Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

22 Chapter 1: Cells and Genomes
parts of the genetically specified molecule contributes to its chemical behavior.
Cell biologists can analyze the behavior of cells that are engineered to express a
mutant version of the gene.
There is, however, no one simple recipe for discovering a gene’s function, and
no simple standard universal format for describing it. We may discover, for example,
that the product of a given gene catalyzes a certain chemical reaction, and
yet have no idea how or why that reaction is important to the organism. The functional
characterization of each new family of gene products, unlike the description
of the gene sequences, presents a fresh challenge to the biologist’s ingenuity.
Moreover, we will never fully understand the function of a gene until we learn its
role in the life of the organism as a whole. To make ultimate sense of gene functions,
therefore, we have to study whole organisms, not just molecules or cells.
Molecular Biology Began with a Spotlight on E. coli
Because living organisms are so complex, the more we learn about any particular
species, the more attractive it becomes as an object for further study. Each discovery
raises new questions and provides new tools with which to tackle general
questions in the context of the chosen organism. For this reason, large communities
of biologists have become dedicated to studying different aspects of the same
model organism.
In the early days of molecular biology, the spotlight focused intensely on just
one species: the Escherichia coli, or E. coli, bacterium (see Figures 1–13 and 1–14).
This small, rod-shaped bacterial cell normally lives in the gut of humans and other
vertebrates, but it can be grown easily in a simple nutrient broth in a culture bottle.
It adapts to variable chemical conditions and reproduces rapidly, and it can
evolve by mutation and selection at a remarkable speed. As with other bacteria,
different strains of E. coli, though classified as members of a single species, differ
genetically to a much greater degree than do different varieties of a sexually
reproducing organism such as a plant or animal. One E. coli strain may possess
many hundreds of genes that are absent from another, and the two strains could
have as little as 50% of their genes in common. The standard laboratory strain
E. coli K-12 has a genome of approximately 4.6 million nucleotide pairs, contained
in a single circular molecule of DNA that codes for about 4300 different kinds of
proteins (Figure 1–24).
In molecular terms, we know more about E. coli than about any other living
organism. Most of our understanding of the fundamental mechanisms of life—
for example, how cells replicate their DNA, or how they decode the instructions
represented in the DNA to direct the synthesis of specific proteins—initially came
from studies of E. coli. The basic genetic mechanisms have turned out to be highly
conserved throughout evolution: these mechanisms are essentially the same in
our own cells as in E. coli.
Summary
Prokaryotes (cells without a distinct nucleus) are biochemically the most diverse
organisms and include species that can obtain all their energy and nutrients from
inorganic chemical sources, such as the reactive mixtures of minerals released at
hydrothermal vents on the ocean floor—the sort of diet that may have nourished the
first living cells 3.5 billion years ago. DNA sequence comparisons reveal the family
relationships of living organisms and show that the prokaryotes fall into two groups
that diverged early in the course of evolution: the bacteria (or eubacteria) and the
archaea. Together with the eukaryotes (cells with a membrane-enclosed nucleus),
these constitute the three primary branches of the tree of life.
Most bacteria and archaea are small unicellular organisms with compact
genomes comprising 1000–6000 genes. Many of the genes within a single organism
show strong family resemblances in their DNA sequences, implying that they originated
from the same ancestral gene through gene duplication and divergence. Family
resemblances (homologies) are also clear when gene sequences are compared
between different species, and more than 200 gene families have been so highly