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Molecular and Cell Biology: Eukaryotic Cells and Moving Proteins and Organelles

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Question 1.
a. How have Eukaryotic cells solved the problem of moving proteins and organelles from one part of the cell to another, faster than would occur by diffusion? And give a specific example to illustrate how a protein may be moved from part of the cell to another.
b. Describe one mechanism that ensures that proteins are moved to the appropriate place within a cell.

Question 2.
a. Using examples to illustrate your answer name and briefly describe four different types of non-covalent interactions that can occur between and within molecules.
b. How is a Scathard plot generated, and what measure of the inter-molecular interaction is used to determine this?

Question 3.
a. What are three features of a protein domain?
b. Briefly outline there attributes conferred on a protein by having multi-domain architecture. Illustrate your answer using at least two examples of multi-domain proteins.

Question 4.
a. Briefly describe how packaging of DNA into chromatin contributes to DNA protection, compaction and metabolism.
b. Briefly describe one factor of cellular component that contributes to the packaging of the eubacterial chromosome.
c. How is the type of DNA packaging found in Archae similar to that observed in Eukaryotes?

Question 5.
a. In terms of replication origins, how do the chromosomes of E. coli and S. Cerevisiae differ?
b. What is the main advantage to a cell of having a defined starting point for DNA synthesis?

Question 6.
a. Two post-translational modification of proteins and indicate where the modification takes place within the cell and what effect it has on the protein.
b. What is a proteasome, and what function does it have and where is it located within the cell?
c. How are proteins targeted to proteasomes?
d. How do functions of proteasomes and MHC molecules combine to contribute to immune defense?

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Solution Preview

Cellular and Molecular Biology

Question 1.
a. The huge volume inside a eukaryotic cell is compartmentalized into a large number of bacterium-sized parts. Because eukaryotic cells are subdivided, the molecules required for specific chemical reactions are often located within a given compartment and do not need to diffuse long distances to be useful.

Additionally, compartmentalization increases the efficiency of chemical reactions. First, the substrates required for particular reactions can be localized and maintained at high concentration within organelles. Second, groups of enzymes that work together can be clustered on internal membranes instead of floating free in the cytoplasm. Clustering these molecules increases the speed and efficiency of the reactions, because reactants have shorter distances over which to diffuse or be transported.

An example to illustrate how a protein may be moved from part of the cell to another. For example, in localization sequencing a protein might be sent to the nucleus or marked for secretion outside of the cell. Additionally, in the SH2 domain , a protein domain is present in many signaling proteins. For example, the SH2 binds a short amino acid sequence containing a phosphotyrosine, and moves a protein containing it to sites in the plasma membrane in response to certain specific signals.

b. Localization Signaling or Tagging: Which are characteristics of short protein sequences that "tell" a cell where to send a protein. The tags are useful for separating as well as segregating the proteins. They direct the protein to a particular physical location in the cell, such as the nucleus, the membrane, the periplasm, and secretion outside of the cell or elsewhere.

Question 2.
a. Non-covalent bonds determine the shape of many large biological molecules and stabilize complexes composed of two or more different molecules. There are four main types of non-covalent bonds in biological systems: Hydrogen, Vand de Waals, Ionic and, Hydrophobic.

Hydrogen bonds: Water molecules give a classic example of hydrogen bonding. Water molecules contain two hydrogen atoms and one oxygen atom. Two molecules of water can form a hydrogen bond between them. Hydrogen bonds among water molecules are largely responsible for the properties of both liquid water and the crystalline solid form (ice). As such, the hydrogen atom in one water molecule is attracted to a pair of electrons in the outer shell of an oxygen atom in an adjacent molecule. Not only do water molecules hydrogen-bond with one another, they also form hydrogen bonds with other kinds of molecules. In addition, the presence of hydroxyl (?OH) or amino (?NH2) groups makes many molecules soluble in water.

Van der Waals (VDW) interaction /bonds: Van der Waals interactions, involving either transient induced or permanent electric dipoles, occur in all types of molecules, both polar and nonpolar. In particular. VDW interactions, are responsible for the cohesion between molecules of nonpolar liquids and solids, such as heptane, CH3?(CH2)5?CH3, that cannot form hydrogen bonds or ionic interactions with other molecules. When these stronger interactions are present, they override most of the influence of van der Waals interactions. Heptane, however, would ...

Solution Summary

Eukaryotic cells and moving proteins and organelles are examined for molecular and cell biology. Scathard plot is generated and measured.

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Proteins, Enzymes, Synthesis and Division

Question 1:
a) What role do microtubules play in intracellular transport?
b) Describe the structure of microfilaments and microfilament networks and explain how they are assembled and disassembled within a cell.
c) Outline two functions that microfilament networks play in cell motility.
d) What function of intermediate filaments have in eukaryotic cells?

Question 3:
a) What two key factors determine the specificity of Watson-Crick base pairing in B-DNA? For each of these factors, explain why this is the case.
b) What activity of E.coli DNA polymerase 1 is responsible for ensuring correct Watso-Crick pairing during DNAS synthesis?
c) Outline briefly how this activity (given in your answer to part (b)) is achieved by this enzyme.

Question 5:
a) What is a mitotic spindle?
b) Which to classes of motor proteins interact with spindle microtubules during mitosis?
c) What role do these motor proteins play in the process of mitosis?
d) A drug that prevents the assembly of microtubules is applied to a culture of dividing cells for four hours. How will the culture treated with the drug differ from an untreated culture of the same cells, in terms of the numbers of cells in different stages of the cell cycle? In your answer, you should explain how the difference in appearance arises.

Question 6:
a) Describe the cellular location and function of the following membrane-bound vesicles: (i) synaptic vesicle, (ii) phagosome.
b) Describe the roles of two of the following proteins associated with the formation of transport vesicles: Epsin, Dynamin, GGA-proteins, GTP-binding adapter proteins.
c) Give one example of a transport vesicle that moves between the ER and the Golgi apparatus, indicating its coat protein and its direction of movement.

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