Lodish H. - Molecular Cell Biology (5ed, Freeman, 2003) (794361), страница 25
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What amino acids are involved in theformation of disulfide bonds? Does the formation of a disulfide bond increase or decrease entropy (S)?5. In the 1960s, the drug thalidomide was prescribed topregnant women to treat morning sickness. However,thalidomide caused severe limb defects in the children ofsome women who took the drug, and its use for morningsickness was discontinued.
It is now known that thalidomidewas administered as a mixture of two stereoisomeric compounds, one of which relieved morning sickness and theother of which was responsible for the birth defects. Whatare stereoisomers? Why might two such closely related compounds have such different physiologic effects?6. Name the compound shown below. Is this nucleotide acomponent of DNA, RNA, or both? Name one other function of this compound.OC6HN1C2H2NOO3N5C478 CH9CNNO5OPOOOPOOOPOOCH24OHH1HH3OH2OH7. The chemical basis of blood-group specificity resides inthe carbohydrates displayed on the surface of red blood cells.Carbohydrates have the potential for great structural diversity.
Indeed, the structural complexity of the oligosaccharidesthat can be formed from four sugars is greater than that foroligopeptides from four amino acids. What properties of carbohydrates make this great structural diversity possible?8. Ammonia (NH3) is a weak base that under acidic conditions becomes protonated to the ammonium ion in the following reaction:NH3 H n NH4NH3 freely permeates biological membranes, including thoseof lysosomes. The lysosome is a subcellular organelle with apH of about 5.0; the pH of cytoplasm is 7.0.
What is the effect on the pH of the fluid content of lysosomes when cellsare exposed to ammonia? Note: Protonated ammonia doesnot diffuse freely across membranes.9. Consider the binding reaction L R n LR, where L isa ligand and R is its receptor. When 1 103 M L is addedto a solution containing 5 102 M R, 90% of the L bindsto form LR. What is the Keq of this reaction? How will theKeq be affected by the addition of a protein that catalyzes thisbinding reaction? What is the Kd?10. What is the ionization state of phosphoric acid in the cytoplasm? Why is phosphoric acid such a physiologically important compound?11.
The G for the reaction X Y n XY is 1000cal/mol. What is the G at 25C (298 Kelvin) starting with0.01 M each X, Y, and XY? Suggest two ways one couldmake this reaction energetically favorable.REFERENCESAlberty, R. A., and R. J. Silbey. 2000. Physical Chemistry, 3d ed.Wiley.Atkins, P. W. 2000. The Elements of Physical Chemistry, 3d ed.W. H. Freeman and Company.Berg, J. M., J. L. Tymoczko, and L.
Stryer. 2002. Biochemistry,5th ed. W. H. Freeman and Company.Cantor, P. R., and C. R. Schimmel. 1980. Biophysical Chemistry.W. H. Freeman and Company.Davenport, H. W. 1974. ABC of Acid-Base Chemistry, 6th ed.University of Chicago Press.Edsall, J. T., and J. Wyman. 1958. Biophysical Chemistry, vol.1.
Academic Press.Eisenberg, D., and D. Crothers. 1979. Physical Chemistry withApplications to the Life Sciences. Benjamin-Cummings.Gennis, R. B. 1989. Biomembranes: Molecular Structure andFunction. Springer-Verlag, New York.Guyton, A. C., and J. E. Hall. 2000. Textbook of Medical Physiology, 10th ed. Saunders.Hill, T. J. 1977. Free Energy Transduction in Biology. AcademicPress.Klotz, I. M. 1978.
Energy Changes in Biochemical Reactions.Academic Press.ReferencesLehninger, A. L., D. L. Nelson, and M. M. Cox. 2000. Principles of Biochemistry, 3d ed. Worth.Murray, R. K., et al. 1999. Harper’s Biochemistry, 25th ed.Lange.Nicholls, D. G., and S. J. Ferguson. 1992. Bioenergetics 2. Academic Press.Oxtoby, D., H. Gillis, and N.
Nachtrieb. 2003. Principles ofModern Chemistry, 5th ed. Saunders.Sharon, N. 1980. Carbohydrates. Sci. Am. 243(5):90–116.Tanford, C. 1980. The Hydrophobic Effect: Formation of Micelles and Biological Membranes, 2d ed. Wiley.57Tinoco, I., K. Sauer, and J. Wang. 2001. Physical Chemistry—Principles and Applications in Biological Sciences, 4th ed. PrenticeHall.Van Holde, K., W.
Johnson, and P. Ho. 1998. Principles of Physical Biochemistry. Prentice Hall.Voet, D., and J. Voet. 1995. Biochemistry, 2d ed. Wiley.Watson, J. D., et al. 2003. Molecular Biology of the Gene, 5thed. Benjamin-Cummings.Wood, W. B., et al.
1981. Biochemistry: A Problems Approach,2d ed. Benjamin-Cummings.3PROTEIN STRUCTUREAND FUNCTIONElectron density map of the F1-ATPase associated witha ring of 10 c-subunits from the F0 domain of ATPsynthase, a molecular machine that carries out thesynthesis of ATP in eubacteria, chloroplasts, andmitochondria. [Courtesy of Andrew Leslie, MRC Laboratory ofMolecular Biology, Cambridge, UK.]Proteins, the working molecules of a cell, carry out theprogram of activities encoded by genes. This programrequires the coordinated effort of many different typesof proteins, which first evolved as rudimentary moleculesthat facilitated a limited number of chemical reactions.
Gradually, many of these primitive proteins evolved into a widearray of enzymes capable of catalyzing an incredible range ofintracellular and extracellular chemical reactions, with aspeed and specificity that is nearly impossible to attain in atest tube.
With the passage of time, other proteins acquiredspecialized abilities and can be grouped into several broadfunctional classes: structural proteins, which provide structural rigidity to the cell; transport proteins, which control theflow of materials across cellular membranes; regulatory proteins, which act as sensors and switches to control proteinactivity and gene function; signaling proteins, including cellsurface receptors and other proteins that transmit externalsignals to the cell interior; and motor proteins, which causemotion.A key to understanding the functional design of proteinsis the realization that many have “moving” parts and are capable of transmitting various forces and energy in an orderlyfashion.
However, several critical and complex cellprocesses—synthesis of nucleic acids and proteins, signaltransduction, and photosynthesis—are carried out by hugemacromolecular assemblies sometimes referred to as molecular machines.A fundamental goal of molecular cell biologists is to understand how cells carry out various processes essential forlife. A major contribution toward achieving this goal is theidentification of all of an organism’s proteins—that is, a listof the parts that compose the cellular machinery.
The compilation of such lists has become feasible in recent years withthe sequencing of entire genomes—complete sets of genes—of more and more organisms. From a computer analysis ofOUTLINE3.1 Hierarchical Structure of Proteins3.2 Folding, Modification, and Degradationof Proteins3.3 Enzymes and the Chemical Work of Cells3.4 Molecular Motors and the Mechanical Workof Cells3.5 Common Mechanisms for Regulating ProteinFunction3.6 Purifying, Detecting, and Characterizing Proteins5960CHAPTER 3 • Protein Structure and Functiongenome sequences, researchers can deduce the number andprimary structure of the encoded proteins (Chapter 9). Theterm proteome was coined to refer to the entire protein complement of an organism.
For example, the proteome of theyeast Saccharomyces cerevisiae consists of about 6000 different proteins; the human proteome is only about five timesas large, comprising about 32,000 different proteins. Bycomparing protein sequences and structures, scientists canclassify many proteins in an organism’s proteome and deducetheir functions by homology with proteins of known function. Although the three-dimensional structures of relativelyfew proteins are known, the function of a protein whosestructure has not been determined can often be inferred fromits interactions with other proteins, from the effects result(a)MOLECULAR STRUCTUREPrimary (sequence)Secondary (local folding)Tertiary (long-range folding)3.1 Hierarchical Structure of ProteinsQuaternary (multimeric organization)Supramolecular (large-scale assemblies)(b)"off"RegulationSignaling"on"StructureFUNCTIONMovementing from genetically mutating it, from the biochemistry of thecomplex to which it belongs, or from all three.In this chapter, we begin our study of how the structureof a protein gives rise to its function, a theme that recursthroughout this book (Figure 3-1).
The first section examineshow chains of amino acid building blocks are arranged andthe various higher-order folded forms that the chains assume.The next section deals with special proteins that aid in thefolding of proteins, modifications that take place after theprotein chain has been synthesized, and mechanisms that degrade proteins. The third section focuses on proteins as catalysts and reviews the basic properties exhibited by allenzymes. We then introduce molecular motors, which convert chemical energy into motion. The structure and functionof these functional classes of proteins and others are detailedin numerous later chapters. Various mechanisms that cellsuse to control the activity of proteins are covered next. Thechapter concludes with a section on commonly used techniques in the biologist’s tool kit for isolating proteins andcharacterizing their properties.TransportCatalysisAB▲ FIGURE 3-1 Overview of protein structure and function.(a) The linear sequence of amino acids (primary structure) foldsinto helices or sheets (secondary structure) which pack into aglobular or fibrous domain (tertiary structure).
Some individualproteins self-associate into complexes (quaternary structure) thatcan consist of tens to hundreds of subunits (supramolecularassemblies). (b) Proteins display functions that include catalysis ofchemical reactions (enzymes), flow of small molecules and ions(transport), sensing and reaction to the environment (signaling),control of protein activity (regulation), organization of the genome,lipid bilayer membrane, and cytoplasm (structure), and generationof force for movement (motor proteins).
These functions andothers arise from specific binding interactions and conformationalchanges in the structure of a properly folded protein.Although constructed by the polymerization of only 20 different amino acids into linear chains, proteins carry out anincredible array of diverse tasks. A protein chain folds intoa unique shape that is stabilized by noncovalent interactionsbetween regions in the linear sequence of amino acids.
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