Nutritional Biochemistry, Second Edition_1 pptx

In oxygen gas O2, the two oxygen atoms share electrons from their 2py and 2pz orbitals to form two covalent bonds between the same two atoms.. The other atom involved in the hydrogen bon

PREFACE

Nutrition involves the relationship of food and nutrients to health Biochemistry is the science of the chemistry of living organisms As implied by the title, this book emphasizes the overlap between problems of nutrition and the techniques of biochemistry

The nutritional sciences also include many aspects of related disciplines such as physiolog~ food chemistr3~ toxicolog~ pediatrics, and public health Thus, any given problem in the nutritional sciences may also be a problem in one of these disciplines Nevertheless, nutrition is a unique discipline because of its specific goal, that is, improving human health by understanding the role of diet and supplying that knowledge in everyday living

Nutritional sciences employ various experimental techniques The methods used to assess a deficiency can also be used to determine the requirement for a given nutrient Dietary deficient36 a technique applied to animals and microorgan- isms, was used in the discovery of vitamins and in proving the essential nature of certain amino acids and lipids This book features a strong emphasis on the tech- niques used to assess both requirements and deficiencies Two of the most impor- tant techniques, those involving nitrogen balance and the respiratory quotient, are covered in some detail

The book focuses on the details of two or three aspects of problems related to each selected topic Clinical and research data are used to illustrate these problems, and case studies are frequently presented Emphasis on primary data is intended

to encourage readers to use their own trained judgment when examining data from the literature as well as data from their own research experience

The ability to organize facts into a hierarchy of importance is useful in under- standing the biological sciences This book encourages the researcher to employ this method of organization For example, the order of use of energy fuels is described in the chapter on regulation of energy metabolism The order of appear- ance of signs of folate deficiency is detailed in the chapter on vitamins The book also encourages the researcher to accept the potential value of data that are am- biguous or apparently contradictory For example, the chapter on digestion shows that a barely detectable increase in plasma secretin levels can be physiologically

~ 1 7 6 1 7 6

xiv Preface

relevant The section on starvation reveals that the body may suffer from signs of vitamin A deficiency even though substantial amounts of the vitamin are stored in the liver The section on fiber explains how an undigestible nutrient supplies vital energy to cells of the h u m a n body

Some of the dreaded nutritional diseases of the p a s t - - such as scurv~ pellagra, and perniciOus anemia m are discussed in this book Such contemporary problems

as infectious diarrhea, xerophthalmia, protein/energy malnutrition, and folate deficiency are discussed, as are diabetes and cardiovascular disease, two of the most significant nutrition-related diseases The last two conditions can be control- led in part by dietary intervention

This book stresses the importance of nutritional interactions Some nutrients are closely related and usually discussed together Some are antagonistic to each other, whereas others act synergistically Examples of uniquely related nutrients are bean and rice protein, saturated and monounsaturated fatty acids, folate and vitamin B12, vitamin E and polyunsaturated fatty acids, and calcium and vitamin D Some closely related biological molecules are discussed, including insulin and glucagon, cholecystokinin and secretin, and low- and high-density lipoproteins Interactions involving multiple organ systems and multiple cell types are stressed More em- phasis is placed on interorgan relationships than in typical biochemistry textbooks Drugs that influence nutrient metabolism are discussed in various sections These drugs include lovastatin, pravastatin, omeprazole, dilantin, methotrexate, allopurinol, warfarin, furosemide, thiouracil, and diphosphonate Alcohol is also discussed in this context because, depending on its intake, it functions as a food, drug, or toxin

The recommended dietary allowances (RDAs) for various nutrients are dis- cussed RDAs are the quantities in the diet of all nutrients required to maintain

h u m a n health RDAs are established by the Food and Nutrition Board of the National Academy of Sciences, and are published by the National Academy Press The RDA values are revised periodically on the basis of new scientific evidence RDAs are used to define a relationship between various h u m a n populations and the nutrients required by the h u m a n body at various stages of life They are intended to serve as a basis for evaluating the adequacy of diets of groups of people rather than of individuals A comparison between the RDA for a specific nutrient and individual intake of that nutrient can indicate the probability or risk of a deficiency in that nutrient The actual nutritional status with respect to the nutrient can be assessed only by appropriate tests These tests are usually of a biochemical nature, but also may be hematological or histological Nutrient RDAs have been determined for men, women, and children of different ages In most cases, the RDA differs with body weight and, in some cases, with gender For convenience, RDA values are sometimes expressed in terms of an ideal or reference subject such as

"the 70-kg man" or "the 55-kg woman." The current RDAs for all nutrients are listed on the inside back cover RDAs have not been set for a number of required

or useful nutrients The estimated safe and adequate intakes of these nutrients established by the Food and Nutrition Board, are listed on the inside front cover

Concentration in arterial blood

minus that in venous blood

Branched chain amino acid

Branched chain keto acid

Body mass index

Basal metabolic rate

Flavin adenine dinucleotide

Free fatty acid

insulin receptor substrate

Lecithin cholesterol acyl-

N balance Nitrogen balance NTD Neural tube defect

PE Phosphatidylethanolamine PEPCK Phosphoenolpyruvate

carboxylase PER Protein efficiency ratio PLP Pyridoxal phosphate

P P A R Peroxisome proliferator

activated receptor PTH Parathyroid hormone

P U F A Polyunsaturated fatty acid RAR Retinoic acid receptor RBP Retinol binding protein

allowance

RQ Respiratory quotient SAH S-adenosyl-homocysteine SAM S-adenosyl-methionine SREBP Sterol response element

binding protein

TPP Thiamin pyrophosphate TTP Thymidine triphosphate

UV light Ultraviolet light VDR Vitamin D receptor VLDL Very-low-density lipoprotein

ACKNOWLEDGMENTS

FIRST E D I T I O N

My father was the earliest influence on this work He introduced me to all of the sciences This book arose from my teaching notes, and I thank Kristine Wallerius, Lori Furutomo, and my other students for their interest, i thank Professor Mary Ann Williams of the University of California at Berkeley for her comments on writing style and for her friendliness I thank a number of research professors for answering lengthy lists of questions over the telephone I thank Clarence Suelter of Michigan State University for comments on C1 and K, and James Fee of the Los Alamos National Laboratory for aid with oxygen chemistry I thank Sharon Fleming (fiber), Nancy Amy (Mn), and Judy Tumlund (Zn) of the University of California at Berkeley for help with the listed nutrients, i am grateful to Andrew Somlyo of the University of Virginia and Roger Tsien of the University of California

at San Diego for help in muscle and nerve biochemistry I am indebted to Gerhard Giebisch of Yale University for answering difficult questions on renal cell biology

I thank Herta Spencer of the Veterans Administration Hospital in Hines, Illinois, for a lengthy and revealing discussion on calcium nutrition I thank Steven Zeisel (choline) of the University of North Carolina, Wayne Becker (Krebs cycle) of the University of Wisconsin at Madison, Daniel Atkinson (urea cycle) of the University

of California at Los Angeles, and Peter Dallman (Fe) of the University of California

at San Francisco for comments on the listed subjects I am deeply appreciative of Quinton Rogers of the University of California at Davis for his insightful written comments on amino acid metabolism I would like to thank Michelle Walker of Academic Press for her immaculate work and skillful supervision of the production phase of this book Finally; I would like to take this opportunity to thank Professor

E L R Stokstad for accepting me as a graduate student, for the friendly and lively research environment in his laboratory; and for his encouragement for over a decade

ACKNOWLEDGMENTS

S E C O N D EDITION

I am grateful to the following researchers on the University of California at Berkeley campus I thank Gladys Block for patiently answering numerous ques- tions regarding methodology in epidemiology Ronald M Krauss answered several questions and provided inspiration for adding further details on atherosclerosis Maret Traber answered a number of questions on oxidative damage to LDLs, and inspired a change in my focus on this topic I thank Ernst Henle for several enlightening discussions on DNA damage and repair I am grateful to Hitomi Asahara for guidance in biotechnology I thank H S Sul and Nancy Hudson for help in fat cell biochemistry and for providing orientation in the field of human obesity

I acknowledge Penny Kris-Etherton of University of Pennsylvania for helping

me with questions regarding dietary lipids I thank Judy Turnlund of the Western Human Nutrition Center in San Francisco for answering a list of questions about copper and zinc I thank Paul Polakis of Onyx Pharmaceuticals (Richmond, CA) for his insights on new developments on the APC protein and catenin protein I am grateful to Pascal Goldschmidt-Clermont of Ohio State University for answering a few questions regarding the MAP kinase signaling pathway and hydrogen perox- ide I thank Ralph Green of the University of California at Davis for sharing his knowledge on gastric atrophy I am grateful to Paul Fox of the Cleveland Clinic Foundation for advice regarding iron transport, as well as to Anthony Norman of the University of California at Riverside for his insights on vitamin D

I appreciate the perspective given to me by Jeanne Rader of the Food and Drug Administration in Washington, DC, regarding folate supplements I thank Dale Schoeller of the University of Wisconsin Madison for his comments On the energy requirement

I thank Ttm Oliver for his professionalism in editing and typesetting Finall~fi I thank Kerry Willis and Jim Mowery for overseeing this project and for their contributions in the final phases of the work

xvii

Overview

Basic Chemistry

Structure and Bonding of Atoms

Acids and Bases

Illustration of the Use of Response

Elements Using the Example of

STRUCTURES

O V E R V I E W

A review of chemical bonds, acid/base chemistry, and the concept of water solubility is provided first, to assure that readers with various backgrounds begin with the same grounding in beginning chemistry Then the discussion progresses to molecular structures of increasing complexity, including carbohydrates, nucleic acids, and amino acids The concept of water solubility is then ex- panded, and an account of micelles, lipid bilay- ers, and detergents is presented Areview of the genome and the synthesis of messenger RNAis given The reader will return to the topics of DNA and RNA in later chapters, in accounts of the actions of vitamin A, vitamin D, thyroid hormone, and zinc, as well as in commentaries

on the origins of cancer The chapter closes with descriptions of protein synthesis, maturation, and secretion and of the properties of several classes of proteins

B A S I C C H E M I S T R Y This section reviews some elementary chemis- try to establish a basis for understanding the later material on hydrophilic interactions and on water-soluble and water-insoluble nu- trients

1 Classification of Biological Structures

Structure and B o n d i n g of A t o m s

Atomic Structure

An atom consists of an inner nucleus surrounded by electrons The nucleus con- sists of protons and neutrons Each proton has a single positive charge The number of protons in a particular atom, its atomic number, determines the chemi- cal nature of the atom Neutrons have no charge, but the electrons that surround the nucleus each have a single negative charge Generall~ the number of electrons

in a particular atom is identical to the number of protons, so the atom has no overall charge The electrons reside in distinct regions, called orbitals, that sur- round the nucleus The actual appearance of the electron as it moves about in its orbital might be thought of as resembling a cloud Addition of one or more additional electrons to a particular atom produces a net negative charge, whereas removal of one or more electrons results in a net positive charge Atoms with a positive or negative charge are called ions Conversion of a neutral atom (or molecule) to one with a charge is called ionization

The various orbitals available to the electrons represent different energy levels and are filled in an orderly manner If one were creating an atom, starting with the nucleus, the first electron added would occupy the orbital of lowest energ~ the ls orbital Since each orbital is capable of holding two electrons, the second electron added also would occupy the ls orbital The next available orbital, which has an energy slightly higher than that of the ls orbital, is the 2s orbital A completely filled 2s orbital also contains two electrons After the ls and 2s orbitals are filled, subsequent electrons fill the 2px, 2py, and 2pz orbitals These three orbitals (the 2p orbitals) have identical energy levels The orbitals that are next highest in energy are 3s, 3px, 3py, and 3pz Of still greater energy are the 4s and 3d orbitals, as indicated

in Table 1.1 The 4s and 3d orbitals contain electrons at similar energy levels, whereas the 4p orbitals contain electrons of even higher energy The terms "higher" and "lower" energy can be put into perspective by understanding that lower-en- ergy electrons have a more stable association with the nucleus They are dislodged from the atom less easily than higher-energy electrons

The electrons in the filled orbitals of highest energ~ are called valence electrons

These electrons, rather than those at lower energy levels, take part in most chemi- cal reactions Table 1.1 outlines the way that electrons fill orbitals in isolated atoms However, inside molecules, electrons are shared by atoms bonded to each other These electrons occupy molecular orbitals The orderly manner in which electrons fill molecular orbitals resembles the filling of atomic orbitals, but a description of molecular orbitals is beyond the scope of this chapter

The number of electrons that fill the orbitals of an atom is generally equal to the number of protons in its nucleus However, atoms tend to gain or lose electrons to the extent that a particular series of valence orbitals is either full or empty This condition results in an overall decrease in energy of the other electrons in valence orbitals In the inert elements (i.e., helium, neon, and argon), the series of valence orbitals is filled completely For example, the 10 electrons of neon, a stable and chemically unreactive atom, fill all the ls, 2s, and 2p orbitals (see Table 1.1) On the other hand, sodium, which contains 11 electrons, loses one electron under certain

Basic C h e m i s t r y 3 TABLE 1.1 Electronic Structure of Various Atoms

Number of electrons filling the atomic orbital

Covalent and Ionic Bonds

Stable i n t e r a c t i o n b e t w e e n t w o or m o r e a t o m s results in the f o r m a t i o n of a m o l e - cule Typically; the a t o m s in a m o l e c u l e are c o n n e c t e d to e a c h o t h e r b y c o v a l e n t

b o n d s In a n o r d i n a r y c o v a l e n t b o n d , e a c h a t o m i n v o l v e d c o n t r i b u t e s o n e e l e c t r o n

to f o r m a pair T h e t w o a t o m s s h a r e this p a i r of electrons A n electron of o n e a t o m

c a n b e s h a r e d w i t h a s e c o n d a t o m w h e n the s e c o n d a t o m h a s v a l e n c e orbitals t h a t are e i t h e r v a c a n t or h a l f filled T h e h y d r o g e n a t o m , w i t h a n a t o m i c n u m b e r of 1,

c o n t a i n s a half-filled ls orbital In the h y d r o g e n m o l e c u l e (H2), the s h a r i n g of electrons results in f o r m a t i o n of a b o n d i n g orbital A single b o n d i n g orbital occur-

r i n g b e t w e e n t w o a t o m s is e q u i v a l e n t to a single c o v a l e n t b o n d

T h e n i t r o g e n a t o m , w i t h a n a t o m i c n u m b e r of 7, c o n t a i n s filled ls a n d 2s orbitals

a n d half-filled 2px, 2py, a n d 2pz orbitals Because of the p r e s e n c e of t h e s e t h r e e half-filled orbitals, n i t r o g e n a t o m s t e n d to f o r m three c o v a l e n t b o n d s In n i t r o g e n gas (N2), t h e t w o n i t r o g e n a t o m s s h a r e t h e electrons in their 2p orbitals, r e s u l t i n g

in t h e f o r m a t i o n of t h r e e c o v a l e n t b o n d s Since t h e s e b o n d s occur b e t w e e n the

s a m e t w o a t o m s , t h e y c o n s t i t u t e a t r i p l e b o n d In a m m o n i a (NH3), t h e n i t r o g e n

a t o m a n d t h r e e h y d r o g e n a t o m s s h a r e electrons, r e s u l t i n g in the f o r m a t i o n of a

1 Classification of Biological Structures

single bond between the nitrogen atom and each of the hydrogen atoms Note that, in these compounds, the nitrogen atom also contains a pair of electrons in its own filled 2s orbital Two electrons in a filled nonbonding valence orbital are called

a lone pair This lone pair is not directly involved in the covalent bonds just described but contributes to the chemical properties of ammonia

The oxygen atom, with an atomic number of 8, contains filled ls, 2s, and 2px

orbitals and half-filled 2py and 2pz orbitals Because of the two half-filled valence orbitals, oxygen tends to form two covalent bonds In oxygen gas (O2), the two oxygen atoms share electrons from their 2py and 2pz orbitals to form two covalent

bonds between the same two atoms This interaction is called a double bond In

water (H20), the oxygen atom forms a single bond with each of the two hydrogen atoms The oxygen atom contains two lone pairs (in the 2s and 2px orbitals) that contribute to the properties of water

The electrons of the carbon atom, with an atomic number of 6, fill the ls and 2s orbitals and half-fill the 2px and 2py orbitals Since this is the most stable state of the carbon atom, one might expect that, in molecules, the carbon atom would form two covalent bonds However, carbon generally forms four covalent bonds This behavior results in promotion of one electron from the 2s orbital to give a half- filled 2pz orbital In this slightly higher energy state, carbon has four half-filled valence orbitals Formation of four covalent bonds results in a lower energy state for the molecule as a whole The carbon atoms in such molecules do not contain lone pairs

The single bonds described in these examples are formed from two shared electrons, one furnished by each of the two bonded atoms Bonds in which both

of the shared electrons are furnished by one of the atoms can form also Generall3~

such bonds involve a lone pair from the donor atom and an unfilled orbital in the acceptor atom, usually a positively charged ion These bonds are called electron donor-acceptor bonds

When two identical atoms are bonded to each other, the distribution of electrons between them is symmetrical and favors neither atom However, in bonds involv- ing two different atoms, the electrons may shift toward one end of the bond In

such a case, the bond is said to have ionic character and to be an ionic bond The

difference between an ionic and a covalent bond is not absolute, because bond types occur with varying degrees of ionic character An extreme example of an ionic bond is found in sodium chloride (NaC1) In solid crystals of NaC1 or in gaseous NaC1, the sodium atom occurs as Na +, whereas the chlorine atom occurs

as C1- Individual NaC1 molecules do not exist; each positive Na + ion is sur- rounded by negative C1- ions The attraction between the ions is very strong, but the bonding electrons are shifted almost completely to the C1- ions, that is, the bonding is highly ionic in character A molecule that contains one or more bonds with measurable ionic character is called a polar molecule

Hydrogen Bonds

Bonds involving hydrogen may be fully covalent, as in H2, partially covalent and partially ionic, as in H20, or nearly completely ionic, as in HC1 In the more ionic bonds, the electrons are distributed unevenly, skewed away from hydrogen to- ward its partner atom This partial removal of electrons from the hydrogen atom results in partially vacant valence orbitals of hydrogen The partial vacancy can be

Basic Chemistry 5

filled by electrons from an atom in a second molecule, resulting in the phenome- non of hydrogen bonding The hydrogen atoms of water, alcohol, organic acids, and amines can participate in hydrogen bonding The other atom involved in the hydrogen bond can be the oxygen atom of molecules such as water, ethers, ke- tones, or carboxylic acids or the nitrogen atom of ammonia or other amines For example, hydrogen bonds can form between two water molecules:

, - - R ~ C ~ O R Hydrogen bonds are much weaker than covalent bonds In aqueous solution, they are broken and re-formed continuousl~ rapidly; and spontaneously Note that a water molecule can form hydrogen bonds with up to four other water molecules

In liquid water, hydrogen bonds link together most of the molecules

Hydration

The digestion and absorption of organic and inorganic nutrients, as well as all other biochemical processes in living organisms, are influenced by the unique properties of water Water is an interactive liquid or solvent Its chemical interac- tions with solutes are called hydration Hydration involves weak associations of water molecules with other molecules or ions, such as Na +, CI-, starch, or protein Because hydration bonding is weak and transitory, the number of water molecules associated with an ion or molecule at any particular moment is approximate and difficult to measure However, typical indicated hydration numbers are: Na +, 1-2;

K +, 2; Mg 2+, 4-10; Ca 2+, 4-8; Zn 2+, 4-10; Fe 2+, 10; CI-, 1; and F-, 4 (Conway, 1981) Hydration is a consequence of two types of bonding: (1) electron donor-acceptor bonding, and (2) hydrogen bonding The primary type involved depends on the ion

Hydration allows water-soluble chemicals to dissolve in water For example, a crystal of table salt (NaC1) is held together by strong ionic interactions However, when NaC1 is dissolved in water, the Na + and C1- ions become independent hydrated entities The energy produced by hydration of the Na § and C1- ions more than balances the energy required to remove them from the NaC1 crystal lattice

In the Na § ion, a lone pair of electrons from a water oxygen atom fills an empty

6 1 Classification of Biological Structures

valence orbital of Na + to form an electron donor-acceptor bond The C1- ion interacts electrostaticaUy with water h y d r o g e n atoms, as described in the section

on hydrogen bonding

Not all ionicaUy b o n d e d molecules dissolve in water For example, silver chlo- ride is virtually insoluble The energy of hydration of the Ag + and C1- ions is not sufficient to overcome their energy of interaction in the crystal lattice

c o m p o u n d loses its proton it acts as a base, because it can n o w readily accept a proton

Conventionally~ some chemicals are called acids, whereas others are called bases This convention is based on the form the chemical takes in its uncharged state or w h e n it is not in contact with water For example, although the acetate ion that is formed w h e n acetic acid dissociates is a base, acetate ion generally is not called "acetic base."

When an acid (HA) dissociates in water, the dissociated protons do not accu- mulate as free protons Instead, each immediately binds to a molecule of water to form a h y d r o n i u m ion (H30+) The proton binds to one of the available lone pairs

of the oxygen atom In this reaction, water serves as a base:

HA + H20 ~ A- + H30 +

The equilibrium depicted is extremely rapid The lifetime of any given molecule

of H3 O+ is only 10 -13 seconds (Eigen, 1964) Water is an acid as well as a base Pure water partially dissociates to form a hydroxide ion and a proton, which binds to another water molecule:

H20 ~ H O - + H +

The strength of a particular acid is described by its dissociation constant (or

equilibrium constant; K) For water, K is defined by K = [H+][HO-]/[H20] The symbols in brackets refer to molar concentrations (M) of the indicated chemicals The concentration of pure liquid water is 55.6 M In the h u m a n bod3~ the concen- trations of H +, HO-, and most other chemicals are far lower than 55 M, and are in the range of 10 -3 to 10 -8 M

Because the concentration of water is so high in most aqueous solutions, and because its concentration fluctuates very little in most living organisms, the [H20] term conventionally is omitted from the formula for K To omit [H20], set the value

at I to yield a simpler version of the formula: K = [H+][HO-] For pure water at 25~ [H +] = 10 -7 M and [HO-] = 10 -7 M These two concentrations must be

Basic Chemistry 7 identical since the dissociation of one proton from water results in the production

of one hydroxide ion

pH is a Shorthand for Expressing the Proton Concentration

The concentration of H + (which actually occurs as the hydronium ion) in solutions

is expressed as the pH, defined by the formula: pH = -log [H+] To use this formula

to describe pure, uncontaminated water, enter the known concentration of H + This concentration is 10 -7 M Solving the equation gives pH = 7.0 As the formula shows, solutions with high H + levels have a low pH; those with low H + levels have a high

pH A solution that has a pH of 7.0 is said to be neutral Solutions with a lower p H are said to be acidic When considering acidic solutions, biochemists often are concerned with the reactive properties of H + Solutions with a pH greater than 7.0 are said to be alkaline or basic Biochemists may be concerned with reactions involving the hydroxide ion (HO-) in such solutions

Strong Acids are Highly Dissociated in Water; Weak Acids are Slightly

Dissociated in Water

The degree of dissociation of any given acid (HA) in water is expressed in terms

of the distinct value of its dissociation constant, K, defined by the formula K = [H+][A-]/[HA] When comparing weak and strong acids, the strength of the acid conventionally is expressed by its pK, defined as pK = -log K

Strong acids have low pK values; weak acids have high pK values For example, formic acid is moderately strong: pK = 3.75 The pK values for other acids and proton-donating compounds are: phosphoric acid (H3PO4), 2.14; acetic acid (CH3COOH), 4.76; carbonic acid (H2CO3) , 3.8; a m m o n i u m ion (NH4), 9.25; and bicarbonate ion (HCO3), 10.2 The values for K and pK refer to reactions that are reversible in aqueous solution and have attained a condition of equilibrium Consider an imaginary acid, HA, with K = 0.01 (pK = 2.0) When any quantity

of HA is mixed with water, the acid will dissociate to the extent that satisfies the formula [A-][H+]/[HA] = 0.01 The term "any quantity" refers to a broad range of concentrations far below 55.6 M Once a degree of dissociation occurs that results

in levels of HA and A- that satisfy the formula, the net trend toward dissociation stops Although dissociation continues, reassociation occurs at an equal ratẹ Thus,

an equilibrium situation is reached

The lone pair electrons of water (O atom), ammonia (N atom), and amino groups (N atom) influences the behavior and concentrations of hydrogen ions (H +)

in water Hydrogen ions, produced either by dissociation of water or by dissocia- tion of acids, do not occur as free entities in aqueous solutions They associate with the lone pair electrons of other water molecules to form hydronium ions, H3 Ợ This association involves the formation of an electron donor-acceptor bond Electron donor-acceptor bonds involving nitrogen are stronger than those in- volving oxygen, so some nitrogen-containing molecules dissolved in water will bind any H + ions that are present with a greater strength than any single surround-

8 1 Classification of Biological Structures

ing w a t e r molecule For example, if d i m e t h y l a m i n e ( C H 3 - N H - C H 3 ) is a d d e d to water, it tends to r e m o v e H + from molecules of H3 O+ that m a y be present:

H This transfer results in a decrease in the concentration of H3 O+ in the solution Therefore, molecules of this t y p e act as bases

C h e m i c a l G r o u p s

Table 1.2 presents structural formulas of the chemical g r o u p s u s e d to classify

c o m p o u n d s of biological interest The c o m m o n abbreviation for the group, the

n a m e of the group, a n d the n a m e of the class of c o m p o u n d s containing the g r o u p are also given Note that, w h e n a c o m p o u n d contains m o r e t h a n one group, it is

n a m e d from the g r o u p considered m o s t significant "R" represents the rest of the molecule on the other side of a single covalent bond In molecules containing m o r e than one R group, "R" represents the s a m e configuration of a t o m s unless the

g r o u p s are d i s t i n g u i s h e d as R1, R2, a n d so forth

B a s i c C h e m i s t r y 9

TABLE 1.2 Chemical Groups Used to Classify Compounds of Biological Interest

10 1 Classification of Biological Structures

tion of a carboxylic acid with an alcohol Amides are formed by reaction of a carboxylic acid with an amine

Inorganic phosphate and organic phosphates are ionized when dissolved in water Similarl3r inorganic sulfate and organic sulfate are ionized when dissolved

in water In inorganic phosphate and sulfate, the R group is a hydrogen atom

As also illustrated in Figure 1.1, a primary or secondary amine group can function as a weak base The degree to which the group is protonated to the positive ion depends on the dissociation constant of the molecule to which it is attached and on the initial pH of the solution

Counterions

Ionized forms of molecules are nearly always accompanied by counterions of the opposite charge When the counterion is a proton, the ion and proton complex is called an acid When the counterion is a different cation, such as a sodium, potassium, or ammonium ion, the complex is called a salt

M A C R O M O L E C U L E S

In biological systems, atoms tend to form very large molecules called macromole- cules, which can be segregated into four groups: carbohydrates, nucleic acids, proteins, and lipids

Carbohydrates

The term carbohydrate refers to a class of polyhydroxy aldehydes and polyhy- droxy ketones with the general formula (CH20)n The name derives from the composition of the formula unit, that is, carbon plus water All carbohydrates are composed of basic units called monosaccharides Polymers containing two to six monosaccharides are called oligosaccharides; those with more are called polysac- charides Starch, cellulose, and glycogen are examples of polysaccharides Monosaccharides and oligosaccharides are also called sugars

Monosaccharides

The open-chain structure of a monosaccharide is a straight-chain saturated alde- hyde or 2-ketone with three to seven carbon atoms The carbon atoms are num- bered as shown in Figure 1.2 Every carbon, except those of the aldehyde or ketone group, has one hydroxyl group In biological materials, monosaccharides with five and six carbon atoms are most common

In many sugars, such as glucose, the carbon chain can cyclize in two different ways, producing the (~ and j3 isomers These rings are formed by reaction of the

hydroxyl group of the next to last carbon with the aldehyde or keto group, forming

a hemiacetal or hemiketal group, respectively The carbon atoms retain the num- bers assigned to them in the straight-chain form The two ring forms are in equilibrium when the free monosaccharide molecules are in solution

Figure 1.2 also shows the ring and open-chain structures of fructose and ribose The 13 form of ribose occurs in the ribonudeic acid (RNA) The ~ form of 2-deoxyri- bose, a modified form of ribose, occurs in deoxyribonucleic acid (DNA)

12 1 Classification of Biological Structures

is ~(1 -> 4)

Polysaccharides

Several polysaccharides are important in biological systems Starch is a polymer

of glucose monomers connected by a glycosidic linkages Amylose is a straight- chain starch containing only a(1 ~ 4) linkages In amylopectin, the chain is branched at approximately 25-monomer intervals by a(1 ~ 6) glycosidic linkages Glycogen is similar to amylopectin, but branches occur more frequently Cellulose

is a linear polymer of glucose monomers containing ~(1 ~ 4) glycosidic linkages

Nucleic Acids

The two nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid

(RNA) As suggested by their names, these c o m p o u n d s occur most commonly in the nucleus of the cell DNA is the genetic material that contains all the information needed to create a living organism, that is, all the information needed to provide for the structure of an animal; the abilities to reproduce, think, and learn; and some forms of behavior and language DNA generally consists of two linear polymers (or strands) of nucleotides, tightly associated with each other by a series of hydrogen bonds between the two strands The two D N A strands are twisted around each other, and the overall structure is called a double helix The length

of each strand of D N A in each h u m a n cell is about 2 m and contains approximately

11 billion nucleotides DNA actually is only the name of a chemical, while

"genome" is the term used to refer to all of the DNA in any particular cell of a specific organism

Macromolecules 13

When double-stranded DNA (dsDNA) becomes unraveled, the result is two strands of single-stranded DNA (ssDNA) During the normal course of metabo- lism, short stretches of dsDNA are unraveled in the cell to give regions of the chromosome that consist of ssDNA

Figure 1.4 shows the nucleosides of DNA: deoxyadenosine (dA), de- oxythymidine (dT), deoxyguanosine (dG), and deoxycytidine (dC) A nucleoside containing one to three phosphate groups bound to the 5'-carbon of the deoxyri- bose group is called a nucleotide Also shown are the nucleosides of RNA: adeno- sine (A), uridine (U), guanosine (G), and cytidine (C) RNA consists of single polymer strands, not double strands as found in DNA

Figure 1.5 shows the manner in which nucleotide units are joined in the polymer strands of DNA Each phosphate group is bonded to the 3'-carbon of one sugar unit and to the 5'-carbon of the next sugar unit, forming a phosphodiester linkage Adjacent nucleotides of RNA are also joined in this manner

Complementation of Bases Maintains the Double-Stranded Structure of DNA,

and Allows DNA to Code for a Corresponding Polymer during RNA Synthesis

The aromatic rings connected to the ribose moieties of RNA and the deoxyribose moieties of DNA are called nucleic acid bases They are bases because they contain nitrogen atoms that bind protons Complementation is the pattern of hydrogen bond formation that occurs between specific pairs of nucleic acid bases An exam- ple is shown in Figure 1.6 Complementation of the bases in nucleic acids is responsible for the maintenance of the double helix structure of DNA Comple- mentation also guides the transfer of genetic information from the DNA in a parent chromosome to a daughter chromosome, during the process of DNA synthesis, which occurs shortly before the cell divides Finally; complementation allows DNA

to serve as a template during RNA synthesis

In maintaining the structure of DNA, interactions occur between dA and dT, and between dG and dC Adenosine and thymine are complementary bases, while guanine and cytosine are complementary bases

Complementation guides the transfer of information from specific regions of DNA (called genes) during formation of RNA During the synthesis of RNA, the order of occurrence of the bases in DNA guides the order of polymerization of the ribonucleotides to create RNA RNA synthesis does not involve a permanent association of DNA with RNA In RNA synthesis, the association between incom- ing ribonucleotides is fleeting and temporary The exposure of successive DNA bases allows the successive process of matching of free ribonucleotides with the deoxyribonucleotides occurring in the strand of DNA As soon as an incoming free ribonucleotide finds a match (on the DNA template), the free ribonucleotide is covalently attached to the growing strand of RNA

The following bases of DNA and RNA hydrogen bond to each other and therefore are complementary to each other: dA of DNA to U of RNA; dT of DNA

to A of RNA; dG of DNA to C of RNA; and dC of DNA to G of RNA

A description of the event of DNA synthesis allows us to make use of two of the concepts introduced herein During DNA synthesis, incoming free deoxyri- bonucleotides find their match (on the DNA template), but as soon as a match is

14 1 Classification of Biological Structures

FIGURE 1.4 Nucleosides of D N A and RNA The nucleosides are each c o m p o s e d of a base

a n d a 5-membered sugar The b o n d from the sugar to the base involves a carbon-to-nitro- gen bond The base is, in fact, a base because of the nitrogen atoms, which can be pro- tonated

A, T, G, and C, whereas the deoxyribose groups are identified by dR Two hydrogen bonds form between dA and dT; three form between dC and dG This bonding occurs between bases on opposite strands of the double helix During RNA synthesis (transcription), the DNA strands are separated This separation is only momentary The separation allows the RNA bases to hydrogen bond tempo- rarily with the DNA bases, thus governing the order of polymerization of the ribonucleotides Some genes are transcribed using one strand of the DNA, whereas others are transcribed from the opposite strand

16 1 Classification of Biological Structures

made the free deoxyribonucleotide is covalently connected to a growing strand of DNA Thus, descriptions of RNA synthesis and DNA synthesis both make use of the concept of a template The other concept used to describe DNA synthesis is that interactions occur between dA and dT, and between dG and dC

DNA synthesis occurs during the process of replication Replication is the process by which DNA synthesis causes all the DNA in the nucleus to make a duplicate of itself In eukaryotic cells, the process of replication causes the cell to change from a diploid cell to one that is temporarily tetraploid Replication in eukaryotic cells is usually immediately followed by cell division, which results in two cells that are once again diploid

A m i n o A c i d s and Proteins

Figure 1.7 depicts the general formula for a 2-amino acid, also called an (x-amino

acid An oligomer consisting of two amino acids is called a dipeptide The amino acids are bound to each other by a peptide bond, which involves a keto group and

an amino group Amino acid polymers of moderate length are called oligopep- tides, whereas longer polymers are called polypeptides or proteins A typical protein contains about 300 amino acids and has a molecular weight of about 50,000 The polypeptide chains that constitute proteins are linear and contain no branching

Generally; specific proteins can bind to each other in the body to form dimers (duplex structures), trimers, tetramers, or even larger multiples These subunit proteins may be of identical or different structure The different proteins in these multimeric structures are bound to each other by hydrogen bonds and other weak interactions These multimers often perform physiological functions that cannot

be carried out by the individual separated proteins

Examination of proteins with an electron microscope reveals that some are somewhat spherical, others asymmetric, and others long and fibrous The overall shape, function, and chemical properties of a specific oligopeptide or protein are determined by the identities and order of polymerization of its constituent amino acids

Classical Amino Acids

The classical amino acids are those that are incorporated into proteins during polymerization in the cell Table 1.3 lists the 20 classical amino acids in order of one

FIGURE 1.7 Generic structure of an amino acid (left) and generic structure of two amino acids linked by a peptide bond (right)

aIsoleucine has the most lipophilic side chain and arginine has the most hydrophilic side chain

property of the R group (side chain), namel3~ increasing hydrophilicity (decreasing lipophilicity) This order does not reflect an absolute property to which a numeri- cal value might be ascribed, but reflects the observed tendency of the amino acid

to occur in the lipophilic core or on the hydrophilic surface of a protein These observations were made by examining the three-dimensional structures of m a n y proteins with somewhat spherical or globular structures Amino acids with ioniz- able or hydrogen-bonding R groups are more hydrophilic, whereas those with alkane or aromatic R groups are more lipophilic Isoleucine, valine, and leucine are the most lipophilic amino acids; arginine, lysine, and asparagine are the most hydrophilic Lysine, for example, contains a protonated amino group at the end of its side chain

Of all the classical amino acids, with the exception of glycine, only the 2-carbon atom is b o n d e d to four different groups, that is, a carboxyl, hydrogen, amino, and

R group Bonding of four different groups to any carbon atom can occur in two different isomeric arrangements In amino acids, these are called the L-amino acids and D-amino acids Essentially; all the amino acids in the diet and in the b o d y occur

as the L-isomer In this textbook, all references to amino acids are to the L-isomer unless otherwise specified D-Amino acids occur in small quantities in certain

18 1 Classification of Biological Structures

molecules synthesized by invertebrates and bacteria Sometimes isomeric mix- tures containing equal proportions of a certain amino acid in the L and D forms are given to animals as supplements to the diet Such mixtures may be given because they are less expensive than a supplement containing the pure L-amino acid Baker (1984) discussed that some D-amino acids can be converted in the body (isomer- ized) to the L isomer, whereas others tend to be broken d o w n rather than isomer- ized

The simplest amino acids are glycine and alanine The R group of glycine is a hydrogen atom; the R group of alanine is a methyl group

Threonine and serine contain hydroxyl groups that sometimes serve as a point

of attachment for a string of sugar molecules These oligosaccharide strings usu- ally include mannose and glucose as well as other sugars The hydroxyl group of serine also may serve as a point of attachment for a phosphate group The milk protein casein may contain up to 10 phosphoserine residues These negatively charged phosphate ions serve as binding sites for positive calcium ions

Isoleucine, valine, and leucine are the branched-chain amino acids (BCAAs)

They are indispensable (essential), but the risk of developing a dietary deficiency

is low because they are plentiful in most diets The branched-chain amino acids,

in addition to phenylalanine, are the most lipophilic of the amino acids:

CH3 - - S ~ CH2CH2CH - COOH

I

NH2 Methionine

Tyrosine and tryptophan, as well as phenylalanine, are the aromatic amino acids The body can convert phenylalanine to tyrosine Thus, tyrosine is a dispen- sable (nonessential) amino acid

The acidic amino acids are glutamic acid and aspartic acid These amino acids also occur in amide forms as glutamine and asparagine Glutamate is the amino acid present in greatest abundance in a variety of dietary proteins

20 1 Classification of Biological Structures

is toxic to nerves A very small proportion of arginine in the body is broken down

in a pathway that results in the formation of nitric oxide (NO) NO is a hormone used for the regulation of blood flow through certain vessels and used to regulate blood pressure In short, NO is synthesized in the endothelial cells that line blood vessels It then diffuses out of the cells and provokes nearby muscle cells to relax, resulting in dilation of the vessel Vessel dilation also is provoked by other hor- mones, such as acetylcholine and serotonin

Histidine is an indispensable amino acid Its requirement is easily demonstrated

in young, growing animals but is difficult to show in adults Apparently, the signs

of deficiency fail to materialize when adult animals are fed a histidine-free diet because of histidine stored in muscle in the form of a related compound, c a r n o s -

H u m a n and rat muscle contain carnosine, but mouse muscle does not Fish muscle contains a methylated form of carnosine, called anserine, that does not seem to be available to the fish as a source of histidine

Modified Amino Acids

As stated earlier, only classical amino acids are built into polypeptides during amino acid polymerization However, other amino acids, classical amino acids that have been modified after incorporation into the chain, are found in proteins Some

of the modified amino acids found in proteins are listed in Table 1.4 Vitamins are required for the synthesis of some of the modified amino acids For example, vitamin C is required for conversion of proline to hydroxyproline This and other vitamin cofactors are listed in Table 1.4

An unusual amino acid behaves like the classical amino acids The amino acid selenocysteine is incorporated into the polypeptide chain during amino acid polymerization The story of selenocysteine is revealed in the Selenium section in Chapter 10

Modified amino acids that are not part of polypeptides m a y be formed by modification of one of the classical amino acids Among the m a n y examples of this type of modified amino acid are creatine (a modified form of glycine), omithine

TABLE 1.4 Some Modified Amino Acids

Trimethyllysine Hydroxyproline Amidated amino add

None None None Vitamin K Ascorbic acid None None Ascorbic acid Ascorbic acid

22 1 Classification of Biological Structures

TABLE 1.5 Classification of Amino Acids According to Dietary Need

(modified arginine), and homocysteine (modified methionine) Creatine, omi- thine, and homocysteine have well-established functions in the body Kynurenine and formiminoglutamic acid are modified forms of tryptophan and histidine, respectivel~ and are broken d o w n in the b o d y to simpler molecules and result in waste products

Indispensable and Dispensable Amino Acids

In Table 1.5 the classical amino acids are segregated according to their necessity in the diet Those that are required to maintain life are called indispensable (essential)

amino acids Those that m a y be present in the diet but can be omitted without threatening life are called dispensable (nonessential) amino acids The proteins of the most value, from a nutritional point of view, are the ones that contain all the indispensable amino acids as well as a variety of dispensable amino acids

FIGURE 1.8 Formation of a triglyceride A triglyceride consists of a backbone of glycerol that is linked, via ester bonds, to three carboxylic acids

FIGURE 1.9 Tripalmitate Tripalmitate is a triglyceride consisting of a glycerol backbone that is linked, via ester bonds, to three molecules of palmitic acid, a 16-carbon carboxylic acid

Glycogenic and Ketogenic Amino Acids

Amino acids can be classified as glycogenic or ketogenic This classification refers

to the products of catabolism (breakdown) of the amino acid in the body Glyco- genic amino acids can be converted to glucose, whereas ketogenic amino acids form ketone bodies This classification is discussed in the Protein chapter

Lipids

Fats and Oils

The structure of glycerol (1,2,3-trihydroxypropane) is given in Figure 1.8 When this molecule forms a triester with three carboxylic acids (molecules ending in a carboxyl group), the product is called a triglyceride Figure 1.9 shows the structure

of tripalmitate, the triglyceride of palmitic acid Carboxylic acids in which the R group is of the saturated or unsaturated long-chain aliphatic type shown in Figure 1.10 are called fatty acids Triglycerides of fatty acids are called fats if they are solid

at room temperature or oils if they are liquid

Phospholipids

The most common phospholipid, phosphatidylcholine, contains two molecules

of fatty acid and one molecule of choline phosphate attached to a glycerol back- bone (see Figure 1.11) Like all other phospholipids, it is amphipathic The water- soluble end features a phosphate group, an amino group, and two keto groups

Micelles, Bilayer Sheets, and Vesicles

Phospholipids can form organized structures, as shown in Figure 1.12, when suspended in water solutions The small circles represent the ionic water-soluble ends of the phospholipid molecules, containing phosphate and amino groups The

24 1 Classification of Biological Structures

Solubility 25 lines represent the lipophilic "tails." In a micelle, the tails face inward and the water-soluble ends face outward, making the surface hydrophilic and the interior lipophilic

composed of water-soluble groups and the "filling" of alkane tails The alkane groups associate with one another but have little contact with the water above and below

The third structure in Figure 1.12 is a vesicle Vesicles are larger than micelles and contain water in the interior The membrane, or lipid-containing portion, is a bilayer sheet that is curved to form a spheroid

S O L U B I L I T Y

Solubility refers to an interaction between a solute (which m a y be a solid, liquid,

or gas) and a solvent (which is a liquid) A material that is soluble can be dispersed

Micelle

V ~ e

FIGURE 1.12 Phospholipid structures Most biological membranes take the form of a bilayer sheet In addition to containing phosopholipids, biological membranes contain proteins and cholesterol Vesicles are used in biology for transporting and delivering biochemicals from the interior of the cell to the membrane, or to the extracellular fluids (Reprinted by permission from Darnell et al., 1990.)

26 1 Classification of Biological Structures

on a molecular level within the solvent A liquid, such as water, that can act as both

an electron donor and an electron acceptor is called a polar solvent A liquid that does not engage in such interactions, like gasoline or vegetable oil, is called a

nonpolar solvent C o m p o u n d s that are polar or have a charged or ionic character are soluble in polar solvents but not in nonpolar solvents Nonpolar compounds are soluble in nonpolar solvents but not in polar solvents

The relative solubility of materials is relevant to most of the subjects covered in this book The biochemical "machinery" used for digestion, absorption, and trans- port of nutrients throughout the body depends on whether the nutrients are water soluble or fat soluble Relative solubilities are also crucial to the function, compo- sition, and architecture of cells and their surrounding membranes

A nutrient is classified as water soluble if it can be dissolved in water However, this property is relative, not absolute, since all materials dissolve to some degree

in all solvents Therefore, one might arbitrarily choose a concentration limit of 1 millimolar (1.0 mM) to define water solubility, that is, any compound whose saturated solution in water contains more than 1.0 mmol per liter (1.0 mol per 1000 liters) is considered water soluble Cholesterol, for example, is definitely not water soluble A saturated solution is only 0.001 mM A nutrient is classified as fat soluble

if it can be dissolved in fats or oils Again, limits of solubility must be established arbitrarily

Amphipathic Molecules

Parts of large molecules can exhibit the properties of the atoms of those parts of the molecule For example, the end of a long molecule containing charges or ionic bonds can exhibit hydrophilic properties, that is, behave as though the molecule were water soluble If the rest of the molecule is an alkane chain with no charged groups, this other end of the molecule can exhibit lipophilic properties, that is, behave as though the molecule were fat soluble Large molecules are said to be amphipathic if they have one hydrophilic end and one lipophilic end

Water-Soluble and Fat-Soluble Nutrients

Water-soluble nutrients usually contain one or more of the following polar or ionizable groups: carboxyl, amino, keto, hydroxyl, or phosphate (see Table 1.2) Molecules that contain several hydroxyl groups, such as sugars, m a y be very soluble Amino acids are water soluble, although some are more soluble than others Glutamic acid, with two carboxyl groups, is very soluble Compounds containing ionic groups, either positive or negative, interact well with water and tend to be water soluble

A molecule that does not contain polar or ionizable groups is not likely to be soluble in water The structures of biological molecules that are not water soluble generally contain only aromatic or aliphatic (alkane-like) components These groups do not interact well with water and are said to be lipophilic If an alkane (e.g., octane) is added to a container of water, it will not associate with the water but will form a separate layer on top of the water (If the molecule were more dense than water, it would sink to the bottom to form a separate layer.)

Solubility 27

If a piece of fat is added to the container, it will float on the water layer and absorb some of the alkane Some of the alkane will "dissolve" into the fat If an aromatic liquid is added (e.g., benzene), it also will associate with the piece of fat These materials are fat soluble or lipophilic Fat-soluble nutrients associate with fat, not because they are forced away from water by some repulsive force but because their molecules are attracted by those in the fat Water does not "repel" fat Figure 1.13 shows the structures of two molecules that are not water soluble The structure at the left is octane, an alkane The structure in the center is benzene,

an aromatic molecule, which usually is simplified as shown on the right

An aromatic compound can be water soluble if several polar or ionic (water- soluble) groups are bonded to its aromatic ring The structure of vitamin B 6 is based on an aromatic ring, but the ring contains aldehyde, phosphate, hydroxyl, and amine groups Consequently, vitamin B 6 is water soluble

Some lipophilic nutrients are amphipathic because their molecules contain water-soluble groups at one end A fatty acid has a long alkane "tail" with a carboxyl group at one end Abile salt has a large aromatic structure with a carboxyl group at one end

Effective Water Solubility of Fat-Soluble Molecules

Bile salts act as "detergents" in nature to maintain insoluble (fat-soluble) com- pounds in water solution The bile salts form mixed micelles that consist of amphipathic bile salt molecules surrounding the lipophilic (fat-soluble) molecules The hydrophilic ends of the amphipathic molecules face outward, forming a lipophilic environment in the interior of the micelle Bile salt molecules contain acid groups, such as carboxyl and sulfonyl groups, that usually are ionized under physiological conditions

In water solutions, bile salt molecules associate to form micelles only when present in sufficient concentration The critical concentrations for micelle forma- tion are in the low millimolar range The structures of these micelles are not particularly stable They continually change in size and shape by fusing and blending with nearby micelles

Figure 1.14 presents a cross-section of a bile salt micelle and the way in which the micelle solubilizes a molecule of fatty acid The bile salt shown is taurocholate and the fatty acid is palmitic acid Within the micelle, the fatty acid remains in solution and can diffuse over some distance The micelle that results from addition

of the fatty acid molecule is called a mixed micelle because it contains more than one type of molecule In the absence of the bile salt, the fatty acid might adhere to

"o~ _ ~4 .L-.- "b/ Y"" _.,,,.,,.,, ~c-,,-cH,c so.-