Kyle’s Section BIBC100 – Structural [email protected] Summer 2005 Problem Set #91. What kind of organism is T. Thermophilus? Graphically compare the heat capacities and activity levels as a function of temperature for T. Thermophilus and E. Coli. Ans: As its name implies, T. Thermophilus is a bacteria found in very hot environments such as thermal springs. It will have a higher temperature for its heat capacity peak (denaturation) than will E. Coli. This is because its protein structure has evolved to withstand these high temperatures. Likewise, the specific activity peak for T. Thermophilus will be at a higher temperature than E. Coli. 2. Pyrococcus furiosus is also a hyperthermophile, like T. Thermophilus. Describe the structural pattern that stabilizes the glutamate dehydrogenase enzyme in this bacteria in the presence of such high heat. Ans: This enzyme shows a structural pattern similar to salt crystal lattices. Negatively charged amino acids like glutamate form salt bridges with adjacent positively charged amino acid resides like arginine. These ionic interactions are much stronger than hydrophobic interactions. 3. Name the two proteins (microfilaments) that make up the molecular motor in your muscle cells. Ans: Actin & Myosin4. Describe the structure of myosinAns: Myosin has a tetrameric structure of 2 light chains and 2 heavy chains. The two heavy chains include a supercoiling of alpha-helices that end in large head-groups at the N-terminus. The two light chains are attached to each of these heads. 5. What are the 4 steps in the myosin power stroke cycle?Ans: i) ATP binds to myosin head causing it to release from actinii) ATP is hydrolyzed inducing a conformational change in the head group; the head group tilts upward. ADP + Pi remain bound to the head groupiii) Myosin head attaches to actin, causing the release of Piiv) Pi release triggers the “power stroke” where the myosin head moves back to the original position, thus projecting the myosin past the actin.6. What are the two molecular protein motors that bind cytoplasmic vesicles and organelles to microtubules and are responsible for their movement?Ans: Kinesin & Dynein. Kinesin directional movement is opposite that of dynein.7. Describe the structure of a microtubule. What are the monomeric subunits called? What are protofilaments?Ans: A microtubule is a cylindrical, hollow structure. The monomeric subunits are made of a protein called “tubulin”. Tubulin has alpha and beta subunits which form aheterodimer. These heterodimers aline to form a protofilament, and these protofilaments form the ring, cylinder that is the microtubule.8. Name the three types of cytoskeletal fiber proteins. Describe their monomeric proteincomponents. Also describe their function.Ans: i) microfilaments ; Actin & Myosin; contraction, actin can grow, shrinkii) intermediate filaments; Keratin; elasticity & flexibilityiii) microtubules ; Tubulin; rigid support, motility, and cell division9. Describe the movement of cilia. What is “telescoping”?Ans: Cilia move in a swinging motion. Telescoping is the movement of isolated microtubules within a larger fiber. This causes the fiber to swing.10. Explain the supramolecular architecture of eukaryotic cilia? What is a “9 + 2 arrangement”? Ans: There are 9 microtubule dimers in the outer ring. There are also 2 microtubule monomers connected together at the center. The dimer has an complete ring of 13 protofilaments, and an attached ring of 10 protofilaments. The monomers simply have 13 protofilaments. Dynein arms can be found on the outer ring. A protein called“nexin” connects these units of the outer ring.11. Describe the structure of bacterial flagella. How is it that a flagella can elongate and shorten? What drives the rotation of the base unit of the flagella?Ans: The rotating base of flagella has multiple units: C-ring, M-S ring, P-ring, L-ring. A central rod runs through these rings, and this composite spans the width of both the outer membrane, periplasm, and inner membrane. A hook is located just outside the outer membrane. Flagellin proteins can be pumped through an inner channel to the end of an elongating flagella. H+ gradients created by an electron-transfer chain are commonly found to contribute to the energy that drives the rotation.12. How could an ATPase possibly be responsible for the rotation of a flagella motor unit? Describe the structure of ATPase. Ans: 3 alpha subunits, 3 beta subunits, 3 ATP binding sites where energy can be transferred. Along with gamma and delta subunits, these make up the F1 group. The F0 group is made of a ring-like structure. ATP hydrolysis causes this whole thing to rotate, and thus could be used in a molecular motor mechanism. 13. Describe the mechanism of the F0 portion of Na+ driven ATPase. What is the stator? How does sodium facilitate the rotation? Ans: H+ / Na+ in from the periplasmic space and exit towards the cytoplasm. After entering into the F0 subunit, these + charges bind with certain – charged residues like glutamate. This neutralizes these charges, allowing them to now pass through the hydrophobic barrier, or “stator”. After rotating through the barrier, the + charges dissociate, and exit into the cytoplasm.14. What is an antigen? What is an antibody? What does the “AB” stand for in Fab? What does the “C” stand for in Fc? Ans: An antigen is an antibody generator; typically a fragment of a bacterial cell or avirus that is recognized by antibodies of the immune system. Antibodies are proteins that are produced by white blood cells to recognize and tag these antigens for destruction. 15. How does a cell specify an IgG immunoglobulin protein for secretion? Ans: N-linked glycosylation on the Fc subunit. 16. Name the sequence of three amino acids that are always found in N-linked glycosylation.Ans: Asn – X – Ser/Thr17. Describe the structure of immunoglobulin antibodies.Ans: Fc and 2 Fab regions. Disulfide bridges connect the two sides. The Fab units have a light chain attached to a heavy chain, with each having variable and constant regions. 18. What are the different types of heavy chains?Ans: alpha, delta, epsilon, gamma, and mu19. What are the different types of light chainAns: kappa and
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