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BZ 310-2.1
Supplemental Information for the second exam
| Question | Answer |
|---|---|
| What are two structural features shared by all members of the collagen family? | 1: All collagen molecules are trimers consisting of three polypeptide chains. 2: The three polypeptide chains of collagen are wound around each other to form a triple helix. |
| How do collagens give cartilage and other extracellular matrices strength and resistance? | collagen molecules resist pulling forces and provide a scaffold for proteoglycans. |
| How do proteoglycans give cartilage and other extracellular matrices strength and resistance? | They can bind huge numbers of cations which, in turn, bind large numbers of water molecules. As a result, proteoglycans form a porous, hydrated gel that fills the extracellular space like packing material and resists compression forces. |
| The polypeptide chains that make up fibronectin contain binding sites for what? | For numerous components of the extracellular matrix and binding sites for receptors on the cell surface. These binding sites hold the extracellular matrix in a stable attachment to the cell. |
| What are the two major activities of integrins? | 1: Adhesion of cells to their surroundings. (The most important family of receptors that attach cells to their extracellular environment) 2: Transmission of signals between the external environment and the cell interior. |
| Describe the role of focal adhesions as sensory structures. | They collect information about the physical and chemical properties of the extracellular environment and transmit that information to the cell interior. This can impact cell adhesion, proliferation, and survival. |
| List the four distinct families of integral membrane proteins that play a major role in mediating cell-cell adhesion | 1. selectins, 2. immunoglobulin superfamily, 3. integrins, 4. cadherins |
| What are the primary functions of tight junctions and how do they accomplish this? | They encircle a cell like a gasket and make contact with neighboring cells on all sides. They can serve as a barrier to the free diffusion of water and solutes from extracellular compartments within the body like the inside of the intestines. |
| Gap junctions are composed entirely of what? | Complexes of the integral membrane protein, connexin. The resulting complexes are called connexons. |
| How do gap junctions integrate the activities of individual cells into a functional unit such as an organ? | Gap junctions serve as sites of communication between the cytoplasms of adjacent cells. They can facilitate cooperative activities among a group of cells to perform a single function. |
| What are the components of the endomembrane system? | Endoplasmic reticulum, Golgi complex, endosomes, lysosomes, and vacuoles. |
| What are the three primary functions of smooth endoplasmic reticulum highlighted in the text? | 1. Synthesis of steroid hormones in the endocrine cells of the gonad and adrenal cortex; 2. Detoxification of a wide variety of organic compounds; and 3. Sequestration of calcium ions. |
| 1/3 of proteins encoded by a mammalian genome are synthesized on ribosomes attached to rough endoplasmic reticulum. These are; | 1. secreted proteins; 2. integral membrane proteins; and 3. soluble proteins that reside within the endomembrane system (such as those of the lysosome). |
| Proteins which are synthesized on ribosomes that are not attached to rough endoplasmic reticulum are released into the cytosol. These include: | 1. proteins destined to remain in the cytosol; 2. peripheral proteins of the cytosolic surface of membranes; 3. proteins that are transported to the nucleus; and 4. proteins to be incorporated into peroxisomes, chloroplasts, and mitochondria. |
| Provide a short overview of the role of the rough endoplasmic reticulum in the processing of newly synthesized proteins. | The ER provides an environment that facilitates the modification, folding, and assembly of proteins followed by their transport to their designed destination. |
| Where does membrane biosynthesis begin? | The biosynthesis most membranes required by a cell begins in the endoplasmic reticulum. |
| Provide a brief overview of the process and path of a protein through the Golgi complex. | Newly synthesized membrane, secretory, and lysosomal proteins exit the ER and enter the Golgi complex at its cis face and pass across the complex to the trans face. During which proteins synthesized in the rER are sequentially modified as necessary. |
| What is the best studied Golgi activity? | Modification of a protein’s carbohydrate structures and composition. |
| Golgi complex is the site of the synthesis of what? | Most of the cell’s complex polysaccharides. |
| What are the two primary functions of proteins coats as they relate to vesicles? | 1. They cause the membrane to curve and form a budding vesicle; 2. They provide a mechanism for selecting the cargo to be carried by the vesicle. |
| Briefly describe the roles of t-SNARES and v-SNARES in the docking and fusion of vesicles to a target compartment. | A v-SNARE in the vesicle membrane interacts with the t-SNAREs in the target membrane to form a complex that brings the two membranes into close contact allowing for membrane fusion. |
| What is the primary mechanism for properly targeting lysosomal enzymes? | Lysosomal enzymes are modified in the Golgi by the phosphorylation of specific residues. This is recognized by specific receptors in the trans Golgi which capture and direct the lysosomal enzymes to the appropriate clathrin-coated vesicles for transport. |
| Briefly describe the primary functions and mechanisms of the lysosome. | Primary functions include breakdown of materials brought into the cell from the extracellular environment, inactivation and digestion of pathogens, and organelle turnover. |
| The role of vacuoles | 1. storage of macromolecules; 2. storage of toxins for release as defense mechanisms; 3. intracellular digestion. |
| What are the steps in the chemical cycle of a motor protein? | 1. Binding ATP; 2. hydrolysis of ATP; 3. release of products; 4. binding of a new molecule of ATP. |
| Use the axon as an example to describe what it means for most kinesins to be plus end-directed motors. | In the axon, where all microtubules are oriented with their minus ends facing the cell body, kinesin transports vesicles and other cargo toward the synaptic terminals. |
| What are the two well-studied roles for cytoplasmic dynein presented in the text? | 1. Force-generating agent in positioning the spindle and moving the chromosomes during mitosis; 2. Minus-end directed microtubular motor which positions the centrosome and Golgi complex and moving organelles, vesicles, and particles through the cytoplasm. |
| microtubules occurs in two phases | 1. nucleation during which a small portion of the microtubule is initially formed; and 2. elongation. |
| Makeup of the 3 cellular filaments | Microtubules are composed of the protein tubulin, microfilaments are composed of the protein actin, and intermediate filaments are composed of a variety of proteins. |
| The microtubules of the cytoskeleton are typically nucleated by what? | The centrosome where the minus end is associated with the centrosome and plus end (growing end) is situated at the opposite tip. |
| The roles of tropomyosin and troponin as they relate to muscle contraction. | When the sarcomere is relaxed, the tropomyosin of the thin filaments block the myosin binding sites on the actin. When Ca2+ binds to troponin a conformational change occurs causing tropomyosin to shift which exposes the myosin-binding sites on actin. |
| Briefly describe the interrelated roles of muscle fibers, myofibrils, sarcomeres, thick filaments, and thin filaments with regard to muscle contraction. | Skeletal muscles are composed of bundles of muscle fibers which are composed of many myofibrils that are composed of contractile units called sarcomeres which consist of alternating thick and thin filaments. Thick filaments=myosin, thin filaments=actin. |
| Provide one example of the role of transposable elements in adaptive evolution. | They can on occasion link 2 unlinked sections of the genome giving rise to new proteins made up of domains derived from different ancestral genes. |
| Provide a short overview of the process of transcription. | RNA polymerase moves in a 3’ to 5’ direction. As the polymerase progresses, the DNA is unwound and the polymerase assembles a complementary strand of RNA that grows from its 5’ terminus in a 3’ direction. |
| Why is the nucleotide incorporation reaction of transcription essentially irreversible? | The pyrophosphate produced in the first step of polymerization is hydrolyzed, thereby releasing a large amount of free energy. |
| What is the role of the sigma factor of bacterial RNA polymerase? | It increases the enzyme’s affinity for promoter sites in DNA and decreases its affinity for DNA in general. |
| Early phosphorylation events in the CTD of RNA polymerase is thought to be involved in what two key functions in transcription? | The trigger that uncouples RNA polymerase from the transcription factors and promoter allows the enzyme to escape the preinitiation complex and move down the DNA template; Provide binding sites for proteins involved in the early stages of mRNA processing. |
| The functions of the methylguanosine cap of mRNA | 1) prevent the 5’ end of mRNA from being digested by nucleases; 2) aid in the transport of the mRNA out of the nucleus; and 3) facilitate initiation of mRNA translation. |
| The function of the poly(A) tail of mRNA | Along with an associated protein it serves to protect the mRNA from degradation by nucleases. |
| Provide a BRIEF overview of the process of converting a primary transcript into a mature mRNA. | 1. Addition of 5’ methylguanosine cap; 2. Addition of 3’ poly(A) tail; 3. removal of introns. |
| With regard to codons, what is the value of clustering? | Clustering reflects the similarity in codons that specify the same amino acid. As a result spontaneous mutations causing single base changes in a gene often will not produce a change in the amino acid sequence of the corresponding protein. |
| What do the bacterial protein, Rho, and terminator sequences have in common? | Rho is a ring shaped protein in bacteria that is used in roughly half the cases of translation to terminate the translation. In other instances termination is done by a terminator sequence forming a hairpin loop to dislodge the mRNA. |
| What is the role of the TATA (pribnow) box present in some eukaryotic promoters? | The TATA box is a consensus sequence responsible for determining exactly where RNA polymerase should start. |
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