BIOL 3581 Lecture 5: Biotech December 5

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orangehorse801

7 Feb 2017

School

University of Windsor

Department

Biological Sciences

Course

BIOL 3581

Professor

Vacratis

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Document Summary

Main goal is to get an idea of the state of all the proteins in a given cell: can be under certain conditions. This can also be used to characterized sub-proteomes: if you are interested in getting a catalogue of what proteins are expressed in a vacuole, a certain cell type, gives a better idea of certain biological functions. 2d gels: derivatize two different samples with different colour fluorescent tags, that allows you to mix them and load them on a single gel, this overcomes the non-biological variation. It is limited by its resolution and sensitivity. Resolution is the separation power: how well you can separate things from one another. You have to be able to visualize it: coomassie stain requires nano-molar levels, silver stain is a little better. When we are talking about deep proteome coverage, things are at low levels.

Related Questions

1) In the major biosynthetic pathway, what is the order in which mRNA moves through the various organelles?

2) Compare and contrast the structure and function of the smooth endoplasmic reticulum and the rough endoplasmic reticulum?

3) Is SAR1 COPI or COPII? What type of protein is this? What causes SAR1 to active and what protein is necessary for this to occur?
4) Dynamin binds where clathrin meets the plasma membrane. As dynamin binds, it forms a ring that is then pinched so that the vesicle can be released from the plasma membrane. What allows for this to occur?

5) What are three different mechanisms of protein translocation? Briefly describe the state of the proteins when translocated in each of these ways.

6) What is the KDEL sequence stand for and how does it function within the cell? What type of transport is it associated with?

7) In what cellular compartment would a glycoprotein be expected to have its greatest mannose content? Its greatest N-acetylglucosamine content? Its greatest sialic acid content?

8) Would you expect the properties of the cisternal side of Golgi membranes to be more similar to the extracellular or cytosolic side of the plasma membrane? Why?

9) ________ are the site of cellular digestion, in which digestion occurs with the help of 50 __________. _____ digest proteins and ____ digest lipids.

10) Name two proteins you would expect to find as integral components of the RER membrane that would be absent from the SER? Name two proteins of the SER that would not be present in the RER?

Explain the cell theory; know the three basic tenets of the theory.

All cells have to carry out certain functions, what do all cells have in common?

Compare/contrast an Eukaryotic vs a Prokaryotic cell type.

Understand the concept of selective toxicity. What do all effective targets of an antimicrobial agent have in common? What are some characteristics of Prokaryotic cells that can be targeted?

Explain the unity and diversity of prokaryotic cells in terms of evolutionary theories.

Describe the three basic shapes (morphologies) of bacteria.

What are the functions of the plasma membrane, how does the structure of the plasma membrane aid in carrying out these functions?

Describe the fluid mosaic model of the plasma membrane. Draw out the plasma membrane, include the phospholipid bilayer (indicating polar/hydrophilic and nonpolar/hydrophobic components) and peripheral and integral proteins. Also indicate the intracellular (cytoplasmic) and extracellular regions.

What are the functions of the components of the plasma membrane? Phospholipids, proteins?

Transport. Compare/contrast the following mechanisms of transport in terms of the types of molecules transported, with or against the concentration gradient, if any Energy input is required, if a transport molecule is involved, and if Euk and or Prok use this mechanism.

Osmosis (explain the role of aquaporins)

Diffusion

Facilitated Diffusion

Active transport (proton motive force / ATP binding cassette system)

Group translocation

Class 6: Viruses (and Cells, continued)

Making connections: viruses and microbes Match the cell biology concept (on page 1) with an important application of that concept (on page 2). Then answer the follow-up questions at the bottom of page 2.

Cell Biology concepts
1. Bacteria that cannot construct new cell wall material become fragile and break down.
2. During influenza infection, the viral enzyme neuraminidase is required to release new viruses from the host cell in which they were made. Once released, the new viruses can infect many additional cells.
3. Thermus aquaticus is a bacterium found in hot springs and can live at temperatures up to ~80Â°C (175Â°F). It has adapted so that its enzymes are most functional at the elevated temperatures, compared with many organismsâ enzymes that function best ~37Â°C (98Â°F).
4. Until the isolation and investigation of retroviruses, scientists thought that RNA could be copied from DNA, but DNA could not be copied from RNA. Research on this class of viruses led to an update to this âCentral Dogmaâ of biology.
5. Some bacteria have adapted, so that the enzymes involved in making cell wall materials have a slightly different shape and can no longer be bound by certain drugs.
6. Rhizobia are bacteria that colonize the roots of certain plants (legumes, including beans and peas). The host plant benefits from the prokaryotesâ ability to âfixâ nitrogen, converting N2 from the atmosphere into a form that is usable by the plant.
7. Many species of bacteria contain the enzyme cellulase. More than 10 billion such bacteria and other symbiotic microbes may be found in a single milliliter of material from inside the digestive system of ruminant mammals.
8. Fungi, including those that cause athleteâs foot, use ergosterol to maintain healthy membranes. Animal cells do not make ergosterol, they use a similar lipid â cholesterol.
9. During retrovirus infection, a DNA copy is made of the virusâs RNA genome. A cut is made in the host cellâs DNA and the DNA copy of the viral genome is pasted into the host chromosome by a viral enzyme called integrase.
10. Prokaryotic cells contain smaller ribosomes (â70Sâ ribosomes) than eukaryotic cells (â80Sâ ribosomes). Both types of ribosomes synthesize proteins, but the macromolecules they use to do it are somewhat different.

2
Applications
_______ Oseltamivir, also called Tamiflu, binds and inhibits the viral protein neuraminidase.
_______ Clotrimazole is a drug that is used to treat certain infections. It interferes with synthesis of ergosterol, a lipid involved in phospholipid membranes.
_______ Penicillin is a drug that interferes with synthesis of peptidoglycans (these are biological molecules that are part protein and part carbohydrate) that are present in certain cell walls.
_______ HIV is often treated with several drugs that inhibit different parts of the viral replicative cycle. Raltegravir is an example of a drug that interferes with the integration of viral genes into the host cellâs chromosome.
_______ Cows, like other vertebrates, lack the ability to breakdown cellulose. Yet they are able to live on a diet of grass and other vegetation high in cellulose.
_______ Enzymes isolated from extremophiles have been very useful in laboratory research. For example, Taq polymerase facilitates PCR, a revolutionary technique for production of DNAs of particular sequences, which requires cycling reactions through high temperatures.
_______ Plants and animals require nitrogen to make biological macromolecules, however theyâre unable to convert atmospheric nitrogen (N2) into a biologically useful form.
_______ Azithromycin is a drug that binds to 70S ribosomes and blocks synthesis of any new proteins.
_______ Methicillin-Resistant Staphylococcus aureus (MRSA) can cause life-threatening infections of the skin and bloodstream. One of the reasons MRSA infections are so serious is that they are resistant to treatment by many antibiotics, including methicillin and penicillin.
_______ The enzyme reverse transcriptase, isolated from retroviruses, is an important tool in molecular biology research. Scientists interested in learning what genes are turned on in particular cells use it to make DNA copies of RNAs they are studying (The DNA copies are useful because they are more stable).

When you have completed the matching activity, answer these follow-up questions:
â¢ What types of infections can be treated with the following drugs?
o Penicillin
o Clotrimazole
o Azithromycin
o Tamiflu
o Raltegravir
â¢ Why are these drugs (above) safe for you to take? That is, why donât they kill your cells?
â¢ Cancer cells are your own human cells that have become deregulated so that they divide and pile up in an uncontrolled way. Many chemotherapy drugs treat cancer by interfering with cell division and other cell processes.
o Why are there so many more side effects for individuals undergoing chemotherapy than for individuals taking antibiotics?

BIOL 3581 Lecture 5: Biotech December 5

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