All Cells Translate RNA into Protein in the Same Way

All Cells Translate RNA into Protein in the Same Way

The translation of genetic information from the 4-letter alphabet of
polynucleotides into the 20-letter alphabet of proteins is a complex process.
The rules of this translation seem in some respects neat and rational, in other
respects strangely arbitrary, given that they are (with minor exceptions)
identical in all living things. These arbitrary features, it is thought, reflect
frozen accidents in the early history of life chance properties of the earliest
organisms that were passed on by heredity and have become so deeply
embedded in the constitution of all living cells that they cannot be changed
without wrecking cell organization.
The information in the sequence of a messenger RNA molecule is read out in
groups of three nucleotides at a time: each triplet of nucleotides, or
specifies (codes for) a single amino acid in a corresponding protein. Since
there are 64 (= 4 × 4 × 4) possible codons, but only 20 amino acids, there are
necessarily many cases in which several codons correspond to the same amino
acid. The code is read out by a special class of small RNA molecules, the
transfer RNAs (
specific amino acid, and displays at its other end a specific sequence of three
nucleotides an
a particular codon or subset of codons in mRNA (Figure 1-9).
For synthesis of protein, a succession of tRNA molecules charged with their
appropriate amino acids have to be brought together with an mRNA molecule
and matched up by base-pairing through their anticodons with each of its
successive codons. The amino acids then have to be linked together to extend
the growing protein chain, and the tRNAs, relieved of their burdens, have to be
released. This whole complex of processes is carried out by a giant
multimolecular machine, the ribosome, formed of two main chains of RNA,
called ribosomal RNAs (
evolutionarily ancient molecular juggernaut latches onto the end of an mRNA
molecule and then trundles along it, capturing loaded tRNA molecules and
stitching together the amino acids they carry to form a new protein chain
(Figure 1-
rRNAs), and more than 50 different proteins. This
codon,tRNAs). Each type of tRNA becomes attached at one end to aanticodon that enables it to recognize, through basepairing,
All Cells Store Their Hereditary Information in the Same Linear Chemical Code (DNA)

All Cells Store Their Hereditary Information in the Same Linear Chemical Code (DNA)


Computers have made us familiar with the concept of information as a
measurable quantity a million bytes (corresponding to about 200 pages of
text) on a floppy disk, 600 million on a CD-ROM, and so on. They have also
made us uncomfortably aware that the same information can be recorded in
many different physical forms. A document that is written on one type of
computer may be unreadable on another. As the computer world has evolved,
the discs and tapes that we used 10 years ago for our electronic archives have
become unreadable on present-day machines. Living cells, like computers,
deal in information, and it is estimated that they have been evolving and
diversifying for over 3.5 billion years. It is scarcely to be expected that they
should all store their information in the same form, or that the archives of one
type of cell should be readable by the information-handling machinery of
another. And yet it is so. All living cells on Earth, without any known
exception, store their hereditary information in the form of double-stranded
molecules of DNA long unbranched paired polymer chains, formed always
of the same four types of monomers A, T, C, G. These monomers are strung
together in a long linear sequence that encodes the genetic information, just as
the sequence of 1s and 0s encodes the information in a computer file. We can
take a piece of DNA from a human cell and insert it into a bacterium, or a
piece of bacterial DNA and insert it into a human cell, and the information will
be successfully read, interpreted, and copied. Using chemical methods,
scientists can read out the complete sequence of monomers in any DNA
molecule extending for millions of nucleotides and thereby decipher the
hereditary information that each organism contains.
All Cells Replicate Their Hereditary Information byTemplated Polymerization

All Cells Replicate Their Hereditary Information byTemplated Polymerization

which this information is copied throughout the living world.
To understand the mechanisms that make life possible, one must understand
the structure of the double-stranded DNA molecule. Each monomer in a single
DNA strand that is, each nucleotide consists of two parts: a sugar
(deoxyribose) with a phosphate group attached to it, and a
either adenine (A), guanine (G), cytosine (C) or thymine (T) (Figure 1-2). Each
sugar is linked to the next via the phosphate group, creating a polymer chain
composed of a repetitive sugar-phosphate backbone with a series of bases
protruding from it. The DNA polymer is extended by adding monomers at one
end. For a single isolated strand, these can, in principle, be added in any order,
because each one links to the next in the same way, through the part of the
molecule that is the same for all of them. In the living cell, however, there is a
constraint: DNA is not synthesized as a free strand in isolation, but on a
template formed by a preexisting DNA strand. The bases protruding from the
existing strand bind to bases of the strand being synthesized, according to a
strict rule defined by the complementary structures of the bases: A binds to T,
DNA replicationtemplated polymerization is the way in which this information is copied throughout the living world.
and C binds to G. This base-pairing holds fresh monomers in place and thereby
controls the selection of which one of the four monomers shall be added to the
growing strand next. In this way, a double-stranded structure is created,
consisting of two exactly complementary sequences of As, Cs, Ts, and Gs. The
two strands twist around each other, forming a double helix (Figure 1-2E).
The bonds between the base pairs are weak compared with the sugarphosphate
links, and this allows the two DNA strands to be pulled apart
without breakage of their backbones. Each strand then can serve as a template,
in the way just described, for the synthesis of a fresh DNA strand
complementary to itself a fresh copy, that is, of the hereditary information
(Figure 1-3). In different types of cells, this process of
occurs at different rates, with different controls to start it or stop it, and
different auxiliary molecules to help it along. But the basics are universal:
DNA is the information store, and which this information is copied throughout the living world
The Fragment of Genetic Information Corresponding to One Protein Is One Gene

The Fragment of Genetic Information Corresponding to One Protein Is One Gene


DNA molecules as a rule are very large, containing the specifications for
thousands of proteins. Segments of the entire DNA sequence are therefore
transcribed into separate mRNA molecules, with each segment coding for a
different protein. A gene is defined as the segment of DNA sequence
corresponding to a single protein (or to a single catalytic or structural RNA
molecule for those genes that produce RNA but not protein).
In all cells, the
manufacturing its full repertoire of possible proteins at full tilt all the time, the
cell adjusts the rate of transcription and translation of different genes
independently, according to need. Stretches of
interspersed among the segments that code for protein, and these noncoding
regions bind to special protein molecules that control the local rate of
transcription (Figure 1-11). Other noncoding DNA is also present, some of it
serving, for example, as punctuation, defining where the information for an
individual protein begins and ends. The quantity and organization of the
regulatory and other noncoding DNA vary widely from one class of organisms
to another, but the basic strategy is universal. In this way, the genome of the
cell that is, the total of its genetic information as embodied in its complete
DNA sequence dictates not only the nature of the cell's proteins, but also
when and where they are to be made.
All Cells Transcribe Portions of Their Hereditary Information into the Same Intermediary Form (RNA)

All Cells Transcribe Portions of Their Hereditary Information into the Same Intermediary Form (RNA)

To carry out its information-storage function, DNA must do more than copy
itself before each cell division by the mechanism just described. It must also
express its information, putting it to use so as to guide the synthesis of other
molecules in the cell. This also occurs by a mechanism that is the same in all
living organisms, leading first and foremost to the production of two other key
classes of polymers: RNAs and proteins. The process begins with a templated
polymerization called transcription, in which segments of the DNA sequence
are used as templates to guide the synthesis of shorter molecules of the closely
related polymer
of translation, many of these RNA molecules serve to direct the synthesis of
polymers of a radically different chemical class the
In RNA, the backbone is formed of a slightly different sugar from that of
DNA ribose instead of deoxyribose and one of the four bases is slightly
different uracil (U) in place of thymine (T); but the other three bases A, C,
and G are the same, and all four bases pair with their complementary
counterparts in DNA the A, U, C, and G of RNA with the T, A, G, and C of
DNA. During transcription, RNA monomers are lined up and selected for
polymerization on a template strand of DNA in the same way that DNA
monomers are selected during replication. The outcome is therefore a polymer
molecule whose sequence of nucleotides faithfully represents a part of the
cell's genetic information, even though written in a slightly different alphabet,
consisting of RNA monomers instead of DNA monomers.
The same segment of DNA can be used repeatedly to guide the synthesis of
many identical RNA transcripts. Thus, whereas the cell's archive of genetic
information in the form of DNA is fixed and sacrosanct, the RNA transcripts
are mass-produced and disposable (Figure 1-5). As we shall see, the primary
role of most of these transcripts is to serve as intermediates in the transfer of
genetic information: they serve as messenger RNA (
synthesis of proteins according to the genetic instructions stored in the DNA.
RNA molecules have distinctive structures that can also give them other
specialized chemical capabilities. Being single-stranded, their backbone is
flexible, so that the polymer chain can bend back on itself to allow one part of
the molecule to form weak bonds with another part of the same molecule. This
occurs when segments of the sequence are locally complementary: a ...
GGGG... segment, for example, will tend to associate with a ...CCCC...
segment. These types of internal associations can cause an RNA chain to fold
up into a specific shape that is dictated by its sequence (Figure 1-6). The shape
of the RNA molecule, in turn, may enable it to recognize other molecules by
binding to them selectively and even, in certain cases, to catalyze chemical
changes in the molecules that are bound. As we see later in this book, a few
chemical reactions catalyzed by RNA molecules are crucial for several of the
most ancient and fundamental processes in living cells, and it has been
suggested that more extensive catalysis by RNA played a central part in the
early evolution of life (discussed in Chapter 6).
mRNA) to guide the
ribonucleic acid, or RNA. Later, in the more complex processproteins (Figure 1-4).
All Cells Use Proteins as Catalysts

All Cells Use Proteins as Catalysts

Protein molecules, like DNA and RNA molecules, are long unbranched
polymer chains, formed by the stringing together of monomeric building
blocks drawn from a standard repertoire that is the same for all living cells.
Like DNA and RNA, they carry information in the form of a linear sequence
of symbols, in the same way as a human message written in an alphabetic
script. There are many different protein molecules in each cell, and leaving
out the water they form most of the cell's mass.
The monomers of protein, the amino acids, are quite different from those of
DNA and RNA, and there are 20 types, instead of 4. Each amino acid is built
around the same core structure through which it can be linked in a standard
way to any other amino acid in the set; attached to this core is a side group that
gives each amino acid a distinctive chemical character. Each of the protein
molecules, or polypeptides, created by joining amino acids in a particular
sequence folds into a precise three-dimensional form with reactive sites on its
surface (Figure 1-7A). These amino acid polymers thereby bind with high
specificity to other molecules and act as enzymes to catalyze reactions in
which covalent bonds are made and broken. In this way they direct the vast
majority of chemical processes in the cell (Figure 1-7B). Proteins have a host
of other functions as well maintaining structures, generating movements,
sensing signals, and so on each protein molecule performing a specific
function according to its own genetically specified sequence of amino acids.
Proteins, above all, are the molecules that put the cell's genetic information
into action.
Thus, polynucleotides specify the amino acid sequences of proteins. Proteins,
in turn, catalyze many chemical reactions, including those by which new DNA
molecules are synthesized, and the genetic information in DNA is used to
make both RNA and proteins. This feedback loop is the basis of the
autocatalytic, self-reproducing behavior of living organisms (Figure 1-
8).
All Cells Function as Biochemical Factories Dealing with the Same Basic Molecular Building Blocks

All Cells Function as Biochemical Factories Dealing with the Same Basic Molecular Building Blocks

Because all cells make DNA, RNA, and protein, and these macromolecules are
composed of the same set of subunits in every case, all cells have to contain
and manipulate a similar collection of small molecules, including simple
sugars, nucleotides, and amino acids, as well as other substances that are
universally required for their synthesis. All cells, for example, require the
phosphorylated nucleotide
for the synthesis of DNA and RNA; and all cells also make and consume this
molecule as a carrier of free energy and phosphate groups to drive many other
chemical reactions.
Although all cells function as biochemical factories of a broadly similar type,
many of the details of their small-molecule transactions differ, and it is not as
easy as it is for the informational macromolecules to point out the features that
are strictly universal. Some organisms, such as plants, require only the
simplest of nutrients and harness the energy of sunlight to make from these
almost all their own small organic molecules; other organisms, such as
animals, feed on living things and obtain many of their organic molecules
ready-made. We return to this point below.
ATP (adenosine triphosphate) as a building block
All Cells Are Enclosed in a Plasma Membrane Across Which Nutrients and Waste Materials Must Pass

All Cells Are Enclosed in a Plasma Membrane Across Which Nutrients and Waste Materials Must Pass

There is, however, at least one other feature of cells that is universal: each one
is bounded by a membrane the plasma membrane. This container acts as a
selective barrier that enables the cell to concentrate nutrients gathered from its
environment and retain the products it synthesizes for its own use, while
excreting its waste products. Without a plasma membrane, the cell could not
maintain its integrity as a coordinated chemical system.
This membrane is formed of a set of molecules that have the simple physicochemical
property of being
hydrophobic (water-insoluble) and another part that is hydrophilic (watersoluble).
When such molecules are placed in water, they aggregate
spontaneously, arranging their hydrophobic portions to be as much in contact
with one another as possible to hide them from the water, while keeping their
hydrophilic portions exposed. Amphipathic molecules of appropriate shape,
such as the phospholipid molecules that comprise most of the plasma
membrane, spontaneously aggregate in water to form a
small closed vesicles (Figure 1-12). The phenomenon can be demonstrated in a
test tube by simply mixing phospholipids and water together; under
appropriate conditions, small vesicles form whose aqueous contents are
isolated from the external medium.
Although the chemical details vary, the hydrophobic tails of the predominant
membrane molecules in all cells are hydrocarbon polymers (-CH
and their spontaneous assembly into a bilayered vesicle is but one of many
examples of an important general principle: cells produce molecules whose
chemical properties cause them to
needs.
The boundary of the cell cannot be totally impermeable. If a cell is to grow and
reproduce, it must be able to import raw materials and export waste across its
plasma membrane. All cells therefore have specialized proteins embedded in
their membrane that serve to transport specific molecules from one side to the
other (Figure 1-13). Some of these
the proteins that catalyze the fundamental small-molecule reactions inside the
cell, have been so well preserved over the course of evolution that one can
recognize the family resemblances between them in comparisons of even the
most distantly related groups of living organisms.
The transport proteins in the membrane largely determine which molecules
enter the cell, and the catalytic proteins inside the cell determine the reactions
that those molecules undergo. Thus, by specifying the set of proteins that the
cell is to manufacture, the genetic information recorded in the DNA sequence
dictates the entire chemistry of the cell; and not only its chemistry, but also its
form and its behavior, for these too are chiefly constructed and controlled by
the cell's proteins.
2-CH2-CH2-),self-assemble into the structures that a cellmembrane transport proteins, like some of
amphipathic that is, consisting of one part that isbilayer that creates
A Living Cell Can Exist with Fewer Than 500 Genes

A Living Cell Can Exist with Fewer Than 500 Genes

The basic principles of biological information transfer are simple enough, but
how complex are real living cells? In particular, what are the minimum
requirements? We can get a rough indication by considering the species that
has the smallest known genome the bacterium
Mycoplasma genitalium
(Figure 1-14)
environment provides it with many of its small molecules ready-made.
Nevertheless, it still has to make all the large molecules DNA, RNAs, and
proteins required for the basic processes of heredity. It has only 477 genes in
its genome of 580,070 nucleotide pairs, representing 145,018 bytes of
information about as much as it takes to record the text of one chapter of this
book. Cell biology may be complicated, but it is not impossibly so.
The minimum number of genes for a viable cell in today's environments is
probably not less than 200 300. As we shall see in the next section, when we
compare the most widely separated branches of the tree of life, we find that a
core set of over 200 genes is common to them all.
. This organism lives as a parasite in mammals, and its

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