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

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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 ...