Biochemistry, 4th Edition P1 pptx

Grisham University of Virginia With molecular graphic images by Michal Sabat, University of Virginia... Text Designer: Lisa Devendish Photo Researcher: Marcy Lunetta Illustrators: Micha

Physical Constants

*Other values of R: 1.9872 cal/K  mol  0.082 liter  atm/K  mol.

†1 coulomb  1 J/V.

Conversion Factors

Pressure: 1 atm 760 torr  14.696 psi

1 torr 1 mm Hg Temperature: K °C  273

C (5/9)(°F  32) Volume: 1 liter 1  103m3 1000 cm3

Energy: 1 Joule 107ergs 0.239 cal

1 cal 4.184 Joule

Length: 1 nm 10 Å  1 7cm

Mass: 1 kg 1000 g  2.2 lb

1 lb 453.6 g

Useful Equations

The Henderson–Hasselbalch Equation

pH pKa log([A]/[HA])

The Michaelis–Menten Equation

v  Vmax[S]/(K m [S])

Temperature Dependence of the Equilibrium Constant

H °  Rd(ln Keq)/d(1/T)

Free Energy Change under Non-Standard-State Conditions

G  G °  RT ln ([C][D]/[A][B])

Free Energy Change and Standard Reduction Potential

G °  nᏲᏱ°

Reduction Potentials in a Redox Reaction

Ᏹ° Ᏹ°(acceptor) Ᏹ°(donor) The Proton-Motive Force

p    (2.3 RT/Ᏺ)pH

Passive Diffusion of a Charged Species

G  G2 G1 RT ln(C2/C1) ZᏲ

The Standard Genetic Code

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Icons and Colors in Illustrations

The following symbols and colors are used in this text to help in illustrating structures,

reactions, and biochemical principles.

Inorganic phosphate and pyrophosphate are sometimes symbolized by the following icons:

Elements:

Sugars:

Nucleotides:

Amino acids:

Enzymes:

= Oxygen = Nitrogen = Phosphorus = Sulfur = Carbon = Chlorine

= Adenine

= Cytosine

= Non-polar/hydrophobic = Polar/uncharged = Acidic = Basic

Glucose Galactose Mannose Fructose Ribose

P

Inorganic phosphate (Pi) Pyrophosphate (PPi)

P P

= Enzyme activation

= Enzyme inhibition or inactivation

= Enzyme = Enzyme Enzymenames are printed in red

+

Phosphoryl group

These colors are internally consistent within reactions and are generally consistent

within the scope of a chapter or treatment of a particular topic

Red arrows are used to indicate nucleophilic attack

Some examples:

P

–O

–O

O

Hydroxyl group

OH

Amino group

NH3+

Carboxyl group COO–

In reactions, blocks of color over parts of molecular structures are used so that discrete parts of the

reaction can be easily followed from one intermediate to another, making it easy to see where the

reactants originate and how the products are produced

E

F O U RT H E D I T I O N

Reginald H Garrett • Charles M Grisham

University of Virginia With molecular graphic images

by Michal Sabat, University of Virginia

Biochemistry, Fourth Edition

Reginald H Garrett, Charles M Grisham

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1 2 3 4 5 6 7 12 11 10 09 08

To Georgia

To Rosemary

About the Authors

Reginald H Garrettwas educated in the Baltimore city public

schools and at the Johns Hopkins University, where he received

his Ph.D in biology in 1968 Since that time, he has been at the

University of Virginia, where he is currently Professor of

Biol-ogy He is the author of previous editions of Biochemistry, as well

as Principles of Biochemistry (Cengage, Brooks/Cole), and

nu-merous papers and review articles on the biochemical, genetic,

and molecular biological aspects of inorganic nitrogen

metabo-lism His research interests focused on the pathway of nitrate

as-similation in filamentous fungi His investigations contributed

substantially to our understanding of the enzymology, genetics,

and regulation of this major pathway of biological nitrogen

ac-quisition More recently, he has collaborated in systems

ap-proaches to the metabolic basis of nutrition-related diseases

His research has been supported by the National Institutes

of Health, the National Science Foundation, and private

indus-try He is a former Fulbright Scholar at the Universität fur

Bodenkultur in Vienna, Austria, and served as Visiting Scholar at

the University of Cambridge on two separate occasions During

the second, he was Thomas Jefferson Visiting Fellow in Downing

College Recently, he was Professeur Invité at the Université Paul

Sabatier/Toulouse III and the Centre National de la Recherche

Scientifique, Institute for Pharmacology and Structural Biology

in France He has taught biochemistry at the University of

Vir-ginia for more than 40 years He is a member of the American

Society for Biochemistry and Molecular Biology

Charles M Grishamwas born and raised in Minneapolis, Min-nesota, and educated at Benilde High School He received his B.S in chemistry from the Illinois Institute of Technology in

1969 and his Ph.D in chemistry from the University of Min-nesota in 1973 Following a postdoctoral appointment at the Institute for Cancer Research in Philadelphia, he joined the faculty of the University of Virginia, where he is Professor of

Chemistry He is the author of previous editions of Biochemistry and Principles of Biochemistry (Cengage, Brooks/Cole), and

nu-merous papers and review articles on active transport of sodium, potassium, and calcium in mammalian systems, on protein kinase C, and on the applications of NMR and EPR spectroscopy to the study of biological systems He has also

au-thored Interactive Biochemistry CD-ROM and Workbook, a tutorial

CD for students His work has been supported by the National Institutes of Health, the National Science Foundation, the Muscular Dystrophy Association of America, the Research Cor-poration, the American Heart Association, and the American Chemical Society He is a Research Career Development Awardee of the National Institutes of Health, and in 1983 and

1984 he was a Visiting Scientist at the Aarhus University Insti-tute of Physiology Denmark In 1999, he was Knapp Professor

of Chemistry at the University of San Diego He has taught bio-chemistry and physical bio-chemistry at the University of Virginia for 34 years He is a member of the American Society for Bio-chemistry and Molecular Biology

Contents in Brief

Part 1 Molecular Components of Cells

1 The Facts of Life: Chemistry Is the Logic of Biological Phenomena 1

2 Water: The Medium of Life 28

3 Thermodynamics of Biological Systems 48

4 Amino Acids 70

5 Proteins: Their Primary Structure and Biological Functions 93

6 Proteins: Secondary, Tertiary, and Quaternary Structure 134

7 Carbohydrates and Glycoconjugates of Cell Surfaces 181

8 Lipids 219

9 Membranes and Membrane Transport 242

10 Nucleotides and Nucleic Acids 291

11 Structure of Nucleic Acids 316

12 Recombinant DNA: Cloning and Creation of Chimeric Genes 354

Part 2 Protein Dynamics

13 Enzymes—Kinetics and Specificity 382

14 Mechanisms of Enzyme Action 419

15 Enzyme Regulation 452

16 Molecular Motors 481

Part 3 Metabolism and Its Regulation

17 Metabolism: An Overview 511

18 Glycolysis 535

19 The Tricarboxylic Acid Cycle 563

20 Electron Transport and Oxidative Phosphorylation 592

21 Photosynthesis 630

22 Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway 662

23 Fatty Acid Catabolism 697

24 Lipid Biosynthesis 722

25 Nitrogen Acquisition and Amino Acid Metabolism 768

26 Synthesis and Degradation of Nucleotides 813

27 Metabolic Integration and Organ Specialization 839

Part 4 Information Transfer

28 DNA Metabolism: Replication, Recombination, and Repair 862

29 Transcription and the Regulation of Gene Expression 906

30 Protein Synthesis 952

31 Completing the Protein Life Cycle: Folding, Processing, and Degradation 987

32 The Reception and Transmission of Extracellular Information 1008

Abbreviated Answers to Problems A-1

Index I-1

Detailed Contents

Molecular Components of Cells

1 The Facts of Life: Chemistry Is the Logic

of Biological Phenomena 1

1.1 What Are the Distinctive Properties of Living

Systems? 1

1.2 What Kinds of Molecules Are Biomolecules? 4

Biomolecules Are Carbon Compounds 4

1.3 What Is the Structural Organization of Complex

Biomolecules? 5

Metabolites Are Used to Form the Building Blocks

of Macromolecules 5

Organelles Represent a Higher Order in Biomolecular

Organization 7

Membranes Are Supramolecular Assemblies That

Define the Boundaries of Cells 9

The Unit of Life Is the Cell 9

1.4 How Do the Properties of Biomolecules Reflect

Their Fitness to the Living Condition? 9

Biological Macromolecules and Their Building Blocks

Have a “Sense” or Directionality 10

Biological Macromolecules Are Informational 10

Biomolecules Have Characteristic Three-Dimensional

Architecture 11

Weak Forces Maintain Biological Structure

and Determine Biomolecular Interactions 11

Van der Waals Attractive Forces Play an Important

Role in Biomolecular Interactions 12

Hydrogen Bonds Are Important in Biomolecular

Interactions 12

The Defining Concept of Biochemistry Is “Molecular

Recognition Through Structural Complementarity” 14

Biomolecular Recognition Is Mediated by Weak

Chemical Forces 14

Weak Forces Restrict Organisms to a Narrow Range

of Environmental Conditions 15

Enzymes Catalyze Metabolic Reactions 15

The Time Scale of Life 16

1.5 What Is the Organization and Structure of Cells? 17

The Evolution of Early Cells Gave Rise to Eubacteria,

Archaea, and Eukaryotes 17

How Many Genes Does a Cell Need? 18

Archaea and Bacteria Have a Relatively Simple

Structural Organization 19

Part 1 The Structural Organization of Eukaryotic Cells Is More

Complex Than That of Prokaryotic Cells 19

1.6 What Are Viruses? 21

SUMMARY 25 PROBLEMS 26 FURTHER READING 27

2 Water: The Medium of Life 28

2.1 What Are the Properties of Water? 28

Water Has Unusual Properties 28 Hydrogen Bonding in Water Is Key to Its Properties 29 The Structure of Ice Is Based On H-Bond Formation 29 Molecular Interactions in Liquid Water Are Based

on H Bonds 30 The Solvent Properties of Water Derive from Its Polar Nature 30

Water Can Ionize to Form Hand OH 34

2.2 What Is pH? 35

Strong Electrolytes Dissociate Completely in Water 36 Weak Electrolytes Are Substances That Dissociate Only Slightly in Water 37

The Henderson–Hasselbalch Equation Describes the Dissociation of a Weak Acid In the Presence

of Its Conjugate Base 38 Titration Curves Illustrate the Progressive Dissociation

of a Weak Acid 39 Phosphoric Acid Has Three Dissociable H 40

2.3 What Are Buffers, and What Do They Do? 41

The Phosphate Buffer System Is a Major Intracellular Buffering System 41

Dissociation of the Histidine–Imidazole Group Also Serves as an Intracellular Buffering System 42

“Good” Buffers Are Buffers Useful Within Physiological pH Ranges 42

HUMAN BIOCHEMISTRY:The Bicarbonate Buffer System

of Blood Plasma 43

HUMAN BIOCHEMISTRY:Blood pH and Respiration 44

2.4 What Properties of Water Give It a Unique Role

in the Environment? 44

SUMMARY 45 PROBLEMS 45 FURTHER READING 47