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 Acknowledgments
I am grateful to my colleagues at Drexel University College of Medicine who
generously shared their expertise to help make this book as accurate and as
useful to medical (and biomedical graduate) students as possible. I am
particularly appreciative of the support and encouragement provided by my
departmental colleagues Jane Clifford, PhD (Chair); Bradford Jameson, PhD;
and Michael White, PhD. As usual, Ms. Barbara Engle was an invaluable
sounding board throughout the process.
I am thankful for the efforts of the editors and production staff of Lippincott
Williams & Wilkins. Many, many thanks are due to freelancer Kelly Horvath for
her assistance in the editing (and many other aspects) of this book. I also want to
thank Remya Divakaran at SPi Global for her work in the assembly of the
seventh edition.
Contributing Editor, Online Unit Review Questions
Bradford A. Jameson, PhD
Professor
Department of Biochemistry and Molecular Biology
Drexel University College of Medicine
Philadelphia, Pennsylvania
 Dedication
This book is dedicated to my grandchildren, Charlie and Isabella, with the
promise that I will not write another, and to my students, past and present, with
deep gratitude for 25 years of opportunities to teach and learn.
 Contents

UNIT I: Protein Structure and Function

Chapter 1:Amino Acids
Chapter 2:Protein Structure
Chapter 3:Globular Proteins
Chapter 4:Fibrous Proteins
Chapter 5:Enzymes

UNIT II: Bioenergetics and Carbohydrate Metabolism

Chapter 6:Bioenergetics and Oxidative Phosphorylation
Chapter 7:Introduction to Carbohydrates
Chapter 8:Introduction to Metabolism and Glycolysis
Chapter 9:Tricarboxylic Acid Cycle and Pyruvate Dehydrogenase Complex
Chapter 10:Gluconeogenesis
Chapter 11:Glycogen Metabolism
Chapter 12:Monosaccharide and Disaccharide Metabolism
Chapter 13:Pentose Phosphate Pathway and Nicotinamide Adenine
Dinucleotide Phosphate
Chapter 14:Glycosaminoglycans, Proteoglycans, and Glycoproteins

UNIT III: Lipid Metabolism

Chapter 15:Dietary Lipid Metabolism
Chapter 16:Fatty Acid, Triacylglycerol, and Ketone Body Metabolism
Chapter 17:Phospholipid, Glycosphingolipid, and Eicosanoid Metabolism
Chapter 18:Cholesterol, Lipoprotein, and Steroid Metabolism

UNIT IV: Nitrogen Metabolism

Chapter 19:Amino Acids: Nitrogen Disposal
Chapter 20:Amino Acids: Degradation and Synthesis
Chapter 21:Amino Acids: Conversion to Specialized Products
Chapter 22:Nucleotide Metabolism
UNIT V: Integration of Metabolism
Chapter 23:Metabolic Effects of Insulin and Glucagon
Chapter 24:The Feed–Fast Cycle
Chapter 25:Diabetes Mellitus
Chapter 26:Obesity

UNIT VI: Medical Nutrition

Chapter 27:Nutrition: Overview and Macronutrients
Chapter 28:Micronutrients: Vitamins
Chapter 29:Micronutrients: Minerals

UNIT VII: Storage and Expression of Genetic

Information
Chapter 30:DNA Structure, Replication, and Repair
Chapter 31:RNA Structure, Synthesis, and Processing
Chapter 32:Protein Synthesis
Chapter 33:Regulation of Gene Expression
Chapter 34:Biotechnology and Human Disease

Appendix
Index
Figure Sources
Bonus chapter online! Chapter 35: Blood Clotting (Use your scratch-off code
provided in the front of this book for access to this and other free online
resources on .)
 UNIT I
Protein Structure and Function
Amino Acids 1

For additional ancillary materials related to this

chapter, please visit thePoint.

I. OVERVIEW
Proteins are the most abundant and functionally diverse molecules in living
systems. Virtually every life process depends on this class of macromolecules.
For example, enzymes and polypeptide hormones direct and regulate metabolism
in the body, whereas contractile proteins in muscle permit movement. In bone,
the protein collagen forms a framework for the deposition of calcium phosphate
crystals, acting like the steel cables in reinforced concrete. In the bloodstream,
proteins, such as hemoglobin and albumin, transport molecules essential to life,
whereas immunoglobulins fight infectious bacteria and viruses. In short, proteins
display an incredible diversity of functions, yet all share the common structural
feature of being linear polymers of amino acids. This chapter describes the
properties of amino acids. Chapter 2 explores how these simple building blocks
are joined to form proteins that have unique three-dimensional structures,
making them capable of performing specific biologic functions.

II. STRUCTURE
Although >300 different amino acids have been described in nature, only 20 are
commonly found as constituents of mammalian proteins. [Note: These standard
amino acids are the only amino acids that are encoded by DNA, the genetic
material in the cell (see p. 411). Nonstandard amino acids are produced by
chemical modification of standard amino acids (see p. 45).] Each amino acid has
a carboxyl group, a primary amino group (except for proline, which has a
secondary amino group), and a distinctive side chain (R group) bonded to the α-
carbon atom. At physiologic pH (~7.4), the carboxyl group is dissociated,
forming the negatively charged carboxylate ion (−COO−), and the amino group
is protonated (−NH3+) (Fig. 1.1A). In proteins, almost all of these carboxyl and
amino groups are combined through peptide linkage and, in general, are not
available for chemical reaction except for hydrogen bond formation (Fig. 1.1B).
Thus, it is the nature of the side chains that ultimately dictates the role an amino
acid plays in a protein. Therefore, it is useful to classify the amino acids
according to the properties of their side chains, that is, whether they are nonpolar
(have an even distribution of electrons) or polar (have an uneven distribution of
electrons, such as acids and bases) as shown in Figures 1.2 and 1.3.
Figure 1.1 A, B. Structural features of amino acids.

Figure 1.2 Classification of the 20 standard amino acids, according to the charge
and polarity of their side chains at acidic pH, is shown here and continues in
Figure 1.3. Each amino acid is shown in its fully protonated form, with
dissociable hydrogen ions represented in red. The pK values for the α-carboxyl
and α-amino groups of the nonpolar amino acids are similar to those shown for
glycine.
Figure 1.3 Classification of the 20 standard amino acids, according to the charge
and polarity of their side chains at acidic pH (continued from Fig. 1.2). [Note: At
physiologic pH (7.35 to 7.45), the α-carboxyl groups, the acidic side chains, and
the side chain of free histidine are deprotonated.]

A. Amino acids with nonpolar side chains

Each of these amino acids has a nonpolar side chain that does not gain or
lose protons or participate in hydrogen or ionic bonds (see Fig. 1.2). The
side chains of these amino acids can be thought of as “oily” or lipid-like, a
property that promotes hydrophobic interactions (see Fig. 2.10, p. 19).
1. Location in proteins: In proteins found in aqueous solutions (a polar
environment), the side chains of the nonpolar amino acids tend to cluster
together in the interior of the protein (Fig. 1.4). This phenomenon,
known as the hydrophobic effect, is the result of the hydrophobicity of
the nonpolar R groups, which act much like droplets of oil that coalesce
in an aqueous environment. By filling up the interior of the folded
protein, these nonpolar R groups help give the protein its three-
dimensional shape. However, for proteins that are located in a
hydrophobic environment, such as a membrane, the nonpolar R groups
are found on the outside surface of the protein, interacting with the lipid
environment (see Fig. 1.4). The importance of these hydrophobic
interactions in stabilizing protein structure is discussed on p. 19.
Figure 1.4 Location of nonpolar amino acids in soluble and membrane proteins.

Sickle cell anemia, a disease of red blood cells that causes them to become
sickle shaped rather than disc shaped, results from the replacement of polar
glutamate with nonpolar valine at the sixth position in the β subunit of
hemoglobin A (see p. 36).

2. Proline: Proline differs from other amino acids in that its side chain and
α-amino nitrogen form a rigid, five-membered ring structure (Fig. 1.5).
 Proline, then, has a secondary (rather than a primary) amino group. It is
frequently referred to as an “imino acid.” The unique geometry of proline
contributes to the formation of the fibrous structure of collagen (see p.
45), but it interrupts the α-helices found in globular proteins (see p. 16).

Figure 1.5 Comparison of the secondary amino group found in proline with the
primary amino group found in other amino acids such as alanine.

B. Amino acids with uncharged polar side chains

These amino acids have zero net charge at physiologic pH, although the
side chains of cysteine and tyrosine can lose a proton at an alkaline pH (see
Fig. 1.3). Serine, threonine, and tyrosine each contain a polar hydroxyl
group that can participate in hydrogen bond formation (Fig. 1.6). The side
chains of asparagine and glutamine each contain a carbonyl group and an
amide group, both of which can also participate in hydrogen bonds.
Figure 1.6 Hydrogen bond between the phenolic hydroxyl group of tyrosine and
another molecule containing a carbonyl group.

1. Disulfide bond: The side chain of cysteine contains a sulfhydryl (thiol)

group (−SH), which is an important component of the active site of many
enzymes. In proteins, the –SH groups of two cysteines can be oxidized to
form a covalent cross-link called a disulfide bond (−S–S–). Two
disulfide-linked cysteines are referred to as cystine. (See p. 19 for a
further discussion of disulfide bond formation.)

Many extracellular proteins are stabilized by disulfide bonds. Albumin, a

blood protein that functions as a transporter for a variety of molecules, is an
example.
 2. Side chains as attachment sites for other compounds: The polar hydroxyl
group of serine, threonine, and (rarely) tyrosine can serve as a site of
attachment for structures such as a phosphate group. In addition, the
amide group of asparagine, as well as the hydroxyl group of serine or
threonine, can serve as a site of attachment for oligosaccharide chains in
glycoproteins (see p. 165).

C. Amino acids with acidic side chains

The amino acids aspartic acid and glutamic acid are proton donors. At
physiologic pH, the side chains of these amino acids are fully ionized,
containing a negatively charged carboxylate group (−COO−). The fully
ionized forms are called aspartate and glutamate.

D. Amino acids with basic side chains

The side chains of the basic amino acids accept protons (see Fig. 1.3). At
physiologic pH, the R groups of lysine and arginine are fully ionized and
positively charged. In contrast, the free amino acid histidine is weakly basic
and largely uncharged at physiologic pH. However, when histidine is
incorporated into a protein, its R group can be either positively charged
(protonated) or neutral, depending on the ionic environment provided by
the protein. This important property of histidine contributes to the buffering
role it plays in the functioning of such proteins as hemoglobin (see p. 30).
[Note: Histidine is the only amino acid with a side chain that can ionize
within the physiologic pH range.]

E. Abbreviations and symbols for commonly occurring

amino acids
Each amino acid name has an associated three-letter abbreviation and a one-
letter symbol (Fig. 1.7). The one-letter codes are determined by the
following rules.
Figure 1.7 Abbreviations and symbols for the standard amino acids.

1. Unique first letter: If only one amino acid begins with a given letter, then
that letter is used as its symbol. For example, V = valine.
2. Most commonly occurring amino acids have priority: If more than one
amino acid begins with a particular letter, the most common of these
amino acids receives this letter as its symbol. For example, glycine is
more common than glutamate, so G = glycine.
3. Similar sounding names: Some one-letter symbols sound like the amino
acid they represent. For example, F = phenylalanine, or W = tryptophan
(“twyptophan” as Elmer Fudd would say).
4. Letter close to initial letter: For the remaining amino acids, a one-letter
symbol is assigned that is as close in the alphabet as possible to the initial
letter of the amino acid, for example, K = lysine. Furthermore, B is
assigned to Asx, signifying either aspartic acid or asparagine; Z is
assigned to Glx, signifying either glutamic acid or glutamine; and X is
assigned to an unidentified amino acid.

F. Amino acid isomers

Because the α-carbon of an amino acid is attached to four different chemical
groups, it is an asymmetric (chiral) atom. Glycine is the exception because
its α-carbon has two hydrogen substituents. Amino acids with a chiral α-
carbon exist in two different isomeric forms, designated D and L, which are
enantiomers, or mirror images (Fig. 1.8). [Note: Enantiomers are optically
active. If an isomer, either D or L, causes the plane of polarized light to
rotate clockwise, it is designated the (+) form.] All amino acids found in
mammalian proteins are of the L configuration. However, D-amino acids are
found in some antibiotics and in bacterial cell walls (see p. 252). [Note:
Racemases enzymatically interconvert the D- and L-isomers of free amino
acids.]
Figure 1.8 D and L forms of alanine are mirror images (enantiomers).

III. ACIDIC AND BASIC PROPERTIES

Amino acids in aqueous solution contain weakly acidic α-carboxyl groups and
weakly basic α-amino groups. In addition, each of the acidic and basic amino
acids contains an ionizable group in its side chain. Thus, both free amino acids
and some amino acids combined in peptide linkages can act as buffers. Acids
may be defined as proton donors and bases as proton acceptors. Acids (or bases)
described as weak ionize to only a limited extent. The concentration of protons
([H+]) in aqueous solution is expressed as pH, where pH = log 1/[H+] or –log
[H+]. The quantitative relationship between the pH of the solution and
concentration of a weak acid (HA) and its conjugate base (A−) is described by
the Henderson-Hasselbalch equation.

A. Equation derivation
Consider the release of a proton by a weak acid represented by HA:
 The salt or conjugate base, A−, is the ionized form of a weak acid. By
definition, the dissociation constant of the acid, Ka, is:

[Note: The larger the Ka, the stronger the acid, because most of the HA has
dissociated into H+ and A−. Conversely, the smaller the Ka, the less acid has
dissociated and, therefore, the weaker the acid.] By solving for the [H+] in
the above equation, taking the logarithm of both sides of the equation,
multiplying both sides of the equation by −1, and substituting pH = −log
[H+] and pKa = −log Ka, we obtain the Henderson-Hasselbalch equation:

B. Buffers
A buffer is a solution that resists change in pH following the addition of an
acid or base. A buffer can be created by mixing a weak acid (HA) with its
conjugate base (A−). If an acid such as HCl is added to a buffer, A− can
neutralize it, being converted to HA in the process. If a base is added, HA
can likewise neutralize it, being converted to A− in the process. Maximum
buffering capacity occurs at a pH equal to the pKa, but a conjugate acid-
base pair can still serve as an effective buffer when the pH of a solution is
within approximately ±1 pH unit of the pKa. If the amounts of HA and A−
are equal, the pH is equal to the pKa. As shown in Figure 1.9, a solution
containing acetic acid (HA = CH3 – COOH) and acetate (A− = CH3 –
COO−) with a pKa of 4.8 resists a change in pH from pH 3.8 to 5.8, with
maximum buffering at pH 4.8. At pH values less than the pKa, the
protonated acid form (CH3 – COOH) is the predominant species in solution.
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desde su entrada en la fúnebre capilla sintió que su magnánimo
corazón se arrugaba y comprimía.
—Sí, sí; perdono, perdono a todo el mundo —balbució el reo
fijando otra vez toda su atención en los ladrillos del piso—. Vamos ya..
¿No es hora?
Pero su ánimo, rápidamente abatido, forcejeó iracundo en las
tinieblas y se rehizo. Fue como si se hubiera dado un latigazo. La
dosis de energía que desplegara en aquel momento era tal, que solo
estando muerta hubiera dejado la mísera carne de responder a ella
Tenía Sarmiento entre las manos su pañuelo; y apretando los dedos
fuertemente sobre él y separando las manos, lo partió en dos pedazos
sin rasgarlo. Cerrando los ojos murmuraba:
—¡Cayo Graco!... ¡Lucas!... ¡Dios que diste la libertad al mundo...!
El verdugo mostró un saco negro. Era la hopa que se pone a los
condenados para hacer más irrisorio y horriblemente burlesco e
crimen de la pena de muerte. Cuando el delito era de alta traición, la
hopa era amarilla y encarnada. La de Sarmiento era negra
Completaba el ajuar un gorro también negro.
—Venga la túnica —dijo preparándose a ponérsela—. Reputo e
saco como una vestidura de gala y el gorro como una corona de
laurel.[4]
[4] Estas palabras las dijo el valeroso patriota ahorcado el 24 de
agosto de 1825. Su noble y heroico comportamiento en las últimas
horas, da en cierto modo carácter histórico al personaje ideal que es
protagonista de esta obra.

Después le ataron las manos y le pusieron un cordel a la cintura, a

cuyas operaciones no hizo resistencia, antes bien, se prestó a ellas
con cierta gallardía. Incapacitados los movimientos de sus brazos
llamó a Sola y le dijo:
—Hija mía, ven a abrazar por última vez a tu viejecillo bobo.
La huérfana lo estrechó en sus brazos, y regó con sus lágrimas e
cuello del anciano.
—¿A qué vienen esos lloros? —dijo este sofocando su emoción—
Hija de mi alma, nos veremos en la gloria, a donde yo he tenido la
suerte de ir antes que tú. De mi imperecedera fama en el mundo, tú
sola, tú serás única heredera, porque me asististe y amparaste en mis
últimos días. Tu nombre, como el mío, pasará de generación en
generación... No llores: llena tu alma de alegría, como lo está la mía
Hoy es día de triunfo; esto no es muerte, es vida. El torpe lenguaje de
los hombres ha alterado el sentido de todas las cosas. Yo siento que
penetra en mí la respiración de los ángeles invisibles que están a m
lado, prontos a llevarme a la morada celestial... Es como un fresco
delicioso..., como un aroma delicado... Adiós..., hasta luego, hija mía..
No olvides mis dos recomendaciones, ¿oyes? Vete con ese hombre...
¿oyes?..., los apuntes... Adiós, mi glorioso destino se cumple... ¡Viva
yo! ¡Viva Patricio Sarmiento!
Desprendieron a Sola de sus brazos; tomola en los suyos el alcaide
para prestarle algún socorro, y don Patricio salió de la capilla con paso
seguro.
El padre Alelí le ató un crucifijo en las manos, y Salmón quiso
ponerle también una estampa de la Virgen; pero opúsose a ello el reo
diciendo:
—Con mucho gusto llevaré conmigo la imagen de mi Redentor
cuyo ejemplo sigo; pero no esperen vuestras paternidades que yo
vaya por la carrera besando una estampita. Adelante.
Al llegar a la calle, presentáronle el asno en que había de montar, y
subió a él con arrogantes movimientos, diciendo:
—He aquí la más noble cabalgadura cuyos lomos han oprimido
héroes antiguos y modernos. Ya estoy en marcha.
Al llegar a la calle de la Concepción Jerónima y ver el inmenso
gentío que se agolpaba en las aceras y en los balcones, en vez de
amilanarse, como otros, se creció, se engrandeció, tomando
extraordinaria altitud. Revolviendo los ojos en todas direcciones, arriba
y abajo, decía para sí:
«Pueblo, pueblo generoso, mírame bien, para que ningún rasgo de
mi persona deje de grabarse en tu memoria. ¡Oh! ¡Si pudiera yo
hablarte en este momento!... Soy Patricio Sarmiento, soy yo, soy tu
grande hombre. Mírame y llénate de gozo, porque la libertad, por quien
muero, renacerá de mi sangre, y el despotismo que a mí me inmola
perecerá ahogado por esta misma sangre, y el principio que yo
consagro muriendo, lo disfrutarás tú viviendo, lo disfrutarás por los
siglos de los siglos».
El murmullo del pueblo crecía entre los roncos tambores, y a él le
pareció que toda aquella música se juntaba para exclamar:
—¡Viva Patricio Sarmiento!
 El padre Alelí le mostraba el crucifijo que en su mano llevaba, y le
decía que consagrase a Dios su último pensamiento. Después e
venerable fraile rezaba en silencio, no se sabe si por el reo o por sus
jueces. Probablemente sería por estos últimos.
Al llegar a la plazuela, Sarmiento extendió la vista por aquel mar de
cabezas, y viendo la horca, dijo:
—¡Ahí está!... Ahí está mi trono.
Y al ver aquello, que a otros les lleva al postrer grado de
abatimiento, él se engrandeció más y más, sintiendo su alma llena de
una exaltación sublime y de entusiasmo expansivo.
—Estoy en el último escalón, en el más alto —dijo—. Desde aqu
veo al mísero género humano, abajo, perdido en la bruma de sus
rencores y de su ignorancia. Un paso más, y penetraré en la eternidad
donde está vacío mi puesto en el luminoso estrado de los héroes y de
los mártires.
Al pie de la horca, rogáronle los frailes que adorase al crucifijo, lo
que hizo muy gustoso, besándolo y orando en voz alta con entonación
vigorosa.
—Muero por la libertad como cristiano católico —exclamó—. ¡Oh
Dios a quien he servido, acógeme en tu seno!
Quisieron ayudarle a subir la escalera fatal; pero él
desprendiéndose de ajenos brazos, subió solo. El patíbulo tenía tres
escaleras: por la del centro subía el reo, por una de las laterales e
verdugo y por la otra el sacerdote auxiliante. Cada cual ocupó su
puesto. Al ver que el cordel rodeaba su cuello, Sarmiento dijo con
enfado:
—¿Y qué? ¿No me dejan hablar?
Los sacerdotes habían empezado el Credo. Callaron. Juzgando que
el silencio era permiso para hablar, el patriota se dirigió al pueblo en
estos términos:
—Pueblo, pueblo mío, contémplame y une tu voz a la mía para
gritar: ¡Viva la...!
Empujole el verdugo y se lanzó con él.
Cayeron de rodillas los sacerdotes que habían permanecido abajo
y elevando el crucifijo, exclamaron consternados:
—¡Misericordia, Señor!
La muchedumbre lanzó el trágico murmullo que indicaba su
curiosidad satisfecha y su fúnebre espanto consumado.
El padre Alelí dijo tristemente:
—Desgraciado, sube al limbo.
 XXIX

¿Qué sabía él?... A pesar de ser fraile discreto y gran sabedor de

teología, ¿qué sabía él si su penitente había ido al limbo, o a otra
parte? ¿Quién puede afirmar a dónde van las almas inflamadas en
entusiasmo y fe? ¿Habrá quien marque de un modo preciso la esfera
donde el humano sentido merecedor de asombro y respeto, se trueca
en la enajenación digna de lástima? Siendo evidente que en aquella
alma se juntaban con aleación extraña la excelsitud y la trivialidad
¿quién podrá decir cuál de estas cualidades a la otra vencía?
Glorifiquémosle todos. Murió pensando en la página histórica que no
había de llenar, y en la fama póstuma que no había de tener. ¡Oh, Dios
poderoso! ¡Cuántos tienen esta con menos motivo, y cuántos ocupan
aquella habiendo sido tan locos como él, y menos, mucho menos
sublimes!

fin de «el terror de 1824»

Madrid, octubre de 1877.

 *** END OF THE PROJECT GUTENBERG EBOOK EL TERROR DE
1824 ***

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