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Molecular and Cell Biology

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1. The three components of the eukaryotic cytoskeleton are microtubules, microfilaments and intermediate filaments.
a) State the principle protein component of the microtubules, and briefly describe the structure of a microtubule.
b) Describe how microfilaments polymerize from their monomer components. Include a description of the protein component(,0) treadmilling, and the role of ATP and capping proteins.
c) The following proteins all interact with microfilaments: ezrin, ARP complex, cofilin, myosin, fimrin. Describe the functions of three of these proteins within the cell.
d) Give one example of a protein that may form intermediate filaments and describe the type of structures that intermediate filaments produce.

3. a) Briefly describe the main differences between integral and peripheral membrane proteins in terms of their location and interactions with the lipid bilayer.
b) Describe the arrangement of secondary structural elements in one type of multipass transmembrane protein.
c) How can antibodies raised against segments of amino acid in a membrane protein be used to provide information on the structure of that protein?

4. a) Briefly describe how the core eukaryotic nucleosome is formed from its protein components and the location of the DNA strand, in relation to the nucleosome.
b) How is the local structure of chromatin maintained during genomic DNA replication?
c) Describe what occurs to nuclear DNA in a cell that has undergone apoptosis, and explain the characteristic pattern shown by DNA from an apoptotic cell, when it is examined by agarase gel electrophoresis.

5. a) List three ways in which mature mRNA differs from the primary transcript.
b) Which of the features of mature eukaryotic mRNA, identified in )a), influence the stability of mRNA and how?
c) Briefly explain what is meant by RNA editing, how this process can occur and how it affects the protein that the RNA encodes.

8. a) Briefly describe what is meant by the term 'growth cone.'
b) What effects do the molecules netrin and semaphorin have on the process of neurit outgrowth?
c) What type of molecules are cadherins, and what effect do they have on neurite outgrowth?
d) Describe how netrin, semaphorin and slit control the growth of the axons of commissural neurons across the midline and towards the brain during development.

10. a) Briefly describe the G2 checkpoint which is sensitive to DNA damage. Use diagrams as appropriate to explain how the activities of the phosphatase Cdc25 and kinase Weee1 play a role in the control of entry into M phase.
b) Explain how the positive feedback loop in this checkpoint functions.
c) What are the two principal external causes of double-strand breaks in DNA?
d) Briefly outline two mechanisms by which double-strand breaks are repaired by a cell.

11. a) Give one example of a cell-type that may be mobile within the tissues of an adult mammal, and explain how motility contributes to the normal function of that cell.
b) Define the term 'chemotaxis' and give one example of a molecule that can induce chemotaxis.
c) Explain with the aid of a labelled diagram how molecules that induce chemotaxis can act on a cell to cause its polarization. The diagram should include information on the receptor for the chemotactic molecule and the intracellular signals and events that follow activation of the receptor.

12. a) Explain the difference between reactive oxygen species and free radicals, and give one example of each.
b) What cellular process is the main source of free radicals in eukaryotes and where does it take place?
c) What biological molecules can be damaged by interaction with free radicals? Give one example of the way that a free radical can interact with a biological molecule to change its structure.
d) Explain the different between primary and secondary antioxidant defenses, giving one example of each.

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The solution discusses molecular and cell biology.

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1) Microtubules - made from polymers of tubulin
Structure: cylindrical arrangement of tubulin, typically in the form of alpha and beta tubulins binding end to end, in alternating sequence (so alpha-beta-alpha etc.)

Microfilaments - made of linear polymers of actin

Actin as a protein monomer is polarized - its two ends are distinctly different from each other. Trimers of G-actin are formed spontaneously, after which ATP-bound actin binds to one end (the "barbed" or + end), using ATP as an energy substrate to attach to the existing strand. On the "pointed" or negative end, ADP-actin actually dissociates, but much more slowly. Where the rate of addition and growth on the barbed end is the same as the dissociation rate at the pointy end, the microfilament treadmills - it's essentially moving in the directly of the barbed end. As the barbed end extends, the pointy end dissociates, and when this is at the same rate, the entire microfilament looks like it's moving forward. Capping proteins at either end of the microfilament are in place in order to ensure that growth and dissociation don't continue forever, as a certain length is required for the microfilament to achieve it's function.

Ezrin: resides in between the plasma membrane and the associated cytoskeleton. Functions in adhesion, migration and organization of cytoskeleton to plasma membrane.

Cofilin: actin-associated protein which catalyzes the dissociation of ADP-actin from the pointy ends of microfilaments.

Myosin: Microfilaments are known to actually function in moving cells and cell components around, and achieves this using actin-myosin complexes similar to those found in muscles. Myosin binds to actin (and vice versa), then pull and contract in order to achieve movement.

Desmin is a protein which polymerizes to form intermediate filaments. They produce the infrastructure behind sacromeres of muscles, which are essential to the functional contraction of muscular tissue.

3) Integral vs. Peripheral membrane proteins

Integral proteins are those which are permanently installed into the plasma membrane, and are often comprised of multiple transmembrane components. Where that isn't the case, they often include components which strongly reinforce their positioning inside a plasma membrane using components which are hydrophobic, thereby keeping them anchored to the inside of lipid bilayers.

Peripheral membrane proteins are only associated with the plasma membrane temporarily, sometimes by attaching themselves to integral proteins. Other times, they exist on the peripheral layer of the plasma membrane only, floating on a singular side of the plasma membrane.

Secondary structural elements of the beta-barrel multi-pass transmembrane proteins are the alternating hydrophobic and hydrophillic parts of the beta sheets. When a beta-barrel protein is embedded in the plasma membrane, often times these hydrophobic ...

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