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1.1 Cellular Foundations 3

organisms contain many different types of cells, which concentrated solution containing enzymes and the RNA
vary in size, shape, and specialized function. Despite molecules that encode them; the components (amino
these obvious differences, all cells of the simplest and acids and nucleotides) from which these macromolecules
most complex organisms share certain fundamental are assembled; hundreds of small organic molecules called
properties, which can be seen at the biochemical level. metabolites, intermediates in biosynthetic and degrada-
tive pathways; coenzymes, compounds essential to many
Cells Are the Structural and Functional Units enzyme-catalyzed reactions; and inorganic ions.
All cells have, for at least some part of their life, either
of All Living Organisms a nucleoid or a nucleus, in which the genome—the
Cells of all kinds share certain structural features complete set of genes, composed of DNA—is replicated
(Fig. 1–3). The plasma membrane defines the periph- and stored, with its associated proteins. The nucleoid, in
ery of the cell, separating its contents from the sur- bacteria and archaea, is not separated from the cytoplasm
roundings. It is composed of lipid and protein molecules by a membrane; the nucleus, in eukaryotes, is enclosed
that form a thin, tough, pliable, hydrophobic barrier within a double membrane, the nuclear envelope. Cells
around the cell. The membrane is a barrier to the free with nuclear envelopes make up the large domain Eukarya
passage of inorganic ions and most other charged or (Greek eu, “true,” and karyon, “nucleus”). Microorgan-
polar compounds. Transport proteins in the plasma isms without nuclear membranes, formerly grouped
membrane allow the passage of certain ions and mole- together as prokaryotes (Greek pro, “before”), are now
cules; receptor proteins transmit signals into the cell; recognized as comprising two very distinct groups: the
and membrane enzymes participate in some reaction domains Bacteria and Archaea, described below.
pathways. Because the individual lipids and proteins of
the plasma membrane are not covalently linked, the
entire structure is remarkably flexible, allowing changes
Cellular Dimensions Are Limited by Diffusion
in the shape and size of the cell. As a cell grows, newly Most cells are microscopic, invisible to the unaided eye.
made lipid and protein molecules are inserted into its Animal and plant cells are typically 5 to 100 mm in diam-
plasma membrane; cell division produces two cells, each eter, and many unicellular microorganisms are only 1 to
with its own membrane. This growth and cell division 2 mm long (see the inside back cover for information on
(fission) occurs without loss of membrane integrity. units and their abbreviations). What limits the dimen-
The internal volume enclosed by the plasma mem- sions of a cell? The lower limit is probably set by the
brane, the cytoplasm (Fig. 1–3), is composed of an minimum number of each type of biomolecule required
aqueous solution, the cytosol, and a variety of suspended by the cell. The smallest cells, certain bacteria known as
particles with specific functions. These particulate com- mycoplasmas, are 300 nm in diameter and have a volume
ponents (membranous organelles such as mitochondria of about 10214 mL. A single bacterial ribosome is about
and chloroplasts; supramolecular structures such as ribo- 20 nm in its longest dimension, so a few ribosomes take up
somes and proteasomes, the sites of protein synthesis a substantial fraction of the volume in a mycoplasmal cell.
and degradation) sediment when cytoplasm is centrifuged The upper limit of cell size is probably set by the
at 150,000 g (g is the gravitational force of Earth). What rate of diffusion of solute molecules in aqueous systems.
remains as the supernatant fluid is the cytosol, a highly For example, a bacterial cell that depends on oxygen-
consuming reactions for energy extraction must obtain
molecular oxygen by diffusion from the surrounding
medium through its plasma membrane. The cell is so
small, and the ratio of its surface area to its volume is so
Cytoplasm large, that every part of its cytoplasm is easily reached
Plasma membrane by O2 diffusing into the cell. With increasing cell size,
Ribosomes however, surface-to-volume ratio decreases, until
50 mm
1 mm Nucleus metabolism consumes O2 faster than diffusion can sup-
Nucleoid
Nuclear membrane ply it. Metabolism that requires O2 thus becomes impos-
Membrane-bounded sible as cell size increases beyond a certain point, plac-
organelles ing a theoretical upper limit on the size of cells. Oxygen
Bacterial cell Animal cell is only one of many low molecular weight species that
must diffuse from outside the cell to various regions of
FIGURE 1–3 The universal features of living cells. All cells have a nucleus its interior, and the same surface-to-volume argument
or nucleoid containing their DNA, a plasma membrane, and cytoplasm. applies to each of them as well.
The cytosol is defined as that portion of the cytoplasm that remains in the
supernatant after gentle breakage of the plasma membrane and centrifu-
gation of the resulting extract at 150,000 g for 1 hour. Eukaryotic cells
There Are Three Distinct Domains of Life
contain a variety of membrane-bounded organelles (mitochondria, chloro- All living organisms fall into one of three large groups
plasts) and large particles (ribosomes, for example), which are sedimented (domains) that define three branches of the evolution-
by this centrifugation and can be recovered from the pellet. ary tree of life originating from a common progenitor
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4 The Foundations of Biochemistry

Eukarya
Animals
Green Entamoebae Slime
Bacteria nonsulfur Archaea molds
bacteria Fungi
Gram-
Methanosarcina
positive Plants
Proteobacteria bacteria Methanobacterium
Halophiles Ciliates
(Purple bacteria) Thermoproteus Methanococcus
Cyanobacteria Pyrodictium Thermococcus Flagellates
Flavobacteria
Trichomonads

Thermotogales

Microsporidia
Diplomonads

Last universal common ancestor

FIGURE 1–4 Phylogeny of the three domains of life. Phylogenetic rela- also be constructed from similarities across species of the amino acid
tionships are often illustrated by a
family tree
of this type. The basis sequences of a single protein. For example, sequences of the protein
for this tree is the similarity in nucleotide sequences of the ribosomal GroEL (a bacterial protein that assists in protein folding) were compared to
RNAs of each group; the more similar the sequence, the closer the loca- generate the tree in Figure 3
35. The tree in Figure 3
36 is a
consensus

tion of the branches, with the distance between branches representing tree, which uses several comparisons such as these to derive the best
the degree of difference between two sequences. Phylogenetic trees can estimates of evolutionary relatedness among a group of organisms.

(Fig. 1–4). Two large groups of single-celled microor- material (as summarized in Fig. 1–5). There are two
ganisms can be distinguished on genetic and biochemical broad categories based on energy sources: phototrophs
grounds: Bacteria and Archaea. Bacteria inhabit soils, (Greek trophē, “nourishment”) trap and use sunlight, and
surface waters, and the tissues of other living or decaying chemotrophs derive their energy from oxidation of a
organisms. Many of the Archaea, recognized as a distinct chemical fuel. Some chemotrophs oxidize inorganic fuels—
domain by Carl Woese in the 1980s, inhabit extreme HS2 to S0 (elemental sulfur), S0 to to or
environments—salt lakes, hot springs, highly acidic bogs, to for example. Phototrophs and chemotrophs
and the ocean depths. The available evidence suggests may be further divided into those that can synthesize all of
that the Archaea and Bacteria diverged early in evolu- their biomolecules directly from CO2 (autotrophs) and
tion. All eukaryotic organisms, which make up the third those that require some preformed organic nutrients made
domain, Eukarya, evolved from the same branch that by other organisms (heterotrophs). We can describe an
gave rise to the Archaea; eukaryotes are therefore more organism’s mode of nutrition by combining these terms.
closely related to archaea than to bacteria. For example, cyanobacteria are photoautotrophs; humans
Within the domains of Archaea and Bacteria are are chemoheterotrophs. Even finer distinctions can be
subgroups distinguished by their habitats. In aerobic made, and many organisms can obtain energy and carbon
habitats with a plentiful supply of oxygen, some resi- from more than one source under different environmental
dent organisms derive energy from the transfer of elec- or developmental conditions.
trons from fuel molecules to oxygen within the cell.
Other environments are anaerobic, virtually devoid of Bacterial and Archaeal Cells Share Common Features
oxygen, and microorganisms adapted to these environ- but Differ in Important Ways
ments obtain energy by transferring electrons to nitrate
The best-studied bacterium, Escherichia coli, is a usu-
(forming N2), sulfate (forming H2S), or CO2 (forming
ally harmless inhabitant of the human intestinal tract.
CH4). Many organisms that have evolved in anaerobic
The E. coli cell (Fig. 1–6a) is an ovoid about 2 mm
environments are obligate anaerobes: they die when
long and a little less than 1 mm in diameter, but other
exposed to oxygen. Others are facultative anaerobes,
bacteria may be spherical or rod-shaped. It has a pro-
able to live with or without oxygen.
tective outer membrane and an inner plasma mem-
brane that encloses the cytoplasm and the nucleoid.
Organisms Differ Widely in Their Sources of Energy Between the inner and outer membranes is a thin but
and Biosynthetic Precursors strong layer of a high molecular weight polymer (pepti-
We can classify organisms according to how they obtain doglycan) that gives the cell its shape and rigidity. The
the energy and carbon they need for synthesizing cellular plasma membrane and the layers outside it constitute
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1.1 Cellular Foundations 5

All organisms

Energy source
Chemical Light

Chemotrophs Phototrophs

Carbon source Carbon source

CO2 Organic compounds CO2 Organic compounds

Chemoautotrophs Chemoheterotrophs Photoautotrophs Photoheterotrophs

Final electron acceptor Use H2O to reduce CO2?

O2 Yes No

Hydrogen-, sulfur-, All animals; most fungi, Oxygenic Anoxygenic Green nonsulfur
iron-, nitrogen-, and protists, bacteria photosynthesis photosynthetic bacteria,
carbon monoxide- (plants, algae, bacteria (green and purple nonsulfur
oxidizing bacteria cyanobacteria) purple bacteria) bacteria

Not O2
Organic Inorganic
compounds compounds

Fermentative …Pseudomonas
bacteria such as denitrificans,
Lactococcus lactis and… for example

FIGURE 1–5 All organisms can be classified according to their source of energy (sunlight or oxidizable chemical compounds) and their source
of carbon for the synthesis of cellular material.

the cell envelope. The plasma membranes of bacteria The cytoplasm of E. coli contains about 15,000
consist of a thin bilayer of lipid molecules penetrated ribosomes, various numbers (10 to thousands) of copies
by proteins. Archaeal plasma membranes have a similar of each of 1,000 or so different enzymes, perhaps 1,000
architecture, but the lipids can be strikingly different organic compounds of molecular weight less than 1,000
from those of bacteria (see Fig. 10–12). Bacteria and (metabolites and cofactors), and a variety of inorganic
archaea have group-specific specializations of their cell ions. The nucleoid contains a single, circular molecule
envelopes (Fig. 1–6b–d). Some bacteria, called gram- of DNA, and the cytoplasm (like that of most bacteria)
positive because they are colored by Gram’s stain contains one or more smaller, circular segments of DNA
(introduced by Hans Peter Gram in 1882), have a thick called plasmids. In nature, some plasmids confer resis-
layer of peptidoglycan outside their plasma membrane tance to toxins and antibiotics in the environment. In
but lack an outer membrane. Gram-negative bacteria the laboratory, these DNA segments are especially ame-
have an outer membrane composed of a lipid bilayer nable to experimental manipulation and are powerful
into which are inserted complex lipopolysaccharides tools for genetic engineering (see Chapter 9).
and proteins called porins that provide transmembrane Other species of bacteria, as well as archaea, contain
channels for low molecular weight compounds and ions a similar collection of biomolecules, but each species has
to diffuse across this outer membrane. The structures physical and metabolic specializations related to its envi-
outside the plasma membrane of archaea differ from ronmental niche and nutritional sources. Cyanobacteria,
organism to organism, but they, too, have a layer of for example, have internal membranes specialized to
peptidoglycan or protein that confers rigidity on their trap energy from light (see Fig. 19–67). Many archaea
cell envelopes. live in extreme environments and have biochemical
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6 The Foundations of Biochemistry

(a) Ribosomes Bacterial and archaeal ribosomes are smaller than (b) Gram-positive bacteria
eukaryotic ribosomes, but serve the same function—
protein synthesis from an RNA message. Polysaccharide
Cell envelope
structures differ. Solid layer

Glycoprotein
Nucleoid
Contains one Peptidoglycan
or several long,
circular DNA
molecules. Plasma membrane
Cytoplasm Lipoprotein
(c) Gram-negative bacteria (shown at left)
Pili Provide
points of LPS
adhesion to
surface of Outer membrane
other cells.
Lipoprotein Porin
Peptidoglycan

Periplasm
Plasma membrane
Cytoplasm Lipoprotein
(d) Methanothermus, an extremely heat-tolerant archaeon
Solid layer

Flagella Glycoprotein
Propel cell Pseudo-
through its peptidoglycan
surroundings.
Plasma membrane
Cytoplasm

FIGURE 1–6 Some common structural features of bacterial and archaeal membrane is studded with protein channels (porins) that allow small
cells. (a) This correct-scale drawing of E. coli serves to illustrate some molecules, but not proteins, to diffuse through. The inner (plasma) mem-
common features. (b) The cell envelope of gram-positive bacteria is a single brane, made of phospholipids and proteins, is impermeant to both large
membrane with a thick, rigid layer of peptidoglycan on its outside surface. and small molecules. Between the inner and outer membranes, in the
A variety of polysaccharides and other complex polymers are interwoven periplasm, is a thin layer of peptidoglycan, which gives the cell shape and
with the peptidoglycan, and surrounding the whole is a porous
solid rigidity, but does not retain Gram's stain. (d) Archaeal membranes vary in
layer
composed of glycoproteins. (c) E. coli is gram-negative and has a structure and composition, but all have a single membrane surrounded by
double membrane. Its outer membrane has a lipopolysaccharide (LPS) an outer layer that includes either a peptidoglycanlike structure, a porous
on the outer surface and phospholipids on the inner surface. This outer protein shell (solid layer), or both.

adaptations to survive in extremes of temperature, pres- volumes a thousand to a million times larger than those
sure, or salt concentration. Differences in ribosomal of bacteria. The distinguishing characteristics of eukary-
structure gave the first hints that Bacteria and Archaea otes are the nucleus and a variety of membrane-enclosed
constituted separate domains. Most bacteria (including organelles with specific functions. These organelles
E. coli) exist as individual cells, but often associate in include mitochondria, the site of most of the energy-
biofilms or mats, in which large numbers of cells adhere extracting reactions of the cell; the endoplasmic retic-
to each other and to some solid substrate beneath or at ulum and Golgi complexes, which play central roles in
an aqueous surface. Cells of some bacterial species (the the synthesis and processing of lipids and membrane
myxobacteria, for example) show simple social behavior, proteins; peroxisomes, in which very long-chain fatty
forming many-celled aggregates in response to signals acids are oxidized; and lysosomes, filled with digestive
between neighboring cells. enzymes to degrade unneeded cellular debris. In addi-
tion to these, plant cells also contain vacuoles (which
store large quantities of organic acids) and chloro-
Eukaryotic Cells Have a Variety of Membranous plasts (in which sunlight drives the synthesis of ATP in
Organelles, Which Can Be Isolated for Study the process of photosynthesis) (Fig. 1–7). Also present
Typical eukaryotic cells (Fig. 1–7) are much larger than in the cytoplasm of many cells are granules or droplets
bacteria—commonly 5 to 100 mm in diameter, with cell containing stored nutrients such as starch and fat.
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1.1 Cellular Foundations 7

(a) Animal cell

Ribosomes are protein-
synthesizing machines.
Peroxisome oxidizes fatty acids.

Cytoskeleton supports cell, aids

in movement of organelles.

Lysosome degrades intracellular

debris.
Transport vesicle shuttles lipids
and proteins between ER, Golgi,
and plasma membrane.
Golgi complex processes,
packages, and targets proteins to
other organelles or for export.

Smooth endoplasmic reticulum

(SER) is site of lipid synthesis
and drug metabolism.

Nuclear envelope segregates Nucleolus is site of ribosomal

chromatin (DNA ! protein) RNA synthesis.
from cytoplasm. Nucleus contains the
Rough endoplasmic reticulum
(RER) is site of much protein genes (chromatin).
Plasma membrane separates cell synthesis.
from environment, regulates Nuclear
movement of materials into and envelope Ribosomes Cytoskeleton
out of cell.
Mitochondrion oxidizes fuels to
produce ATP.

Chloroplast harvests sunlight,

produces ATP and carbohydrates. Golgi complex

Starch granule temporarily stores

carbohydrate products of
photosynthesis.

Thylakoids are site of light-

driven ATP synthesis.

Cell wall provides shape and

rigidity; protects cell from
osmotic swelling.

Vacuole degrades and recycles

macromolecules, stores
metabolites. Cell wall of adjacent cell
Plasmodesma provides path
between two plant cells.
Glyoxysome contains enzymes of
the glyoxylate cycle.

(b) Plant cell

FIGURE 1–7 Eukaryotic cell structure. Schematic illustrations of two labeled in red are unique to animal cells; those labeled in green are
major types of eukaryotic cell: (a) a representative animal cell and (b) a unique to plant cells. Eukaryotic microorganisms (such as protists and
representative plant cell. Plant cells are usually 10 to 100 mm in diameter
fungi) have structures similar to those in plant and animal cells, but
larger than animal cells, which typically range from 5 to 30 mm. Structures many also contain specialized organelles not illustrated here.
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8 The Foundations of Biochemistry

In a major advance in biochemistry, Albert Claude, leaves most of the organelles intact. The homogenate is
Christian de Duve, and George Palade developed methods then centrifuged; organelles such as nuclei, mitochondria,
for separating organelles from the cytosol and from each and lysosomes differ in size and therefore sediment at dif-
other—an essential step in investigating their structures ferent rates.
and functions. In a typical cell fractionation (Fig. 1–8), These methods were used to establish, for example,
cells or tissues in solution are gently disrupted by physical that lysosomes contain degradative enzymes, mitochon-
shear. This treatment ruptures the plasma membrane but dria contain oxidative enzymes, and chloroplasts contain
photosynthetic pigments. The isolation of an organelle
enriched in a certain enzyme is often the first step in the
purification of that enzyme.

Differential
centrifugation The Cytoplasm Is Organized by the Cytoskeleton
and Is Highly Dynamic
Tissue Fluorescence microscopy reveals several types of pro-
homogenization tein filaments crisscrossing the eukaryotic cell, forming
an interlocking three-dimensional meshwork, the cyto-
Low-speed centrifugation skeleton. There are three general types of cytoplasmic
(1,000 g, 10 min) filaments—actin filaments, microtubules, and interme-
diate filaments (Fig. 1–9)—differing in width (from
about 6 to 22 nm), composition, and specific function.
Supernatant subjected to All types provide structure and organization to the cyto-
medium-speed centrifugation
(20,000 g, 20 min) plasm and shape to the cell. Actin filaments and micro-
▲
tubules also help to produce the motion of organelles or
▲ Supernatant subjected of the whole cell.
▲ to high-speed
Tissue ▲
❚

Each type of cytoskeletal component is composed

▲

homogenate ▲ ▲
centrifugation
▲ (80,000 g, 1 h) of simple protein subunits that associate noncovalently
▲
▲ to form filaments of uniform thickness. These fila-
▲
▲

▲
▲

▲ ▲ ments are not permanent structures; they undergo

▲
Supernatant
Pellet subjected to
constant disassembly into their protein subunits and
contains very high-speed reassembly into filaments. Their locations in cells are
whole cells, centrifugation not rigidly fixed but may change dramatically with
nuclei, (150,000 g, 3 h)
cytoskeletons, mitosis, cytokinesis, amoeboid motion, or changes in
plasma cell shape. The assembly, disassembly, and location of
membranes Pellet all types of filaments are regulated by other proteins,
contains
mitochondria,
which serve to link or bundle the filaments or to move
lysosomes, cytoplasmic organelles along the filaments. (Bacteria
peroxisomes contain actinlike proteins that serve similar roles in
Pellet
contains Supernatant those cells.)
microsomes contains The picture that emerges from this brief survey of
(fragments soluble
proteins eukaryotic cell structure is of a cell with a meshwork of
of ER),
small vesicles structural fibers and a complex system of membrane-
enclosed compartments (Fig. 1–7). The filaments disas-
Pellet contains
semble and then reassemble elsewhere. Membranous
ribosomes, large vesicles bud from one organelle and fuse with another.
macromolecules Organelles move through the cytoplasm along protein
FIGURE 1–8 Subcellular fractionation of tissue. A tissue such as liver is filaments, their motion powered by energy-dependent
first mechanically homogenized to break cells and disperse their contents motor proteins. The endomembrane system segre-
in an aqueous buffer. The sucrose medium has an osmotic pressure simi- gates specific metabolic processes and provides surfaces
lar to that in organelles, thus balancing diffusion of water into and out of on which certain enzyme-catalyzed reactions occur.
the organelles, which would swell and burst in a solution of lower osmo- Exocytosis and endocytosis, mechanisms of transport
larity (see Fig. 2
13). The large and small particles in the suspension can (out of and into cells, respectively) that involve mem-
be separated by centrifugation at different speeds. Larger particles sedi- brane fusion and fission, provide paths between the
ment more rapidly than small particles, and soluble material does not cytoplasm and surrounding medium, allowing for secre-
sediment. By careful choice of the conditions of centrifugation, subcellular tion of substances produced in the cell and uptake of
fractions can be separated for biochemical characterization. extracellular materials.
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1.1 Cellular Foundations 9

between the cytoskeleton and organelles are noncova-

lent, reversible, and subject to regulation in response to
various intracellular and extracellular signals.

Cells Build Supramolecular Structures

Macromolecules and their monomeric subunits differ greatly
in size (Fig. 1–10). An alanine molecule is less than 0.5 nm
long. A molecule of hemoglobin, the oxygen-carrying
protein of erythrocytes (red blood cells), consists of nearly
600 amino acid subunits in four long chains, folded into
globular shapes and associated in a structure 5.5 nm in
diameter. In turn, proteins are much smaller than ribo-
somes (about 20 nm in diameter), which are in turn much
smaller than organelles such as mitochondria, typically
1,000 nm in diameter. It is a long jump from simple biomol-
ecules to cellular structures that can be seen with the light
(a) microscope. Figure 1–11 illustrates the structural hierar-
chy in cellular organization.
The monomeric subunits of proteins, nucleic acids,
and polysaccharides are joined by covalent bonds. In
supramolecular complexes, however, macromolecules
are held together by noncovalent interactions—much
weaker, individually, than covalent bonds. Among these
noncovalent interactions are hydrogen bonds (between
polar groups), ionic interactions (between charged
groups), hydrophobic interactions (among nonpolar
groups in aqueous solution), and van der Waals interac-
tions (London forces)—all of which have energies much
smaller than those of covalent bonds. These noncova-
lent interactions are described in Chapter 2. The large
numbers of weak interactions between macromolecules
in supramolecular complexes stabilize these assemblies,
producing their unique structures.

(b) In Vitro Studies May Overlook Important Interactions

FIGURE 1–9 The three types of cytoskeletal filaments: actin filaments, among Molecules
microtubules, and intermediate filaments. Cellular structures can be One approach to understanding a biological process is
labeled with an antibody (that recognizes a characteristic protein) cova- to study purified molecules in vitro (“in glass”—in the
lently attached to a fluorescent compound. The stained structures are test tube), without interference from other molecules
visible when the cell is viewed with a fluorescence microscope. (a)
present in the intact cell—that is, in vivo (“in the
Endothelial cells from the bovine pulmonary artery. Bundles of actin fila-
living”). Although this approach has been remarkably
ments called
stress fibers
are stained red; microtubules, radiating from
revealing, we must keep in mind that the inside of a cell
the cell center, are stained green; and chromosomes (in the nucleus) are
is quite different from the inside of a test tube. The
stained blue. (b) A newt lung cell undergoing mitosis. Microtubules
“interfering” components eliminated by purification
(green), attached to structures called kinetochores (yellow) on the con-
densed chromosomes (blue), pull the chromosomes to opposite poles,
may be critical to the biological function or regulation of
or centrosomes (magenta), of the cell. Intermediate filaments, made of
the molecule purified. For example, in vitro studies of
keratin (red), maintain the structure of the cell. pure enzymes are commonly done at very low enzyme
concentrations in thoroughly stirred aqueous solutions.
In the cell, an enzyme is dissolved or suspended in the
Although complex, this organization of the cyto- gel-like cytosol with thousands of other proteins, some
plasm is far from random. The motion and positioning of of which bind to that enzyme and influence its activity.
organelles and cytoskeletal elements are under tight Some enzymes are components of multienzyme com-
regulation, and at certain stages in its life, a eukaryotic plexes in which reactants are channeled from one
cell undergoes dramatic, finely orchestrated reorgani- enzyme to another, never entering the bulk solvent.
zations, such as the events of mitosis. The interactions When all of the known macromolecules in a cell are
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10 The Foundations of Biochemistry

represented at their known dimensions and concentra- function of individual enzymes and other biomolecules—
tions (Fig. 1–12), it is clear that the cytosol is very to understand function in vivo as well as in vitro.
crowded and that diffusion of macromolecules within
the cytosol must be slowed by collisions with other large SUMMARY 1.1 Cellular Foundations
structures. In short, a given molecule may behave quite u All cells are bounded by a plasma membrane; have
differently in the cell and in vitro. A central challenge of
a cytosol containing metabolites, coenzymes,
biochemistry is to understand the influences of cellular
inorganic ions, and enzymes; and have a set of
organization and macromolecular associations on the
genes contained within a nucleoid (bacteria and
archaea) or nucleus (eukaryotes).
u All organisms require a source of energy to
(a) Some of the amino acids of proteins perform cellular work. Phototrophs obtain energy
from sunlight; chemotrophs oxidize chemical fuels,
"
COO
" " passing electrons to good electron acceptors:
COO COO
! A !A !A inorganic compounds, organic compounds, or
H 3N O C O H H3NO CO H H3NO CO H molecular oxygen.
A A A
CH3 CH2OH CH2 u Bacterial and archaeal cells contain cytosol, a
A
"
Alanine Serine COO nucleoid, and plasmids, all contained within a cell
Aspartate
envelope. Eukaryotic cells have a nucleus and are
multicompartmented, with certain processes
" "
COO COO
!A !A "
COO
H3NO CO H H3NO CO H !A
A A FIGURE 1–10 The organic compounds from which most cellular materi-
H3NO CO H
CH2 CH2 A als are constructed: the ABCs of biochemistry. Shown here are (a) six
A
NH CH2
C A of the 20 amino acids from which all proteins are built (the side chains
CH SH are shaded light red); (b) the five nitrogenous bases, two five-carbon
HC !
NH sugars, and phosphate ion from which all nucleic acids are built; (c) five
Cysteine
OH components of membrane lipids; and (d) D-glucose, the simple sugar
Histidine
from which most carbohydrates are derived. Note that phosphate is a
Tyrosine
component of both nucleic acids and membrane lipids.

(b) The components of nucleic acids (c) Some components of lipids

O O
NH2 COO! COO! CH2OH
C C CH3 CH2 CH2 CHOH
HN CH HN C N CH
CH2 CH2 CH2OH
C CH C CH C CH Glycerol
O N O N O N CH2 CH2
H H H
CH2 CH2
Uracil Thymine Cytosine CH3
CH2 CH2 "
CH3 N CH2CH2OH
NH2 O CH2 CH2
CH3
C C O! CH2 CH2 Choline
N N
N C HN C CH CH2
CH CH HO P OH
HC C C C CH CH2
N N H2N N N O
H H
Phosphate CH2 CH2
Adenine Guanine (d) The parent sugar
CH2 CH2
Nitrogenous bases
CH2 CH2
HOCH2 O H HOCH2 O CH2 CH2 CH 2OH
H
H H CH2 CH2 O
H H H H
H OH H
H OH CH2 CH3 OH H
OH OH OH H Palmitate HO OH
CH2
# -D-Ribose H OH
2-Deoxy-# -D-ribose CH3
Five-carbon sugars Oleate # -D-Glucose