BIOCHEM Wkbook - The Foundations of Biochemistry...

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Unformatted text preview: The Foundations of Biochemistry STEP~BY-STEP GUIDE Major Concepts All cells have common structural elements. All cells are defined by a plasma membrane, which separates the contents of a cell from its surroundings and is a barrier to diffusion. All cells are divided into two major internal regions, the cytoplasm and a nu— clear region. The cytoplasm contains soluble en— zymes, metabolites, and cellular organelles. It is a very active and orgaruzed place, with constantly changing interactions occurring between its components. The contacts between biomolecules are primarily weak, noncovaient interactions, which collectively produce complex structure and functions. The nuclear re~ ' gion contains primarily DNA and associated proteins. .2 Cells can be classified according to the complement of cellular membranes and the complexity of the nu- biomoiecuies are derivatives of hydrocarbons with a variety of attached functional groups. These func~ tional groups determine the chemical behavior of bio- molecules. Biochemistry is three-dimensional. In addition to the functional groups, the overall shape of a biomoiecule greatly affects the types of interac- tions in which it can participate. Most biomolecules are asymmetric. Typically, only one of the possible (chiral) forms is found in living organisms. interac- tions between many biomolecules (cg, enzymes and their substrates) depend upon their ability to differ— entiate between stereoisomers. Living organisms are interdependent; they ex- change energy and matter with each other and the environment. __clear region. ' There are two domains of single~celled nucroorgan- isms, Bacteria and Archaea, which differ in specific biochemical characteristics. Eukaryotes generally are larger than prokaryotes and include all protists, fungi, plants, and animais. The nuclear region of the _. single—celled organisms, the nucleoid, has no mem- brane to separate it from the rest of the cytoplasm. In addition, there are no other internal membranes and no internal organelles. Eukaryotic cells have plasma embraces as well as many membrane—bounded in~ raceliular organelles and a membranebounded nu— Idem. Celts can be alternatively classified based upon " comes of energy and carbon. " matter is composed of low atomic weight laments. fly pgen, oxygen, nitrogen, and carbon are the most ____.un ant elements in biomolecules. The bonding ver- ,___of carbon makes it the most important and _._e.1nlngjclement in biochemical compounds. Most The sun is the ultimate source of (almost) all energy used ‘oy organisms. The anabolic reactions that use en- ergy to form biological macromolecules and the cata- bolic reactions that liberate energy constitute the metabolic pathways. Most of these reactions require enzymes in order to proceed at useful rates; these bio logical catalysts lower the activation energy. Meta~ bolic reactions can be linked through ATP, which can capture or release stored energy as needed by cells. A thermodynamic system can be a single, simple chemical reaction or an entire organism. The transfer of energy in a single reaction or in an or- ganism can be described by three thermodynamic quantities: (Gibbs) free energy, G; enthalpy, H; and entropy, S. These quantities are related by the equation communes) pter l The Foundations of Biochemistry 2 Che absolute temperature (in degrees where T is the change in free energy Kelvin, or K). AG describes the lipids, proteins, and carbo that occurs in a chemical reaction. partmentalize cells, whereas chromosomes (supra— molecular complexes of DNA and proteins) encode aneonsly only if AG nega~ ‘ and store genetic information. Btornolecnles first arose by chemical evolution. ergy. Reactions are at eqmlihrium if AG r- O. The conditions under which his arose on Earth can» not be absolutely determined, but chemical evolution The standard free-energy change, AG” is a physical constant and can be calculated from the equilibrium can be simulated in simplicity of the chemical reactions that probably led constant, K1, 1 AG” 3 #RT an; . Cl Cl urn the rates of the forward to the formation of small biomolecules, and eventually to macromolecules, the evolution of life seems to be For a system at equilibri and reverse reactions are equal; no further not change possible on other planets. occurs in the system. the laboratory. Considering the Information needeafor theformalion anafanclt‘on of what to R 8 vi 9 W all living organisms is contained in their genetic Part of this chapter is a 1' material, which is usually DNA. and 0f DNA genie chemical principles. You may find it helpful to The linear sequence of nucleotides in a sh: DTOVideS iflfflmaiiflfi SPBCi-‘fyifig the l'meal‘ Sequence consult a good inorganic or organic chemistry text for ems made by an Orgafir additional background information. Using this and of amino acids in all the prot 181’“- In turn, the complemeflt 0f 91131983115 determines other texts as sources, make sure that you thoroughly definitions and concepts. the repertoire of metabolic reactions and functions understand the fguomg that an organism can perform. (In some viruses, the ‘ . I s Covalent bonds and their relationship to the num- ber of unpaired electrons. genetic material is RNA.) * The significance of the atomic numbers. Biological systems have a hierarchy of structure. ' G Stereoisomerism; chirality. A relatively small 3 used to construct 'macro- . Electronegatmty' are the building block n be arranged - Nucleophilic and electrophili molecules. Macromolecules can the into supramolecular complexes. Different classes of eview of organic and inor- c centers in reactions. on» Topics for Discussion of the following questio ortant points of the chapter. ns, especially in the context of study group discussions, should help you Answering each derstand the imp 1.1 Cellular Foundations 1. What distmgui shes living organisms from inanimate obiects‘? Cells Are the Structural and Functional Units of All living Organisms n scale. To put cells into per» 2. Cellular dimensions are difficult to imagine on a home leshows the relative sizes of spective it is helpful to magnify them. The following tab cells and their components magnified 10,000-fold (from micrometer to millimeter hen magnified 10,000-fold, is about the size of a large scale). A typical eukaryotic cell, w with familiar objects that are approximately the sizes platter. Complete the table below indicated and assemble them on a large serving platter. Stepry-Step Guide 3 ""‘"“':'fl:mm;um:mwm% "mmw'm-JmLm-r-mmf “27.12:: » a | CeEI or Celiular Component Size at 10,000 x (mm) Equivalent Size Object l VI . § oak. 3;; H” ‘. Lysosome 10 \ ; _ r — ‘Q‘w are-e fl flagellum, diameter 0.35 2 I ; r i figsiefii m is:er Nacleoid 10 . ~ ' g - mi“ film“ 1 if = t' :1 10—100 . i ChEoroplast 20 x80 paagvmo g algal i FE ii ‘ . I f M Nucieas 100 Ea”? (31 @{Ms $639 3% Eukaryotic cell 500 (50 cm} Large serving piatter SE ii i Cellular Dimensions Are Limited by Diffusion 3. What sets the lower limit of ceii size? The upper limit? ‘ There Are Three Distinct Domains of Life 4. Why are eukaryotes considered to be more closeiy related to the archaea than to bacteria? , wacg Emerge} 06+ “the eree. in “first $633 we? fif‘i’rffi .33. ‘* e ‘< r a I": Q where. {at} time! or; s2 5. Why are cyanobacteria considered among the most self-sufficient groups of organisms? Escherichia coii ls the Most-Studied Bacterium 6. What are the structurai features of prokaryotes that distinguish them from eukaryotes, which are discussed in the next section of the text? “ Nucleoiei , loci: or? erfiaeehes E ukaryatic Cells Have a Variety of Membranaus Organelles, Which Can Be Isolated for Study ‘7. What might be an advantage of compartmentalization of coils? . r . ~ Miami: "for are @am‘z‘ro meager“ aa stair? o: 5? iii-7‘ i :‘ae‘i LS dis—Eage— §roeoe its 154141 We? _ 5 8. What are the differing characteristics of organelles that aiiow researchers to separate and isolate there. from. one another? ‘ 1 ‘ i ‘ g 'l » The egsaeiier veg whale ; ‘ivt‘w‘lj 4 Chapter 1 The Foundations of Biochemistry The Cytoplasm ls Organized by Gyroskeleton and Is Highly Dynamic proteins? What are the functions of the cy— 9. What are the three classes of cytoskeletai toskeleton? Aggy, ) m; army‘iflmgxfi a. 2, 9.5. (xv/166415,? 10. How do the organelles and cytoskeieton interact? " mow couoicmifi Cells Build Supramolecular Structures 11. What are the bonds and/or interactions that are important at each of the three levels of cell structure? In Vitro Studios May Overlook important interactions among Molecules 12. What are the advantages, and the disadvantages, of the in vitro approach to studying biomoiecules‘? , l , _ L .. ,r . .- air a Can cash; {daemon/wowsonata ISU‘D’flf‘éh oiosvs.?5€a:‘.. ion/fit" W33 W I . See :th orcdivl'fi in wit/0: 1.2 Chemical Foundations 13. What are the four mo 10,0,H3C) 14. What is the importance of tr at common eiements in living organisms? . ace eiements to ordinal life? Biomolecules Are Compounds of Carbon with a Variety of Functional Groups 15. What is meant by the “bonding versatility" of carbon? h I" C the “fart-v3 6'3 s" v ' I ., . t. . 16. What factors influence the strength, 1ength, and rotation of carbon bonds? .3 5' {’27: 5: 8, ~ The as a; imdeI C ,3, a,3,,;,.:,,,ig, [my a so do ma" 17'. Review the common fazrdiies of functional groups or organic compounds that are en~ countered in biomolecoles. Cells Contain a Universal Set of Small Molecules 18. What is the definition of tabolome? , " , a I] , ., 3‘5:ch CGHBC‘Hon o 3W1 61‘ H mgificmias m “31%: w C Macromolecules Are the Major Constituents of Cells 19. at are macromoiecoles a how are the cate rized‘? ~— (migratch wit 4: 7&10‘00 Motirflrv’aégr W Of 0‘ «from gimrftrr moifcuffs (9. Proteins and nucleic acids are always considered Mormational macromoiecules, while polysaccharides are not always considered so; why is this the case? 1.3 Physical Foundations it Step—By-Step Guide 5 Three-Dimensional Structure is Described by Configuration and Conformation 21. What are the three types of modeis that are used to represent the three-dimensional structure of moiecules? What different kinds of information are provided by each type ofmodel? Skeletal l; boil } s'lfck! Sidboiqr 22. What is the difference betweena diastereomer and an enantiomer? ennnnemer‘. rm rror image 0E2: m5+a'refiwt€f: non-mirror“ imajéS Louis Pasteur and Optical Activity: In Vino, Verna; 23. Use the structural formulas of Pasteur’s two forms of tartaric acid to foliow the dew scription of RS nomenclature in the text. 24. How does the high potential energy of the eclipsed conformation affect the dynamics of ethane? There {5‘ gruff: rotation fihdm‘i fit «:31. Qwé {amwaf‘ .lsimc‘aerrc Casey”. pr. moff' stable 25. What are the advantages and disadvantages of the techniques of xnray crystailography and NMR spectroscopy? interactions between Biomoleouies Are Stereospeoific 26. Why do cells produce only one form of a chiral compound rather than a racemic ndxture? bwL‘l’f Sl‘m'ilar/ Chg‘m‘i CQMPOMWdf \Mli’tl "invifi‘r' CeisfiWIS‘fii‘w, Om‘U Owfl gap-{wt ear/(j Prone, restful ,‘WUQ {grew}: as”! v’l Living Organisms Exist in a Dynamic Steady State, Never at Equilibrium with Their Surroundings f: as 5) ( 5:5 9 27. What is the difference between dynamic steady state and equilibrium? Make sure you understand these terms; the concepts vviil recur constantly throu heat the text. 953 f yfigifl’f‘fii‘diwfi come. €44 mug Ll Cerifiw mp‘fi‘an dz flogpmgfltcmfu‘m vaé/g Brganisms Transform Energy and Matter from Their Surroundings 28c Is it possible to design a ciosed system that incorporates living organisms? Why or Why not? He harness la aqua agentst also pie-pend an 44¢ merit-r M fin: Mailer“? it“) 3 e i n/extreci energy" The Flow of Electrons Provides Energy for Organisms 29. What happens (in terms of ~gestaronlrjlow) to the reactant that is oxidized? a Electrovws a re lgg I (at; Tee oedoii ace! resent-eat“ Creating and Maintaining Order Requires Work and Energy 30. What are the qualities thzat determine the free energy (G) in a system? .3 A . 2 Vin ctr“ ~ re or”: that uteri" “3 1639mm [L 53:3}??? ‘53“) 31. How are cells able to synthesize polymers if such reactions are themodynamicaiiy unfavo able? \ . y * ,‘Lgmohrwgc‘a'hcmf are Winona Cal/«Mao! wile QW’ZfiC-T‘WC GweS‘. W‘fl m6“? 4 C) i Chapter 1 “the Foundations of Biochemistry Energy Coupling Links Reactions in Biology energy transductions, and entropy, explain the following 32. In terms of potential energy, moving, excreting. Where do the sun and ATP fit normal human daily activities: eating, into this scheme? Entropy: The Advantages of Being Disorganized 33. Does the oxidation of glucose represent an increase or decrease in entropy have a positive or negative AG? ? Does it Jim and AG" auantify a Reaction’s Tendency to Proceed Spontaneously 34. What are the two ways of expressing a driving force on a reaction? Enzymes Promote Sequences of Chemical Reactions 35. Why are enzymes essential in biochemical reactions?a 1. - of * "Raga 5538595; map {truce-lows Garter. sweeter" “Serif 36. How do enz es overcome activation barriers? a 0 fl- ,4; "meg he} hesitates ‘m piece we” aim-"‘5 a 37. Why is the option of increasing temperature to overcome these barriers not possibie in livin coils? ~ a _,. ‘ , m, ' - l a separatism Inctteét Yiéflifieii‘iqfi “5‘53 tisueiamé if? 1M?) be daegci‘t’l’vafirgfe‘a’tfi’l “to little it 653-3533"- Metabollsm ls Regulated to Achieve Balance and Economy 38. What would be the negative consequences to the celi of making too much of one metabolite? 1.4 Genetic Foundations Genetic Continuity ls Vested in Single DNA Molecules 39. Why can we not describe the “average” behavior of a DNA molecuie? The Structure of DNA Allows for its Replication and Repair with Near-Perfect Fidelity 40. How do complementary strands assure continuity of information? The Linear Sequence in DNA Encodes Proteins with Three-Dimensional Structures 41. How are the instructions contained in the linear sequence of DNA translated into a three~dimensional enzyme or structural protein? Cent mi 5! ego/m Step-By—Step Guide 7 42. What forces contribute to the three-dimensional structure? non C,an {391+ 15 Evolutionary Foundations Changes in the Hereditary instructions Allow Evolution 43. How can a change in the DNA instructions affect the final form of a protein? Biomolecules First Arose by Chemical Evolution 44. Under what environmental conditions are the first biomolecules thought to have been formed? 45. What energy sources may have been available to drive prehiotic evolntlon‘? = RNA or Related Precursors May Have Been the First Genes and Catalysts 46. What are the lines of evidence suggesting that RNA or a similar molecule was both the first gene and the first catalyst? Biological Evolution Began More Than Three and a Half Billion Years Ago 47. How might it be possibie to determine if a fossil carbon compound were of biological origin? The First Cell Probably Used inorganic Fuels 48. Why is it likely that autotrophs evolved only after the appearance of heterotrophs? Euiraryotic Cells Evolved from Simple Precursors in Several Stages 49. How are nuclei thought to have evolved? Molecular Anatomy Reveals Evolutionary Relationships 50. Compare the definitions of homologs, paralogs, and orthologs. Functional Genomics Shows the Allocations of Genes to Specific Cellular Processes 51. What is the difference between E. coir; and H. sapie'ns in terms of percentage of genes devoted to membrane transporters? Genomic Comparisons Have lncreasing importance in Human Biology and Medicine 52. What would you predict would be the difference between a chimpanzee andH. sapiens in terms of percentage of genes devoted to membrane transporters? 8 Chapter 1 The Foundations of Biochemistry Discussion Questions for Study Groups v Why are the six compiex characteristics detailed in the first part of this chapter necessary to define “life” completely? 0 The fossil record indicates that organisms evolved mechanisms to adapt to dramatic changes in the composition of Earth’s atmosphere. How can we use this information in evaluating the consequences of modem giobal weaning? - Why would the development of impermeable layers of lipid—like compounds have favored continued chemical evolution? . .vawMWme-w-ru - - - «WWW SELF-TEST Do You Know the Terms? AGRflSS 1. 11. or supramolecular complex. 19. Describes a reaction for which the freemenergy change (AG) is negative. 7. 21. The internal components of cells and the aqueous solution in which they are suspended. 9. 22. Molecules having the same composition and order of atomic connections, but different spatial arrangements 10. among the atoms. . 13. DOWN 15- 1. Mitochondria are thought to have evolved from bacteria ' -_ - that formed associations with the ancestors of 16. - - modern eukaryotes. Proteins encoded by two genes that share similar 18. _ I. nucleotide sequences. - Enzymes enhance the rate of chemical reactions by 20. 12. 14. 17. : lowering the G; free . Amino acids are the subunits of proteins. . The randomness of the components of a chemicai system; S. Amino acid is to as monomer is to pciymer. . The complete set of genetic material needed for the growth and deveiopment of an organism. Glycine is the only amino acid lacking an phi ml? asymmetric or carbon. Reactions requiring an input of energy from the surroundings are thermic reactions. In - reactions, electrons ‘ are transferred from a more reduced to a more oxidized mole- cole. A type of weak inter~ action that stabilizes the native conforma— tion of a biomolecizle EMEEEE g N M I Eflflflfififl EEEEEEM V fiflfléfififififlflfil 2%“ fl Eflflfifigfififi a r EEEEEEEEQMEEE energy that constitutes an energy barrier between reactants and products. flfififlfiflflflfiflfl 1 e o Self»Test 9 W mamamanag bflflflfl! E H An equirnolar mixture of the D and L isomers of an optically active compound is a mixture. Describes a reaction for which the free-energy change {AG} is positive. Structural components of membranes; energy storage molecuies. The energy or heat content of a system; H. Organisms that can synthesize most of the molecules necessary for their growth from simple compounds, such as (302 and NH3. A system that exchanges energy and material with its surroundings is said to be . Membrane-bounded compartment, present only in eukaryotes, that contains chromosomes. »synthetic organisms convert solar energy into ' ATP. 10 Chapter 1 The Foundations of Biochemistry ANSWERS Do You Know the Terms? ACROSS 1. 4. 5. 6. 8. 11. 12. 14. 17. 19. 21. 22. energy monomeric entropy protein genome chiral endo ozddation-reduction noncovaient exergonic cytopiasm stereoisomers DOWN 1. 2. 3. 7. 9. 10. .13. 15. 16. 18. 20. endosymbiotic homoiogs activation racemic endergonic lipids enthalpy autotrophs open nucieus photo ...
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BIOCHEM Wkbook - The Foundations of Biochemistry...

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