John Kuriyan, Boyana Konforti, David Wemmer The field of biochemistry is entering an exciting era in which genomic information is being integrated into molecular-level descriptions of the physical processes that make life possible.
Figure 5.42 Schematic representation of the reactions catalyzed by (a) glutathione reductase and (B) thioredoxin reductase. (A) Glutathione is a tripeptide and, in the oxidized form, two molecules of glutathione are linked by a disulfide bond (the bond between the two orange circles). The enzyme glutathione reductase uses the reducing power of nAdph to break the disulfide bond, releasing oxidized nAdp and reduced glutathione. The first residue in glutathione is a glutamate residue that is linked to the cysteine through its sidechain carboxyl group (denoted γ-Glu). (B) Thioredoxin reductase catalyzes the same reaction, but the disulfide bond that it breaks is within a protein, thioredoxin, that is about 100 residues long.
γ-Glu Cys
Gly
glutathione reductase
S
γ-Glu Cys
γ-Glu Cys
NADPH NADP
Gly
oxidized glutathione
γ-Glu Cys
(A)
(B) 5′
3′
5′
5′
3′
5′
3′
5′
5′
3′
3′ DNA
Figure 2.2 Double-helical structure in DNA and RNA.
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RNA
3′
Gly
reduced glutathione
(B) thioredoxin protein Cys Cys
S
•
thioredoxin reductase
S
Cys
SH
Cys
SH
NADPH NADP
reduced thioredoxin
5.27 Disulfide reductases utilize NaDPh- and FaD-binding domains to catalyze the reduction of disulfide bonds in their substrates 302look at one example of how specialized functions arise from comWe shall now CHAP TERproteins. 7: Entr The proteins we shall discuss are members of bining domains into larger op a class of enzymes known as disulfideyreductases. The general reaction catalyzed Figure 7.8isIm by these enzymes the transfer of electrons from the ring of FADH2 to the tagge Figuflavin a g in g +flu re 7.8in d moof oresfinally and a trsubstrate nicotinamide lecNADP (en a virusring cently to a disulfide bond u opy 32 moleparticle les. In this _v1) 11 cule, resulting and e breakage of the disulfide bond (see _Chapter virus c in the reduction ontain is the recep xperiment, s to (blue st for an explanation of sioxidation andr. reduction). The two substrates we shall conx RNA ructure molec The byglutathione, s)ath u le dye m Figure 5.42). sider are small tripeptide, and thioredoxin, a protein ( olecule at are bou s molec s. Upthat helpndto maintain the redox balance of the cell, and ules caagents Both are reducing n bind to six dye headp iece. W enzymes to onconvert disulfide e viru them from the oxidized to the reduced state. hen flu reductase oresc s view particle ence microsc ed through a ope, e is ach viru oresce observedreductase 5.28fluThioredoxin a s s glutathione n a ce. d spot o and et al., apted f green and P. (Afrom fr a common ancestor, but o G m 200diverged u o, RNA H. Zha 7. With n 1 g evolution 3: 179 permis Spriarose convergent 3–1 ng Harb through si or Pre on from Cold 802, ss.)
A
Important calculations and derivations explained in boxes.
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Qualitative and quantitative end-of-chapter problems, with selected solutions available online to students.
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Chapter summaries, with key concepts delineated by chapter section.
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Further reading and references at the end of each chapter.
Each of the enzymes contains four components: the NADPH, the FAD, the disulfide bond of the enzyme, and the substrate. We shall first discuss how glutathione reductase is constructed, and then compare the structure of this enzyme with that of the related thioredoxin reductase. Although both enzymes utilize very similar dinucleotide-binding domains and are likely to have evolved from a common ancestor, the manner in which theynare is very different. umorganized ber o ep nd mo fisrecfolded The polypeptide chain of glutathione areductase domains lecules tor–liinto gandthree comple we edomain xpect towithare bound core a central adopts (Figure 5.43). First, there is an FAD-binding xes in to eathat see? th chNADPH, recepto e microsco a Rossmann fold. A second dinucleotide-binding domain, which binds Individ pe rc ual rec is inserted into the first domain and se also contains aepRossmann fold. Insertions omplex, wh and ask how para to r at kind comple tion be m of distr any ligxand, of one domain into the structure of another nottwuncommon long as ing poware es caas e e n n ibution re b er of lig ceptorare able to e fold entifie do the insertion occurs within a flexible eexternal both comple id ht mdomains cules w loop, d ic in ro x it th e sc h em in one opes known is large ofFinally, properly and carry out their functions. is not hass the fluoresca C-terminal comdomain, enough icroscope if p le ig e x h n to b the sp t enou (Fig the ste interactions interface domain, is involved in mediating corresponding e detec pwise molecwith ules bthe TML07 ted inofd gh for individ ure 7.9). The atial reducleading .09_v2. bleach reductase, domain in another molecule of glutathione toouthe ndformation ividua resolv ual fl tion to e ed ai 7.9, we by the light, in fluoresce ach recepto lly. Neverthe uorescent m a dimer (Figure 5.44). r nc olle in is beca fer that there as indicated e intensity a can be coun ss, the numb in ted s in use the er a 60 level. fluoresc re two fluore Figure 7.9. In dividual mo by observin sce lec g th ence in tensity nt molecule e example sh ules become s is o wit w reduce 40 d in tw hin the field n in Figure 7.6 P o o f vie ascal’ steps to s the ba w. This for a s triangle de ckgrou 20 nd eries scribe o s f the m binary Consid er a m u event ltiplic ultime recepto ity of s ric rec 0 r outco eptor c ligand complex ca mes om n m tor is in olecules. If w be bound to plex with M no liga bindin e assum depen 0 n d g o d, or it ent of f ligand 2 e that e sites fo th 4 which s bound to a e others, th ach of the lig can be boun r a ligand. Th 6 time (m en th 8 d a re inutes by the e bound liga ceptor com the probab nd binding si to 1, 2, 3, ..., e Figure ) ilit n p m M te 7 fluore .9 Countin (numb ultiplicity W ds can be rea lex is proport y of seeing a s in the rece g the scent rr e (M io p nu m fluore recepto r of positive o , N), where anged amon nal to the n certain numb scenc olecules in mber of u g e u r N m th r tc c e b a regio spots omple . One is of in x (tota omes) and M the numbe e binding site er of ways in n Analog 7.8 is o the sample the fluoresc of l numb r of lig s. This is the to shown o ent bserve u e a is s r n to o g d ta iv f m l numb microsc in Figu th events d in a e the mu flu re ). er of b olecules bou n ltiplicit e number of fluoresc ope, and the orescence inding w y W(M in sites in nd , N) is g ays of obtain of time ence is reco tensity of the ing N h iven by rded a . As th eads in : s e mole region cules in a function a serie a becom bsorb light, s of M c the th e oin toss We can W (M , longer bleached (t ey eventually N es, M u ) = ! ha fl ligand se Equation is redu uoresce), an t is, they no N !( M − molecu 7.7 to w d the in ced. Th N p le stepw e te ri le )! s o te n x b b si e se o dow sw ty un ise red rvation uction this re multip ith different d (N, the nu n the multip s in inte of two gio (7.7) li m n li nsity in fluoresc n shows th schem cities for rece umbers of b ber of positi cities for va a rious n atically ve outc ptors c inding (Adapte ent molecule t there are tw u o o ro in si m n m s te w d o ta b F e in s (M from H ers o igure inin s) to in P P. Guo . Zhan the region ,R entries ascal’s triang 7.10. This g 1 to 10 bind , the numbe receptor co f permis NA 13: 1793 g et al., and . m d r in le corr ing site si –1802 espond iagram is kn The nu the row are s (or ev of events). Th , 2007 Press.) on from Co o m th s w e . ld Spri mial co bers in Pasc e multiplicit to a series o n as Pascal’ nts) are sho e ng Harb With w al’s tria ies for f events s efficien or n tr N posi ngle are each b ts exhib with M iangle. Eac tiv in except omial coeffi it many fasc known as bin e outcomes (N trials, and th h inating cient is for the omial e = 0, 1, n numbe th c rs on th e sum of th umerical rela oefficients. 2, ..., M). The bin e ti e edge s, whic two numbe onships. Fo o r rs imm h are a ll 1. ediately example, above it,
September 2012 1,032 Pages • 900 Illustrations Paperback • 978-0-8153-4188-8 • £50.00
+60 mV
Noteworthy biological examples, many building from seminal discoveries, with key terms highlighted throughout the text.
reductase their active sites
ity
Figure 2.2 (na_60_v1)
•
SH
intens
The Molecules of Life deepens our understanding of how life functions by illuminating the physical principles underpinning many complex biological phenomena, including how nerves transmit signals, the actions of chaperones in protein folding, and how polymerases and ribosomes achieve high fidelity.
Gly
SH
S
oxidized thioredoxin
The Molecules of Life is a new textbook that provides an integrated physical and biochemical foundation for undergraduate students majoring in biology or health sciences. This new generation of molecular biologists and biochemists will harness the tools and insights of physics and chemistry to exploit the emergence of genomics and systems-level information in biology, and will shape the future of medicine. The book integrates fundamental concepts in thermodynamics and kinetics with an introduction to biological mechanism at the level of molecular structure. The central theme is that the ways in which proteins, DNA, and RNA work together in a cell are connected intimately to the structures of these biological macromolecules. The structures, in turn, depend on interactions between the atoms in these molecules, and on the interplay between energy and entropy, which results in the remarkable ability of biological systems to self-assemble and control their own replication.
(A)
Figure 11.27 (TML11.27_v2.ai)
voltage
PHYSICAL AND CHEMICAL PRINCIPLES
KEY FEATURES
ChaPTEr 5: evolutionary Variation in proteins
0 mV –60 mV 0
time B
axon hillock axon
synaptic terminals
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The Molecules of Life
230
0 mV –60 mV 0
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Figure 11.27 Transmission of an action potential down on axon
CONTENTS Part I. Biological Molecules
Part IV. Molecular Interactions
1. 2. 3. 4. 5.
12. Molecular Recognition 13. Specificity of Macromolecular Recognition 14. Allostery
From Genes to RNA to Proteins Nucleic Acid Structure Glycans and Lipids Protein Structure Evolutionary Variation in Proteins
16. Principles of Enzyme Catalysis 17. Diffusion and Transport
Part VI. Assembly and Activity 18. Folding 19. Fidelity in DNA and Protein Synthesis
Part V. Kinetics and Catalysis 15. Rates of Molecular Processes
Part II. Energy and Entropy 6. 7. 8.
Energy and Intermolecular Forces Entropy Linking Energy and Entropy
Figure 18.41 (folding_groel_v1) 1KP8 (A)
intermediate domain
Part III. Free Energy 9. Free Energy 10. Chemical Potential and the Drive to Equilibrium 11. Voltages and Free Energy
apical domain
(B) αH hydrophobic sidechains
hydrophobic sidechains face inner chamber
hydrophobic sidechains pulled away from inner chamber
αI ATP
equatorial domain
GroEL
A sample chapter and detailed table of contents are available at
(C)
GroEL–GroES
Figure 18.41 Conformational changes in GroEL-GroES.
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ONLINE RESOURCES Online resources are available for students and for instructors who are adopting or recommending the book for their course at www.garlandscience.com/TMOL.
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• Artwork in JPEG & PowerPoint® formats. • Movies and animations. • Solutions to end-of-chapter problems.
Explore a New Approach to Physical Chemistry for the Life Sciences
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For students:
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THE AUTHORS JOHN KURIYAN is Professor of Molecular and Cell Biology and of Chemistry at the University of California, Berkeley. He began his career at Rockefeller University, New York and has been an Investigator of the Howard Hughes Medical Institute since 1990. His laboratory uses x-ray crystallography to determine the three-dimensional structures of proteins involved in signaling and replication, as well as biochemical, biophysical, and computational analyses to elucidate mechanisms. Kuriyan was elected to the US National Academy of Sciences in 2001.
PRAISE FOR THE MOLECULES OF LIFE BOYANA KONFORTI is the launch Editor of Cell Reports, an open-access journal that covers all of biology with a focus on short papers. Konforti earned her PhD at Stanford University in the Biochemistry Department with Ronald W. Davis studying the mechanism of DNA recombination. Her postdoctoral studies at Rockefeller University with Magda Konarska, and Columbia University with Anna Pyle were on the mechanisms of RNA splicing. Konforti has been a professional editor for over 13 years; most recently she was Chief Editor of Nature Structural & Molecular Biology.
DAVID WEMMER is Professor of Chemistry at the University of California, Berkeley and has served as Vice Chair, Assistant Dean, and Executive Associate Dean since joining the faculty in 1985. His research in structural biology uses magnetic resonance methods to investigate the structure of proteins and DNA toward a better understanding of how these molecules function. Systems studied include DNA-ligand complexes, covalent DNA adducts, protein-DNA complexes, and diverse proteins involved in cellular regulatory processes. Wemmer is a Fellow of the AAAS and a member of Phi Kappa Phi and Sigma Xi.
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