BCOR 103 1st EditionExam # 2 Study Guide Lectures: 8 - 14Lecture 8 (February 10)The cytoskeleton is the architectural material of the cell. The key activities that it is associated with are: cell shape, positioning organelles, macromolecular metabolism, a track for the transport of materials within the cell, cell movement, and transduction between cells. Cytoskeletal StructuresFilament System Major Protein Subunit Structure Diameter Major Function(s)Microtubules α , β- Tubulins Hollow Tube, 22nmCell Polarity,Cell Division,Intracellular TransportIntermediateFilamentsVariable FibrousProtein Rope-like Fiber, 10nmBasic Support,Cell Shape, ResistStressMicrofilaments ActinGlobular ProteinChain 6nmCell Elasticity,Cell MotilityThick Filaments Myosin (Muscle-like)Rough Bipolar Fiber15nm ContractilityIntermediate Filament Proteins assemble in a building-block like sequence. Starting with one α-helical region, then a coiled dimer of the two, then a combined staggered dimer, the association of eight tetramers, which come together to make up filaments. This building-block process produces a stress resistant filament. There are N and C terminal domains that project to the surface to provide binding sites for other components. Without filaments, a layer of cells would not stretch and remain intact, they would rupture.Dynamic Instability refers to the growth and collapse of microtubules. A growing microtubule lengthens when GTP binds to tubulin molecules. The microtubule can collapse when GTP hydrolysis occurs, and the microtubule peels itself away. Additionally, some microtubules become stable when they meet a capping protein at the cell membrane. Others do not get capped and so they grow and shrink over and over.Lecture 9 (February 12) There are seven different MAPs that should be known. The first is γ-tubulin ring complex which initiates the formation of a microtubule. The second MAP to know is XMAP215 which polymerizes the (+) end of the microtubule. Next is Kinesins 8 and 13 which depolymerize the (+) end of the microtubule. CLASP and EB1 controls (+) tracking. Katanin controls severing the microtubule. Tau, MAP1, MAP2, and MAP4 work to stabilize the microtubule lengthwise. Lastly, CLASP is also involved in rescue functions of the microtubules. Kinesin is made up of two “heavy chains” and “light chains” connected by an alpha helix. The heavy chains are two globular proteins that attach to the microtubule. The light chains attach tothe vesicle or protein being transported within the cell. The kinesin works with ATP to move its proteins along the microtubule in the direction toward the positive end of the microtubule. Dynein serve a similar function to kinesin, except it moves its materials toward the negative endof the microtubule. Dynein also has a different structure from kinesin. Dynein has two heavy chains that link with the microtubule, but the other side is made up of lots of light chains, approximately seven. The light chains bond with the material being moved and the other heavychains move along the microtubule. G actin is the molecule that actin fibers are made up of. Actin monomers (G actin) come together to form dimers, then trimers, and eventually a microfilament with a positive and negative end. These microfilaments layer together called monomer polymerizing. The dimer “formin” can regulate the (+) end of the microfilament. Actin works with the motor proteins that are microfilament based “myosin.” There are many different types of myosin proteins. We will focus on the mechanism. The myosin head that is connected to a microfilament works in tandem with ATP to attach and release to a parallel actin filament. Myosin uses ATP to move up actin. This is primarily seen in muscles, it is how they contract. Lecture 10 (February 17) There are three types of RNA involved in protein synthesis. Those three types are: transfer RNA (abbreviated tRNA), messenger RNA (abbreviated mRNA) and ribosomal RNA (abbreviated rRNA). Transfer RNA is responsible for decoding sections of the nucleic acid sequence code into the correct order of amino acids that are in a protein; tRNA also brings energy that is needed in these synthetic processes. Messenger RNA encodes genetic information that details the specificsequence of amino acids for a protein. Ribosomal RNA provides the core component of ribosomes. This ribosomal RNA codes for “Peptidyl-Transferase” which is the major active part of ribosomes.The genetic code is essentially how all of the genetic information of an organism is stored. There are four bases used by humans, and 20 amino acids that those four bases code for. The little bits of information are called “codons.” Codons are made up of three nucleotide bases, forexample adenine guanine cytosine (AGC) codes for the amino acid serine. Please note that other codons can code for the same amino acid; for example the codon UCU also codes for serine. The ribosome is by far the most abundant organelle in the cell. This is true for both eukaryotes and prokaryotes. The structure and function of ribosomes in the cell is similar for both eukaryotes and prokaryotes, yet the eukaryotic ribosome is slightly larger on all accounts than a prokaryotic ribosome. A ribosome is made up of two parts: a large subunit and a small subunit. The primary process a ribosome is responsible for is to synthesize proteins. Lecture 11 (February 19)The production and synthesis of proteins by ribosomes is important, but it is not sufficient for efficient cell processing. The proteins need to be organized into complexes in order for cell processes to take place. This activity is protein targeting. There are two classes of eukaryotic ribosomes: membrane-bound ribosomes and free ribosomes. Membrane-bound ribosomes areassociated with the rough endoplasmic reticulum (rough ER) and the proteins that they producehave three specific criteria. First, these proteins remain associated with some type of membrane, whether it is the nuclear membrane, the ER, the Golgi, or the plasma membrane. Second, these proteins are encased in small vesicles. Third, these proteins are secreted from the cell. Free ribosomes, like they sound, are not bound to any membranes at all. The proteins produced by free ribosomes that are found in the cytoplasm, mitochondria and chloroplasts, and the cytoskeleton. The Endoplasmic Reticulum has two subgroups: the rough