and break down the food and foreign objects brought into the cell by phagocytosis. - Lysosomes help get rid of undigested materials

Mitochondria

- Eukaryotes have mitochondria while prokaryotes do not. - The mitochondria are enclosed by a double membrane (remember the inner and outer membrane discussed in relation to the electron transport chain) - Mitochondria have their own circular DNA, this is one of the components of the endosymbiosis theory. - The mitochondria have their own ribosomes that synthesize some of their proteins - 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.

Why do cells need transport proteins? Why can't components just diffuse through the membrane bi-layer?

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.

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.

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 past 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 plasma membrane surfaces.

How many times do fission and fusion 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 from 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.

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.

Starting at the RER, we have 2 fission events and 2 fusion events.

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?

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.

Explain how nerve cells provide examples of both local and long-distance signaling.

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.

Describe the 3 stages of cell signaling.

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.)