12.1.1 What is life?
No completely satisfactory definition of life – or of “living things” – has yet been devised. Most simple definitions of life – something that grows spontaneously, or something that replicates itself – fail because they either include demonstrably nonliving things or exclude certain particular living organisms.
Crystals such as snow or pyrite grow but are not biological in nature; offspring of separate but related species such as mules (offspring of a donkey and a horse) are almost invariably unable to reproduce, yet clearly are living.
Some biologists lean toward a definition that incorporates the concept ofDarwinian evolution, defined broadly to mean
reproduction, variation of characteristics from one generation to another, and natural selection whereby some individuals with specific traits gain an advantage over others and hence are more successful in producing offspring. In this context, one work- ing definition of life might be “a self-sustained chemical system capable of undergoing Darwinian evolution,” as devised by Uni- versity of California biologist Gerald Joyce and colleagues.
There are two major drawbacks to this definition. First, it has become clear that, although species do evolve, the classical Darwinian concept of natural selection is only one factor that comes into play in such evolution. Second, the definition may
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4.0 nonvascular land plants and others (this black section) early vascular plants
pteridophytes
mass extinction mass extinction mass extinctionmass extinction
mass extinction (asteroid impact) gymnosperms
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land arthropod and other families land vertebrate families (known) marine vertebrate and invertebrate families land plant species (incomplete)
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angiosperms
megascopic eukaryotes develop and diversify
oldest traces of invertebrates; oldest large algae oldest body fossils of invertebrates
eukaryotes diversify; sexual reproduction develops eukaryotes develop (or earlier) O2-rich atmosphere; aerobic respiration develops; some anaerobes become extinct
aerobic photosynthesis develops first widespread diverse stromatolites
trace O2 released inorganically oldest fossil-like objects first anaerobic bacteria
oldest whole rocks; oceans present
intense bombardment4.5 billion years agoOrigin of Earth photosynthetic bacteria major banded iron formations youngest detrital uraninitesaerobic prokaryotes diversify anaerobic prokaryotes diversify
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2.0 1.8 1.6 1.4 1.2 1.0 .9 .9 .7 .6.5 .4.3.2
.2 geologictime,billionsofyearsbeforepresent Figure12.1SchematichistoryoflifeonEarth,showingwherekeymilestonesinthehistoryoflifelikelyoccurredrelativetogeologiceventsonEarth.BeginningattheVendian–Cambrian diversificationoflife(Chapter18),theriseandfallwithtimeofthenumberoffamiliesoflandandmarinecreaturesisdepicted.
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be unnecessarily narrow in that “life” on other planets might not undergo Darwinian evolution, but might still involve bio- chemical reactions resembling those on Earth; non-Darwinian evolution might have occurred in the very earliest, primitive organisms on our planet as well. The definition also excludes
“artificial life,” experiments in computer information replica- tion described in Chapter 13, but could easily allow inclusion of such experiments by replacing the phrase “chemical system” by
“material system,” as has been suggested by NASA Ames plane- tary scientist Chris McKay. Finally, a more general definition of life – perhaps too general in that it might apply to some nonliving systems – is “a system that possesses the ability (homeostasis) of maintaining form and function through feedback processes in the face of changing environments.”
What is required to maintain terrestrial life? Many different things are required for different forms of life, but the essen- tials are organic (carbon-based) molecules for structure and pro- cesses, liquid water as an energy and information transporting medium, and a source of usable energy (most often from the Sun, but Earth’s heat can be a source as well).
12.1.2 Basic structure of life
All known life-forms live on Earth and are based on the same small set of molecular units and chemical reactions. Four types of essential molecules areorganic(contain carbon and hydro- gen) and account for most biological processes and structures:
proteins, nucleic acids, carbohydrates, and lipids. Carbohy- drates are molecules in which the hydrogen and oxygen atoms form a whole number (that is, 1, 2, 3 . . . ) of water molecules.
Some classes of carbohydrates (sugars) are produced by plants using sunlight as an energy source, and water and carbon diox- ide as the raw materials. This process, photosynthesis, led to fundamental changes in Earth’s atmospheric composition early in its history, as we see in Chapter 17.
The molecules that provide the primary structural material for life, as well as contribute crucially to its functioning, are calledproteins(from the Greek wordproteios, or primary, hence
“primary substance”). Proteins are long chains (orpolymers) of relatively small molecular units (monomers), called amino acids.
An example structure of an amino acid is shown in Figure 12.2.
The “R” group distinguishes the particular amino acid – it could be hydrogen or methyl (CH3) or more complicated combinations of hydrogen, carbon, and oxygen. Of the vast variety of possible amino acids, only about 20 are found to be the building blocks of the major proteins of life.
Long-chain proteins fold into tight bundles, which give rise to the physical and chemical behaviors associated with particular proteins. A typical protein chain may contain from about 50 to 1,000 amino acid molecules strung together. The total number of possible proteins is vastly more than the relatively few (of order 100,000) that actually occur in terrestrial life. Of those that do occur in cells, some play a role in defining the cellular structure, some act to transport or store molecular compounds, and others act as catalysts to control the rates of biochemical reactions; the latter are calledenzymes.
Proteins cannot make copies of themselves; in the absence of some directive agent or template, the faithful production of
oxygen
nitrogen hydrogen
(a)
(b)
carbon
H
H H
N
R C C
O
OH
Figure 12.2(a) Atomic structure of the amino acid alanine, used in proteins. (b) Schematic structure of many amino acids, including most biological ones, where “R” represents a functional group of atoms that defines the particular amino acid.
proteins from the simpler amino acids would not occur in cells.
Nucleic acids are molecules that form the building blocks of the templates, which we consider next.
12.1.3 Information exchange and replication
The information-carrying and replicating (or genetic) compo- nents of terrestrial life are types of nucleic acids called DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). DNA molecules are long double chains normally twisted into a helical structure. The side rails of the double chains consist of a string of alternating sugar and phosphate molecules. Sugar is a simple carbohydrate. Many common sugars, such as glucose, have the chemical formula C6H12O6; others have slightly different ratios of carbon to hydrogen and oxygen. Phosphate molecules, or phosphate groups, form high-energy bonds in living systems; a phosphate group involves phosphorus and, for example, would have the formula PO3H2.
The cross-ties of the DNA chain consist of pairs of four differ- ent types ofbases: adenine (A), thymine (T), guanine (G), and cytosine (C). These bases consist of carbon, nitrogen, oxygen, and hydrogen in complicated ring structures (Figure 12.3). The combination of a base with the sugar and phosphate backbone is called anucleotide.
The pairing of the nucleotide bases is restricted: A with T, and G with C. Thus, the two sides of the chain (conjugates) are
O O
O O O
N H
H N
N
N N
H N3
N N
NH2
NH2
H2N
CH3
H
N H
N H uracil
adenine guanine
cytosine
beta-glycoside link to purine or pyrimidine O
P O O
HO OH
−O
−O
thymine Pyrimidines:
Beta-D-ribonucleotide Purines:
N
N O
N H
H N
O
P O
−O
−O
beta-glycoside link to purine or pyrimidine
O
HO H
Beta-D-deoxyribonucleotide Nucleotides:
(b) (a)
Figure 12.3(a) The five types of nucleic acid bases in DNA and RNA, showing the characteristic ring structure. (b) Two types of nucleotides are produced from the bases: (top) a ribonucleotide that is the foundation for RNA and (bottom) a deoxyribonucleotide that is the foundation for DNA.
Empty vertices correspond to carbon paired with zero or one hydrogen atoms; double lines indicate two shared pairs of electrons. Redrawn from Mason (1991).
redundant to each other because, from the letter on one side, you know what the letter on the other side must be. In replication, the net result is that the two sides of the chain are split, with each side reconstituting (through the mediation of enzymes) its conjugate, resulting in two copies of the original DNA.
12.1.4 Formation of proteins
Protein synthesis is governed by DNA, through the interme- diation of RNA. The synthesis begins when DNA, instead of replicating to make new DNA, transcribes RNA. RNA differs from DNA in two aspects: the sugar is of a different form, and the nucleic acid base uracil (U) is present in place of thymine (T).
These are relatively minor structural changes in the molecule (Figure 12.3), a fact that we return to in Chapter 13 as we con- sider the origin of the genetic code.
Thus, a chain of RNA contains a long sequence of molecular monomers chosen from among the four nucleic acid bases A, U, G, C. This chain of monomers can be “read” as a sequence of three-letter “words” constructed from a four-letter “alphabet.”
Each three-letter word is called a codon. Some examples of words areGUA,AAG,UGA. The number of possible words is 4×4×4=64.
Each codon codes for a specific amino acid; thus, the sequence of codons in an RNA molecule (which, remember, is ultimately derived from the sequence in the original DNA) specifies a sequence of amino acids. This amino acid sequence consti- tutes the synthesized protein. A particular amino acid generally is coded for by more than one codon, because 64 codons are available for the 20 amino acids commonly used in terrestrial biology.
The actual protein synthesis is a bit more complicated, with messenger RNAcarrying the protein-structure information from
the DNA,transfer RNAattaching to specific amino acids and aligning them based on the messenger RNA sequence, and ribosomal RNA(located in a cellular structure called the ribo- some) receiving the ordered amino acid sequence (ferried by the transfer RNA) and acting as a catalyst for final assembly of the amino acid chains. Other RNA molecules assist in DNA replication and in the construction of the messenger RNA. This diverse range of roles for a single kind of molecule makes tempt- ing the proposal that, at some time in the distant past, RNA was central to the genesis of life as we know it. By contrast, DNA, which is not terribly dissimilar to RNA, has a very specialized function as a record of the genetic information of the individual organism and (in separate DNA strands) of certain structures in the cell. This essential but much more limited role compared to that of RNA suggests that DNA is a subsequent, derived molecule.
A length of DNA that carries the genetic information that is ultimately expressed as a single protein is called a gene.
The genetic code is the complete sequence of nucleotides in DNA, which determines the form and function of an organism’s proteins. All living organisms on Earth that have been examined use DNA and RNA to record and express the proteins of which they are made.
12.1.5 Mutation and genetic variation
The replication process sketched above operates with high fidelity. Errors are rare but occur. These errors are called muta- tions. Such errors, changes in the structure of the DNA, may have a variety of causes such as chemical impurities in the envi- ronment or radiation (ultraviolet photons or particle radiation).
Other errors or changes may be a result of accidental mixing or crossover of DNA chains in normal cells. Mutations give rise to
mitochondria Golgi apparatus (a) Eukaryotic cell
(b) Prokaryotic cell
peroxisome lysosome
microtubules
endoplasmic reticulum nuclear envelope
chloroplast DNA
cell membrane cell wall
ribosome cytoplasm
DNA
flagella 1 micron
10–30 microns
Figure 12.4(a) Generalized eukaryotic cell, with structures and organelles shown. (b) Prokaryotic cell (a bacterium).
changes in organisms. This genetic variation is usually harmful but sometimes not.
Such variation forms the biochemical basis for the evolu- tion of one species from another, via natural selection within a given environment or through environmental changes in the ecosystem itself. The large-scale pressures for the evolu- tion of species are discussed in Chapter 18, but, without the imperfection and vulnerability in the genetic code that allows changes (both good and bad), such evolution would not be possible, or too slow to be relevant to the history of life on Earth.
Since it is now possible to analyze the genome of an organism and determine the sequence of base pairs, the concept of a molec- ular clock based on the mutation rate has assumed great impor- tance in estimating when different organisms diverged from one another. The rate of mutation varies from species to species, and even between different components of DNA within a given species – for example the mutation rate of DNA contained in the mitochondria of eukaryotes (see next section) is generally higher than that of the DNA in the nucleus. This molecular clock may have errors of factors of ten or more. In some cases, the muta- tion rate can be cross-checked with other evidence. For example, the differences in DNA among different peoples can be cross- checked with the migration patterns established by archeology to determine a mutation rate. And in closely related species, such as humans and chimpanzees, it is reasonable to assume mutation rates that are similar, allowing a molecular determination of how long ago the two lineages diverged from a common lineage; to some extent this can be cross-checked by dating fossil remains (Chapter 20).