Molecular Biology

Preface

                My interest in how nature replicates began when Dr Ken O’Kief of TRW asked, while we were reviewing a signal processor design, “could you design a computer that could replicate itself? ”  My thoughts were focused on how automate fabrication of the signal processor we were discussing – after a short pause I said “no, there is no way of solving the parts supply problem.”   The with a slight smile Ken said “I’m looking at one.”  It took a moment to realized what he had just said.  We humans are computers that replicate!!.  I had been taking a night class in Biology and at lunch told Ken of a booklet describing the DNA molecule and a text book “Molecular Biology” by Watson --  this had prompted his question.  I kept pondering how nature solves the supply problem?  When observing contaminate moving in a pool, I said, that’s it.  Life began in water, a sea of molecular soup, kept in constant motion.  The DNA code that evolved was immersed in it’s supply of parts, combining parts by magnetic attraction per patterns that survived – atom’s doing what come s naturally.

The following contributed to our understanding of genetics

 

 

Biology I

Biology is Organic Chemistry and Chemistry is about Atoms and Molecules

            Organic compounds contain carbon.  Large organic molecules are called Monomers. Polymers  are strings of Monomers, like pearls on a necklace.  Polymers  can be digested by hydolysis (water break), the reversal of dehydration.  

 

            Carbohydrates include sugar, monosaccharides are simple sugar; disaccharides are double sugar; Polysaccharides are long chains of sugar units.  Glucose & Fructose are isomers that have the same molecular formula but their atoms are arranged differently. Glucose is to cells what gasoline is to an engine, given to ambulance patients.  Beer, candy, milk, malts are double sugars.  Starch & grain are examples of Polysaccrarides, excess is stored in liver and muscle cells. 

Plants store glucose as starch.  Animals store glucose as glycogen in muscles for physical activity. Starch can be converted to Glycogen.   Cellulose is the most abundant organic compound on earth.

Prokaryotes, ancient cells, in a cow’s digestive tract can convert cellulose to a digestible form – the by product of this chemical action is large amounts of methane.

            Lipids are hydrophobic ( water-fearing) whereas Carbohydrates are hydrophilic (water loving),

            Fats consist largely of triglycerides, saturated and unsaturated.  Broken chains are unsaturated, but can by be “hydrogenated” and made saturated.  Vegetable oils & fish are unsaturated.  Plant oils as coco butter are saturated.

 

            Steroids include cholesterol, testosterone & estrogen.  At right water fearing and water loving amino acids.

 

            The human body has tens of thousands of different kinds of Proteins which is a polymer constructed of amino acid monomers. 

            The thousands of kinds of proteins are made from just 20 kinds of amino acids by varying the sequence of codes.  Polypeptide chains, proteins, has a chain sequence specified by an inherited gene.  These codes are stored in nucleic acid molecules.

  

Nucleic acids are polymers called Nucleotides.  Each DNA nucleotide, above left,  has one of the following four bases shown at right:  Adenine (A), guanine (G), cytosine (C), or thymine (T).

            Nucleic acids are information storage molecules that provide the directions for building proteins.  The name nuclei comes from their location in the nuclei of eukaryotic cells (subsequently described).   Each nucleotide monomer consists of three parts: a sugar, a phosphate & a nitrogenous base.  There are two types of nucleic acids: DNA and RNA  The genetic material humans and other organisms inherit from their parents, consists of giant molecules of DNA. Within the DNA are genes, specific stretches of DNA that program the amino acid sequences (primary structure) of proteins. Those programmed instructions, however, are written in a kind of chemical code that must be translated from "nucleic acid language" to "protein language." A cell's RNA molecules help translate.

 

 

  

(a) A DNA strand is a polymer of nucleotides linked into a backbone, with appendages consisting of the bases. A strand has a specific sequence of the four bases, abbreviated A, G , C, and T.

(b)  A double helix consists of two DNA stands held together by bonds between bases.  The bonds are individually weak – but they zip thi tow stands together with a cumulative strength that gies the double helix it’s stability. The base pairing si specific: A always pairs with T; G always pairs with C.

            The above right RNA nucleotide differs from the previous DNA nucleotide as it has nitrogenous base Uracil (U) in place of (T).   RNA is usually found in single strand only while DNA is a double strand helix.

 

                The DNA double helix is a sugar-phosphate back bone.  Phosphorous  is a large atom, of a kind produced only in a large supernova star.   Proteins are the supply source when building cells from DNA & RNA patterns. 

            A protein's shape is sensitive to the surrounding environment. An unfavorable change in temperature, pH, or some other quality of the aqueous environment can cause a protein to unravel and lose its normal shape. This is called denaturation of the protein.

            Given an environment suitable for that protein (so that it doesn't denature), the primary structure of a protein causes it to fold into its functional shape. Each kind of protein has a unique primary structure and therefore a unique shape that enables it to do a certain job in a cell.  Each polypeptide chain has a sequence specified by an inherited gene.

 

 

            Prior to the electron microscope it was impossible to see even large molecules.  Humans were oblivious of their existence.

            Nucleic acids are polymers of monomers called nucleotides.  Each nucleotide is itself a complex organic molecule with three parts. At the center of each nucleotide is a five-carbon sugar, deoxyribose in DNA and ribose in RNA. Attached to the sugar is a negatively charged phosphate group containing a phosphorus atom bonded to oxygen atoms (PO4-). Also attached to the sugar is a nitrogen-containing base (nitrogenous base) made of one or two rings. (It is called a base because it behaves like a base, or alkali, in aqueous solutions.) The sugar and phosphate are the same in all nucleotides; only the base varies. Each DNA nucleotide has one of the following four bases: adenine (abbreviated A), guanine (G), cytosine (C), or thymine (T). Thus, all genetic information is written in a four-letter alphabet-A, G, C, T -the bases that distinguish the four nucleotides that make up DNA.

Nucleotide monomers are linked into long chains called polynucleotides, or DNA strands. Nucleotides are joined together by covalent .bonds between the sugar of one nucleotide and the phosphate of the next. This results in a sugar-phosphate backbone, a repeating pattern of sugar-phosphate-sugar-phosphate, with the bases hanging off the backbone like appendages. Polynucleotides vary in length from long to very long, so the number of possible polynucleotide sequences is very great. One long DNA strand contains many genes, each a specific series of hundreds or thousands of nucleotides. And each of these genes stores information in its unique sequence of nucleotide bases. In fact, it is this information that cells translate into an amino acid sequence to make a specific protein.

How can the cells of parents copy their genes to pass along to offspring? Inheritance is based on DNA actually being double-stranded, with the two DNA strands wrapped around each other to form a double helix. In the central core of the helix, the bases along one DNA strand hydrogen-bond to bases along the other strand. This base pairing is specific: The base A can pair only with T, and G can pair only with C. Thus, if you know the sequence of bases along one DNA strand, you also know the sequence along the complementary strand in the double helix. This unique base pairing is the basis of DNA’s ability to act as the molecule of inheritance.

What about RNA? As its name-ribonucleic acid-implies, its sugar is ribose rather than deoxyribose. By comparing the RNA nucleotide in, Figure 3.27 with the DNA nucleotide in Figure 3.24 you can see that the RNA ribose sugar has an extra -OH group compared with the DNA deoxyribose sugar (deoxy means "without an oxygen"). Another difference between RNA and DNA is that instead of the base thymine, RNA has a similar but distinct base called uracil (U). Except for the presence of ribose and uracil, an RNA polynucleotide chain is identical to a DNA polynucleotide chain. However, RNA is usually found only in a single-stranded form, while DNA usually exists as a double helix.

Figure 10-2

Figure 10.2 The structure of a DNA polynucleotide. A molecule of DNA contains two polynucleotides, each a chain of nucleotides. Each nucleotide consists of a nitrogenous base, a sugar (blue), and a phosphate group (gold). The nucleotides are linked, the sugar of one connected to the phosphate of the next, forming a sugar-phosphate backbone, with the bases protruding from the sugars. The chemical structure at the right shows the details of a DNA nucleotide. The sugar has five carbon atoms (shown in red for emphasis) and is called deoxyribose. The phosphate group has given up an H+ ion, acting as an acid. Hence, the full name for DNA is deoxyribonucleic acid.

The Structure and Replication of DNA

DNA was known as a chemical in cells by the end of the nineteenth century, but Mendel and other early geneticists did all their work without any know-ledge of DNA’s role in heredity. By the late 1930s, experimental studies had convinced most biologists that a specific kind of molecule, rather than some complex chemical mixture, was the basis of inheritance.  Attention focused on chromosomes, which were already known to carry genes. By the 1940s, scientists knew that chromosomes consisted of two types of chemicals: DNA and protein. And by the early 1950s, a series of discoveries had convinced the scientific world that DNA was the hereditary material.

What came next was one of the most celebrated quests in the history of science -- the effort to figure out the structure of DNA. A good deal was already known about DNA. Scientists had identified all its atoms and knew how they were covalently bonded to one another. What was not understood was the specific arrangement that gave DNA its unique properties – the capacity to store genetic information, copy it, and pass it - from generation to generation. A race was on to discover how the structure of this molecule could account for its role in heredity. We will describe that momentous discovery shortly. First, look at the underlying chemical structure of DNA and its chemical cousin RNA.

DNA and RNA: Polymers of Nucleotides I

Both DNA and RNA are nucleic acids, which consist of long chains (polymers) of chemical units (monomers) called nucleotides.  A very simple diagram of a nucleotide polymer, or polynucleotide. This sample polynucleotide chain shows only one possible arrangement of the four different types of nucleotides ( abbreviated A, C, T and G) that make up DNA. Polynucleotides tend to be very long and can have any sequence of nucleotides, so a great number of polynucleotide chains are possible.

The nucleotides are joined to one another by covalent bonds between the sugar of one nucleotide and the phosphate of the next. This results in a sugar-phosphate backbone, a repeating pattern of sugar-phosphate-sugar-phosphate. The nitrogenous bases are arranged like appendages along this backbone. Zooming in on our polynucleotide we see that each nucleotide consists of three components: a nitrogenous base, a sugar (blue), and a phosphate group (gold). Examining a single nucleotide even more closely, we see the chemical structure of its three components. The phosphate group, with a phosphorus atom (P) at its center, is the source of the acid in nucleic acid. (The phosphate has given up a hydrogen ion, H+ , leaving a negative charge on one of its oxygen atoms.) The sugar has five carbon atoms: four in its ring and one extending above the ring. The ring also includes an oxygen atom. The sugar is called deoxyribose because, compared to the sugar ribose, it is missing an oxygen atom. The full name for DNA is deoxyribonucleic acid, with the nucleic part coming from DNA’s location in the nuclei of eukaryotic cells. (some, mDNA, is located in the mitochondria.) The nitrogenous base ( thymine, in our example) has a ring of nitrogen and carbon atoms with various functional groups attached. In contrast to the acidic phosphate group, nitrogenous bases are basic; hence their name.

 

Left   Co discoverers Watson & Crick    Right   rope-ladder model of a double helix. The ropes at the sides represent the sugar-phosphate backbones. Each wooden rung stands for a pair of bases connected by hydrogen bonds.

The four nucleotides found in DNA differ only in their nitrogenous bases (Figure 3.25). At this point, the structural details are not as important as the fact that the bases are of two types. Thymine (T) and cytosine (C) are single-ring structures. Adenme (A) and guanme (G) are larger, double-ring structures. (The one-letter abbreviations can be used for either the bases alone or for the nucleotides containing them.) Recall that RNA has the nitrogenous base uracil (U) instead of thymine ( uracil is very similar to thymine). RNA also contains a slightly different sugar than DNA (ribose instead of deoxyribose). Other than that, RNA and DNA polynucleotides have the same chemical structure.

Watson and Crick's Discovery of the Double Helix

The celebrated partnership that resulted in the determination of the physical structure of DNA began soon after a 23-year-old American named James D. Watson journeyed to Cambridge University, where Englishman Francis Crick was studying protein structure with a technique called X-ray crystallography . While visiting the laboratory of Maurice Wilkins at King's College in London, Watson saw an X-ray crystallographic photograph of DNA, produced by Wilkins's colleague Rosalind Franklin. The photograph clearly revealed the basic shape of DNA to be a helix (spiral). On the basis of Watson's later recollection of the photo, he and Crick deduced that the diameter of the helix was uniform. The thickness of the helix suggested that it was made up of two polynucleotide strands-in other words, a double helix.

Using wire models, Watson and Crick began trying to construct a double helix that would conform both to Franklin's data and to what was then known about the chemistry of DNA. After failing to make a satisfactory model that placed the sugar-phosphate backbones inside the double helix, Watson tried putting the backbones on the outside and forcing the nitrogenous bases to swivel to the interior of the molecule. It occurred to him that the four kinds of bases might pair in a specific way. This idea of specific base pairing was a flash of inspiration that enabled Watson and Crick to solve the DNA puzzle.

At first, Watson imagined that the bases paired like with like - for example A with A, C with C. But that kind of pairing did not fit with the fact 

Three representations of DNA. (a) In this model, the sugar-phosphate backbones are blue ribbons, and the bases are complementary shapes in shades of green and orange. (b) In this more chemically detailed structure, you can see the individual hydrogen bonds (dashed lines). You can also see that the strands run in opposite directions; notice that the sugars on the two strands are upside down with respect to each other. (c) In this computer graphic of a DNA double helix, each atom is shown as a sphere, creating a space-filling model, that the DNA molecule was a uniform diameter. In AA pair (made of double-ringed bases) would be almost twice as wide as a CC pair (made of single-ringed bases), causing bulges in the molecule. It soon became apparent that a double-ringed base on one strand must always be paired with a single-ringed base on the opposite strand. Moreover, Watson and Crick realized that the individual structures of the bases dictated the pairings even more specifically. Each base has chemical side groups that can best form hydrogen bonds with one appropriate partner. Adenine can best form hydrogen bonds with thymine, and guanine with cytosine. In the biologist's shorthand, A pairs with T, and G pairs with C. A is also said to be "complementary" to T, and G to C.

You can picture the model of the DNA double helix proposed by Watson and Crick as a rope ladder having rigid, wooden rungs, with the ladder twisted into a spiral (Figure 10.4). Figure 10.5 shows three more detailed representations of the double helix. The ribbon like diagram in Figure 10.5a symbolizes the models of the bases with shapes that emphasize their complementarities. Figure 10.5b is a more chemically precise version showing only four base pairs, with the helix untwisted and the individual hydrogen bonds specified by dashed lines; you can see that the double helix has an antiparallel arrangement-that is, the two sugar-phosphate backbones are oriented in opposite directions. Figure 10.5c is a computer graphic showing every atom of part of a double helix.

Although the base-pairing rules dictate the side-by-side combinations nitrogenous bases that form the rungs of the double helix, they place no restrictions on the sequence of nucleotides along the length of a DNA strand. In fact, the sequence of bases can vary in countless ways.

In April 1953, Watson and Crick shook the scientific world with a succinct, two-page announcement of their molecular model for DNA in the journal Nature. Few milestones in the history of biology have had as broad an impact as their double helix, with its AT and CG base pairing. In 1962, Watson, Crick, and Wilkins received the Nobel Prize for their work. {Franklin may have received the prize as well, had she not died from cancer in 1958.)

In their 1953 paper, Watson and Crick wrote that the structure they proposed "immediately suggests a possible copying mechanism for the genetic material." In other words, the structure of DNA also points toward a molecular explanation for life's unique properties of reproduction and inheritance, as we see next.

DNA Replication

When a cell or a whole organism reproduces, a complete set of genetic instructions must pass from one generation to the next. For this to occur, there must be a means of copying the instructions. Watson and Crick's model for DNA structure immediately suggested to them that DNA replicates by a template mechanism-each DNA strand can serve as a mold, or template, to guide reproduction of the other strand. The logic behind the Watson-Crick proposal for how DNA is copied is quite simple. If you know the sequence of bases in one strand of the double helix, you can very easily determine the sequence of bases in the other strand by applying the base-pairing rules: A pairs with T (and T with A), and G pairs with C (and C with G). For example, if one polynucleotide has the sequence ATCG, then the complementary polynucleotide in that DNA molecule must have the sequence TAGC.

Figure 10.6 shows how the template model can account for the direct copying of a piece of DNA. The two strands of parental DNA separate, and each becomes a template for the assembly of a complementary strand from a supply of free nucleotides. The nucleotides are lined up one at a time along the template strand in accordance with the base-pairing rules. Enzymes link the nucleotides to form the new DNA strands. The completed new molecules, identical to the parental molecule, are known as daughter DNA molecules (no gender should be inferred from this name).

Although the general mechanism of DNA replication is conceptually simple, the actual process is complex and requires the cooperation of more than a dozen enzymes and other proteins. The enzymes that actually make the covalent bonds between the nucleotides of a new DNA strand are called DNA polymerases. As an incoming nucleotide base-pairs with its complement on the template strand, a DNA polymerase adds it to the end of the growing daughter strand (polymer ). The process is both fast and amazingly accurate; typically, DNA replication proceeds at a rate of 50 nucleotides per second, with only about one in a billion incorrectly paired. (This is like parallel signal processing) In addition to their roles in DNA replication, DNA polymerases and some of the associated proteins are also involved in repairing damaged DNA. DNA can be harmed by toxic chemicals in the environment or by high-energy radiation, such as X-rays and ultraviolet light

 

DNA replication begins at specific sites on a double helix, called origins of replication. It then proceeds in both directions, creating what are called replication "bubbles" (Figure 10.8). The parental DNA strands open up as daughter strands elongate on both sides of each bubble. The DNA molecule of a eukaryotic chromosome has many origins where replication can start simultaneously, shortening the total time needed for the process. Eventually, all the bubbles merge, yielding two completed double-stranded daughter DNA molecules.

DNA replication ensures that all the somatic cells in a multicellular organism carry the same genetic information. It is also the means by which genetic instructions are copied for the next generation of the organism.

 

How an Organism's DNA Genotype Produces Its Phenotype

Knowing the structure of DNA, we can now define genotype (genetic makeup) and phenotype (the expressed traits of an organism) more precisely.  An organism's genotype is the sequence of nucleotide bases in its DNA. The molecular basis of the phenotype lies in proteins with a variety of functions. For example, structural proteins help make up the body of an organism, and enzymes catalyze its metabolic activities. What is the connection between the genotype and the protein molecules that more directly determine the phenotype? Recall that DNA specifies the synthesis of proteins. A gene does not build a protein directly, but rather dispatches instructions in the form of RNA, which in turn programs protein synthesis. This central concept in biology is summarized in Figure 10.9. The chain of command is from DNA in the nucleus of the cell to RNA to protein synthesis in the cytoplasm (the parts supply) . The two main stages are transcription, the transfer of genetic information from DNA into an RNA molecule, and translation, the transfer of the information in the RNA into a protein.

The relationship between genes and proteins was first proposed in 1909, when English physician Archibald Garrod suggested that genes dictate phenotypes through enzymes, the proteins that catalyze chemical processes. Garrod's idea came from his observations of inherited diseases. He hypothesized that an inherited disease reflects a person's inability to make a particular enzyme, and he referred to such diseases as "inborn errors of metabolism." He gave as one example the hereditary condition called alkaptonuria, in which the urine appears dark red because it contains a chemical called alkapton. Garrod reasoned that normal individuals have an enzyme that breaks down alkapton, whereas alkaptonuric individuals lack the enzyme. Garrod's hypothesis was ahead of its time, but research conducted decades later proved him right. In the intervening years, biochemists accumulated evidence that cells make and break down biologically important molecules via metabolic pathways, as in the synthesis of an amino acid or the breakdown of a sugar. Each step in a metabolic pathway is catalyzed by a specific enzyme. If a person lacks one of the enzymes, the pathway cannot be completed.

The major breakthrough in demonstrating the relationship between genes and enzymes came in the 1940s from the work of American geneticists George Beadle and Edward Tatum with the orange bread mold Neurospora crassa. Beadle and Tatum studied strains of the mold that were unable to grow on the usual simple growth medium.  Each of these strains turned out to lack an enzyme in a metabolic pathway that produced some molecule the mold needed such as an amino acid. Beadle and Tatum also showed that each mutant was defective in a single gene. Accordingly, they formulated the one gene-one enzyme hypothesis, which states that the function of an individual gene is to dictate the production of a specific enzyme.

The one gene-one enzyme hypothesis has been amply confirmed, but with some important modifications. First it was extended beyond enzymes to include all types of proteins. For example, alpha-keratin, the structural protein of your hair, is the product of a gene. So biologists soon began to think in terms of one gene-one protein. Then it was discovered that many proteins have two or more different polypeptide chains, and each polypeptide  is specified by its own gene. Thus, Beadle and Tatum's hypothesis has come to be restated as one gene-one polypeptide.

  

From Nucleotide Sequence to Amino Acid Sequence: An Overview

Stating that genetic information in DNA is transcribed into RNA and then translated into polypeptides does not explain how these processes occur. Transcription and translation are linguistic terms, and it is useful to think of nucleic acids and polypeptides as having languages, too. To understand how genetic information passes from genotype to phenotype, we need to see how the chemical language of DNA is translated into the different chemical language of polypeptides.

What exactly is the language of nucleic acids? Both DNA and RNA are polymers made of monomers in specific sequences that carry information, much as specific sequences of letters carry information in English. In DNA, the monomers are the four types of nucleotides, which differ in their nitrogenous bases (A, T, C, and G). The same is true for RNA, although it has the base U instead of T.

DNAs language is written as a linear sequence of nucleotide bases, a sequence such as the one you see on the enlarged DNA strand in Figure 10.10.  Specific sequences of bases, each with a beginning and an end, make up the genes on a DNA strand. A typical gene consists of thousands of nucleotides, and a DNA molecule may contain thousands of genes.

When DNA is transcribed, the result is an RNA molecule. The process is called transcription because the nucleic acid language of DNA has simply been rewritten (transcribed) as a sequence of bases of RNA; the language is still that of nucleic acids. The nucleotide bases of the RNA molecule are complementary to those on the DNA strand. As you will soon see, this is because the RNA was synthesized using the DNA as a template.

Translation is the conversion of the nucleic acid language into the polypeptide language. Like nucleic acids, polypeptides are polymers, but the monomers that make them up -- the letters of the polypeptide alphabet are the 20 amino acids common to all organisms. Again, the language is written in a linear sequence, and the sequence of nucleotides of the RNA molecule dictates the sequence of amino acids of the polypeptide. But remember, RNA is only a messenger; the genetic information that dictates the amino acid sequence is based in DNA.

What are the rules for translating the RNA message into a polypeptide? In other words, what is the correspondence between the nucleotides of an RNA molecule and the amino acids of a polypeptide? Keep in mind that there are only four different kinds of nucleotides in DNA (A, G, C, T) and RNA (A, G, C, U). In translation, these four must somehow specify 20 amino acids. If each nucleotide base coded for one amino acid, only 4 of the 20 amino acids could be accounted for. What if the language consisted of two-letter code words? If we read the bases of a gene two at a time, AG, for example, could specify one amino acid, while AT could designate a different amino acid. However, when the four bases are taken two by two, there are only 16 (that is, 41 possible arrangements-still not enough to specify all 20 amino acids.

Triplets of bases are the smallest "words" of uniform length that can specify all the amino acids. There can be 64 ( that is, 43) possible code words of this type-more than enough to specify the 20 amino acids. Indeed, there are enough triplets to allow more than one coding for each amino acid. For example, the base triplets AAT and AAC could both code for the same amino acid - and, in fact, they do.

Experiments have verified that the flow of information from gene to protein is based on a triplet code. The genetic instructions for the amino acid sequence of a polypeptide chain are written in DNA and RNA as a series of three-base words called codons. Three-base codons in the DNA are transcribed into complementary three-base codons in the RNA, and then the RNA codons are translated into amino acids that form a polypeptide. Next we turn to the codons themselves.

The Genetic Code

In 1799, a large stone tablet was found in Rosetta, Egypt, carrying the same lengthy inscription in three ancient scripts: Greek, Egyptian hieroglyphics, and Egyptian written in a simplified script. The Rosetta stone provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code.

In cracking the genetic code, the set of rules relating nucleotide sequence to amino acid sequence, scientists wrote their own Rosetta stone. It was based on a series of elegant experiments , that revealed the amino acid translations of each of the nucleotide - triplet code words. The first codon was deciphered in 1961 by American biochemist Marshall Nirenberg. He synthesized an artificial RNA molecule by linking together identical RNA nucleotides having uracil as their base. No matter where this message started or stopped, it could contain only one type of triplet codon: uuu. Nirenberg added this "poly U" to a test tube mixture containing ribosomes and the other ingredients required for polypeptide synthesis. This mixture translated the poly U into a polypeptide containing a single kind of amino acid, phenylalanine. In this way, Nirenberg learned that the RNA codon UUU specifies the amino acid phenylalanine (Phe). By variations on this method, the amino acids specified by all the codons were determined.

Figure 10.11 The dictionary of the genetic code, listed by RNA codons. The three bases of an RNA codon are designated here as the first, second, and third bases. Practice using this dictionary by finding the codon UGG. This is the only codon for the amino acid tryptophan (Trp), but most amino acids are specified by two or more codons. For example, both UUU and UUG stand for the amino acid phenylalanine (Phe). Notice that the codon AUG not only stands for the amino acid methionine (Met) but also functions as a signal to "start" translating the RNA at that place. Three of the 64 codons function as "stop" signals. Anyone of these termination codons marks the end of a genetic message.

As Figure 10.11 shows, 61 of the 64 triplets code for amino acids. The triplet AUG has a dual function: It not only codes for the amino acid methionine (Met) but can also provide a signal for the start of a polypeptide chain. Three of the other codons do not designate amino acids. They are the stop codons that instruct the ribosomes to end the polypeptide.

In Figure 10.11 that there is redundancy in the code but no ambiguity. For example, although codons UUU and UUC both specify phenylananine (redundancy), neither of them ever represent any other amino acid (no redundancy).  The codons in the figure are the triplets found in RNA. They have a straightforward, complementary relationship to the codons in DNA. The nucleotides making up the codons occur in a linear order along the DNA and RNA, with no gaps or "punctuation" separating the codons.

Almost all of the genetic code is shared by all organisms, from the simplest bacteria to the most complex plants and animals. The universality of the genetic vocabulary suggests that it arose very early in evolution and was passed on over the eons to all the organisms living on Earth today. Such universality is extremely important to modern DNA technologies. Because the code is the same in different species, genes can be transcribed and translated after transfer from one species to another, even when the organisms are as different as a bacterium and a human, or a firefly and a tobacco plant (Figure 10.11.). This allows scientists to mix and match genes from various species-a procedure with many useful applications.

Transcription: From DNA to RNA

Let's look more closely at transcription, the transfer of genetic information from DNA to RNA. An RNA molecule is transcribed from a DNA template by a process that resembles the synthesis of a DNA strand during DNA replication. Figure 10.13a is a close-up view of this process. As with replication, the two DNA strands must first separate at the place where the process will start. In transcription, however, only one of the DNA strands serves as a template for the newly forming molecule. The nucleotides that make up the new RNA molecule take their places one at a time along the DNA template strand by forming hydrogen bonds with the nucleotide bases there. Notice that the RNA nucleotides follow the same base-pairing rules that govern DNA replication, except that U, rather than T, pairs with A. The RNA nucleotides are linked by the transcription enzyme RNA polymerase.

Figure 10.13b is an overview of the transcription of an entire gene. Special sequences of DNA nucleotides tell the RNA polymerase where to start and where to stop the transcribing process.

Initiation of Transcription The "start transcribing" signal is a nucleotide sequence called a promoter, which is located in the DNA at the beginning of the gene. A promoter is a specific place where RNA polymerase attaches. The first phase of transcription, called initiation, is the attachment of RNA polymerase to the promoter and the start of RNA synthesis. For any gene, the promoter dictates which of the two DNA strands is to be transcribed (the particular strand varying from gene to gene).

RNA Elongation During the second phase of transcription, elongation, the RNA grows longer. As RNA synthesis continues, the RNA strand peels away from its DNA template, allowing the two separated DNA strands to come back together in the region already transcribed.

Termination of Transcription In the third phase, termination, the RNA polymerase reaches a special sequence of bases in the DNA template called a terminator. This sequence signals the end of the gene. At this point, the polymerase molecule detaches from the RNA molecule and the gene.

In addition to producing RNA that encodes amino acid sequences, transcription makes two other kinds of RNA that are involved in building polypeptides. We discuss these kinds of RNA a little later.

The Processing of Eukaryotic RNA

In prokaryotic cells, which lack nuclei, the RNA transcribed from a gene immediately functions as the messenger molecule that is translated, called messenger RNA (mRNA). But this is not the case in eukaryotic cells. The eukaryotic cell not only localizes transcription in the nucleus but also modifies, or processes, the RNA transcripts there before they move to the cytoplasm for translation by the ribosomes.

One kind of RNA processing is the addition of extra nucleotides to the ends of the RNA transcript. These additions, called the cap and tail, protect the RNA from attack by cellular enzymes and help ribosomes recognize the RNA as mRNA.

 

(a) A close-up view of transcription                            (b)  Transcription of a gene

Figure 10.13 Transcription. (a) As ANA nucleotides base-pair one by one with DNA bases on one DNA strand (called the template strand), the enzyme ANA polymerase links the ANA nucleotides into an ANA chain. The orange shape in the background is the ANA polymerase. (b) The transcription of an entire gene occurs in r three phases: initiation, elongation, and termination of the ANA. The section of DNA t where the ANA polymerase starts is called the promoter; the place where it stops is , called the terminator.

  

Figure 10-14                                                      Figure 10-15

Figure 10.14 The production of messenger RNA in a eukaryotic cell. Both exons and introns are transcribed from the DNA. Additional nucleotides, making up the cap and tail, are attached It the ends of the RNA transcript. The exons are spliced together. The Iroduct, a molecule of messenger RNA (mRNA), then travels to the :ytoplasm of the cell. There the coding sequence will be translated.

Figure 10.15 The structure of tRNA. (a) The RNA polynucleotide is a "rope" whose appendages are the nitrogenous bases. Dashed lines are hydrogen bonds, which connect some of the bases. The site where an amino acid will attach is a three nucleotide segment at one end (purple). Note the three-base anti codon at the bottom of the molecule (dark green). The overall shape of a tRNA molecule is like the letter L. (b) This is the representation of tRNA that we use in later diagrams.

Another type of RNA processing is made necessary in eukaryotes by noncoding stretches of nucleotides that interrupt -- nucleotides that actually code for amino acids. It is as if unintelligible sequences of letters were randomly interspersed in an otherwise intelligible document. most genes of plants animals, It turns out, include such internal noncoding regions, which are called introns. (The functions of introns, if any, and how introns evolved remain a mystery.) The coding regions -- the parts of a gene that are expressed - are called exons. As Figure 10.14 illustrates, both exons and introns are transcribed from DNA into RNA. However, before the RNA leaves the nucleus, the introns are removed, and the exons are joined to produce an mRNA molecule with a continuous coding sequence. This process is called RNA splicing. RNA splicing is believed to playa significant role in humans in allowing our approximately 35,000 genes to produce many thousands more polypeptides. This is accomplished by varying the exons that are included in the final mRNA. With capping, tailing, and splicing completed, the "final draft" of eukaryotic mRNA is ready for translation.

Translation: The Players

As we have already discussed, translation is a conversion between different languages-from the nucleic acid language to the protein language-and it involves more elaborate machinery than transcription.

Messenger RNA (mRNA) The first important ingredient required for translation is the mRNA produced by transcription. Once it is present, the machinery I used to translate mRNA requires enzymes and sources of chemical energy, such as ATP. In addition, translation requires two heavy-duty components: ribosomes and a kind of RNA called transfer RNA.

Transfer RNA (tRNA) Translation of any language into another language requires an interpreter,  person or device that can recognize the words of one language and convert them into the other. Translation of the genetic message carried in mRNA into the amino acid language of proteins also requires an interpreter. To convert the three-letter words ( codons ) of nucleic acids to the one-letter, amino acid words of proteins, a cell uses a molecular interpreter, a type of RNA called transfer RNA. abbreviated tRNA (Figure 10.15).

 

Figure 10-16                                                                   Figure 10-17

Figure 10.16 The ribosome. (a) A simplified diagram of a ribosome, showing its two subunits and sites where mRNA and tRNA molecules bind. (b) When functioning in polypeptide synthesis, a ribosome holds one molecule of mRNA and two molecules of tRNA. The growing polypeptide is attached to one of the tRNAs.

Figure 10.17 A molecule of mRNA. The pink ends are nucleotides that are not part of the message; that is, they are not translated. These nucleotides, along with the cap and tail (yellow),

help the mRNA attach to the ribosome.

A cell that is ready to have some of its genetic information translated into polypeptides has in its cytoplasm a supply of amino acids, either obtained from food or made from other chemicals. The amino acids themselves cannot recognize the codons arranged in sequence along messenger RNA. It is up to the cell's molecular interpreters, tRNA molecules, to match amino acids to the appropriate codons to form the new polypeptide. To perform this task, tRNA molecules must carry out two distinct functions: ( 1) to pick up the appropriate amino acids, and (2) to recognize the appropriate codons in the mRNA. The unique structure of tRNA molecules enables them to perform both tasks-

As shown in Figure 10.15a, a tRNA molecule is made of a single strand of RNA - one polynucleotide chain-consisting of about 80 nucleotides. The chain twists and folds upon itself, forming several double-stranded regions in which short stretches of RNA base-pair with other stretches. At one end of the folded molecule is a special triplet of bases called an anticodon. The anticodon triplet is complementary to a codon triplet on mRNA. During translation, the anticodon on tRNA recognizes a particular codon on mRNA by using base-pairing rules. At the other end of the tRNA molecule is a site where an amino acid can attach. Although all tRNA molecules are similar, there is a slightly different version of tRNA for each amino acid.

Ribosomes  Ribosomes are the organelles that coordinate the functioning of the mRNA and tRNA and actually make polypeptides. As you can see in Figure 10.16a, a ribosome consists of two subunits. Each subunit is made up of proteins and a considerable amount of yet another kind of RNA, ribosomal RNA (rRNA). A fully assembled ribosome has a binding site for mRNA on its small subunit and binding sites for tRNA on its large subunit. Figure 10.16b shows how two tRNA molecules get together with an mRNA molecule on a ribosome. One of the tRNA binding sites, the P site, holds the tRNA carrying the growing polypeptide chain, while another, the A site, holds a tRNA carrying the next amino acid to be added to the chain. The anticodon on each tRNA base pairs with a codon on mRNA. The subunits of the ribosome act like a vise, holding the tRNA and mRNA molecules close together. The ribosome can then connect the amino acid from the A site tRNA to the growing polypeptide.

 ‘

Figure 10.18      Figure 10.19

Figure 10.18 The initiation of translation. (1) An mRNA molecule binds to a small ribosomal subunit. A special initiator tRNA then binds to the start codon, where translation is to begin on the mRNA. The initiator tRNA carries the amino acid methionine (Met); its anticodon, UAC, binds to the start codon, AUG.  (2) A large ribosomal subunit binds to the small one, creating a functional ribosome. The initiator tRNA fits into the P site on the ribosome.

Figure 10.20

Translation: The Process

Translation can be divided into the same three phases as: transcription initiation, elongation, and termination.

Initiation This first phase brings together the mRNA, the first amino acid with its attached tRNA, and the two subunits of a ribosome. An mRNA molecule, even after splicing, is longer than the genetic message it carries (Figure 10.17) .Nucleotide sequences at either end of the molecule are not part of the message, but along with the cap and tail in eukaryotes, they help the mRNA bind to the ribosome. The initiation process determines  exactly where translation will begin so that the mRNA codons will be translated into the correct sequence of amino acids. Initiation occurs in two steps, as shown in Figure 10.18. 

            Elongation Once initiation is complete, amino acids are added one by one to the first ammo acid. Each addition occurs ill a three-step elongation process (Figure 10.19).

Step (1)  Codon recognition.  The anticodon of an incoming tRNA molecule, carrying its ammo acid, pairs with the mRNA codon in the A site of the ribosome.

Step (2) Peptide bond formation. The polypeptide leaves the tRNA in the P site and attaches to the amino acid on the tRNA in the A site. The ribosome catalyzes bond formation. Now the chain has one more amino acid.

Step (3) Translocation. The P site tRNA now leaves the ribosome, and the ribosome translocates (moves) the remaining tRNA, carrying the growing polypeptide, to the P site. The mRNA and tRNA move as a unit. This movement brings into the A site the next mRNA codon to be translated, and the process can start again with step (1).

            Termination Elongation continues until a stop codon reaches the ribosome's A site. Stop. codons-UAA, UAG, and UGA-do not code for amino acids but instead tell translation to stop. The completed polypeptide, typically several hundred ammo acids long, is freed, and the ribosome splits into its subunits.

Review: DNA > RNA > Protein

Figure 10.20 reviews the flow of genetic information in the cell, from DNA to RNA to protein. In eukaryotic cells, transcription-the stage from DNA to RNA-occurs in the nucleus, and the RNA 8 Peptide bond formation is processed before it enters the cytoplasm. Translation is rapid; a single ribosome can make an average-size polypeptide in less an a minute. As it is made a polypeptide coils and folds, assuming a three-dimensional shape, its tertiary structure. Several polypeptides may come together, forming a protein with quaternary structure.

What is the overall significance of transcription and transcription? These are the processes whereby genes control the structures and activities of cells location or, more broadly, the way the genotype produces the phenotype.  The chain command originates with information in the gene, a specific linear sequence of nucleotides in the DNA.  The gene serves as a template, dictating the transcription of a complementary sequence of nucleotides in mRNA. In turn, mRNA specifies the linear sequence in which amino acids appear in a polypeptide. Finally, the proteins that form from the polypeptides determine the appearance and capabilities of the cell and organism.

Mutations

Since discovering how genes are translated into proteins, scientists have been able to describe many heritable differences in molecular terms. For instance, when a child is born with sickle-cell disease, the condition can be traced back through a difference in a protein to one tiny change in a gene. In one of the polypeptides in the hemoglobin protein, the sickle-cell child has a single different amino acid. This difference is caused by a single nucleotide difference in the coding strand of DNA (Figure 10.21 ). In the double helix, a base pair is changed.

The sickle-cell allele is not a unique case. We now know that the various alleles of many genes result from changes in single base pairs in DNA. Any change in the nucleotide sequence of DNA is called a mutation. Mutations can involve large regions of a chromosome or just a single nucleotide pair, as in the sickle-cell allele.

Types of Mutations Mutations within a gene can be divided into two general categories: base substitutions and base insertions or deletions (Figure 10.22 ) .A base substitution is the replacement of one base, or nucleotide, by another. Depending on how a base substitution is translated, it can result in no change in the protein, in an insignificant change, or in a change that might be crucial to the life of the organism. Because of the redundancy of the genetic code, some substitution mutations have no effect. For example, if a mutation causes an mRNA codon to change from GAA to GAG, no change in the protein product would result, because GAA and GAG both code for the same amino acid (Glu). Such a change is called a silent mutation.

Other changes of a single nucleotide do change the amino acid coding, Such mutations are called missense mutations. For example, if a mutation causes an mRNA codon to change from GGC to AGC, the resulting protein will have a serine (Ser) instead of a glycine (Gly) at this position (see Figure 10.22a). Some missense mutations have little or no effect on the resulting protein, but others, as we saw in the sickle-cell case, cause changes in the protein that prevent it from performing normally.

Occasionally, a base substitution leads to an improved protein or one with new capabilities that enhance the success of the mutant organism and its descendants. Much more often, though, mutations are harmful. Some base substitutions, called nonsense mutations, change an amino acid codon into a stop codon. For example, if an AGA (Arg) codon is mutated to a UGA ( stop) codon, the result will be a prematurely terminated protein, which may not function properly.

 

Figure 10.21 The molecular basis of sickle-cell disease. The sickle-cell allele differs from its normal counter-part, a gene for hemoglobin, by only one nucleotide, This difference changes the mRNA codon from one that codes for the amino acid glutamic acid (Glu) to one that codes for valine (Val).

Figure 10.22 Two types of mutations and their effects. Mutations are changes in DNA, but they are represented here as reflected in mRNA and its polypeptide product, (a)1n the base substitution shown here, an A replaces a G in the fourth codon of the mRNA, The result in the polypeptide is a serine (Ser) instead of a glycine (Gly), This amino acid substitution mayor may not affect the protein's function, (b) When a nucleotide is deleted (or inserted), the reading frame is altered, so that all the codons from that point on are misread, The resulting polypeptide is likely to be completely nonfunctional,

Mutations involving the insertion or deletion of one or more nucleotides in a gene often have disastrous effects. Because mRNA is read as a series of nucleotide triplets during translation, adding or subtracting nucleotides may alter the reading frame (triplet grouping) of the genetic message. All the nucleotides that are "downstream" of the insertion or deletion will be regrouped into different codons. For example, consider an mRNA molecule containing the sequence AAG-UUU-GGC-GCA; this codes for Lys-Phe-Gly-Ala. If a U is deleted in the second codon, the resulting sequence will be AAG- UUG-GCG-CAU, which codes for Lys-Leu-Ala-His (see Figure 10.22b). The altered polypeptide is likely to be nonfunctional. Inserting one or two mRNA nucleotides would have a similarly large effect.

Mutagens What causes mutations? Mutagenesis, the creation of mutations, can occur in a number of ways. Mutations resulting from errors during DNA replication or recombination are known as spontaneous mutations, as are other mutations of unknown cause. Other sources of mutation are physical and chemical agents called mutagens. The most common physical mutagen is high-energy radiation, such as X-rays and ultraviolet (UV) light. Chemical mutagens are of various types. One type, for example, consists of chemicals that are similar to normal DNA bases but that base-pair incorrectly when incorporated into DNA. Many mutagens can act as carcinogens, agents that cause cancer. What can you do to avoid exposure to mutagens? Several lifestyle practices can help, including wearing protective clothing and sun screen to minimize direct exposure to the sun’s rays and not smoking. But such precautions are not fool proof; for example, you cannot entirely avoid UV radiation.

Although mutations are often harmful, they are also extremely useful, both in nature and in the laboratory. Mutations are the source of the rich diversity of genes in the living world, a diversity that makes evolution by natural selection possible (Figure 10.23). Mutations are also essential tools for geneticists. Whether naturally occurring or created in the laboratory, mutations are responsible for the different alleles needed for genetic research.

 

 

Basic Concepts in Genetics

Cells are of two basic types: eukaryotic and prokaryotic - Structurally, cells consist of two basic types, although, evolutionarily, the story is more complex  (above) Prokaryotic cells lack a nuclear membrane and possess no membranebounded cell organelles, whereas eukaryotic cells are more complex, possessing a nucleus and membranebounded organelles such as chloroplasts and mitochondria.

The gene is the fundamental unit of heredity - The precise way in which a gene is defined often varies. At the simplest level, we can think of a gene as a unit of information that encodes a genetic characteristic. We will enlarge this definition as we learn more about what genes are and how they function.

Genes come in multiple forms called alleles - A gene that specifies a characteristic may exist in several forms, called alleles. For example, a gene for coat color in cats may exist in alleles that encode either black or orange fur.

Genes encode phenotypes - One of the most important concepts in genetics is the distinction between traits and genes. Traits are not inherited directly. Rather, genes are inherited and, along with environmental factors, determine the expression of traits. The genetic information that an individual organism possesses is its genotype; the trait is its phenotype. For example, the A blood type is a phenotype; the genetic information that encodes the blood type A antigen is the genotype.

Genetic information is carried in DNA and RNA - Genetic information is encoded in the molecular structure of nucleic acids, which come in two types: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are polymers consisting of repeating units called nucleotides; each nucleotide consists of a sugar, a phosphate, and a nitrogenous base. The nitrogenous bases in DNA are of four types (abbreviated A, C, G, and T), and the sequence of these bases encodes genetic information. Most organisms carry their genetic information in DNA, but a few viruses carry it in RNA. The four nitrogenous bases of RNA are abbreviated A, C, G, and U.

Genes are located on chromosomes - The vehicles of genetic information within the cell are chromosomes, which consist of DNA and associated proteins. The cells of each species have a characteristic number of chromosomes; for example, bacterial cells normally possess a single chromosome; human cells possess 46; pigeon cells possess 80. Each chromosome carries a large number of genes.

Chromosomes separate through the processes of mitosis and meiosis - The processes of mitosis and meiosis ensure that each daughter cell receives a complete set of an organism's chromosomes. Mitosis is the separation of replicated chromosomes during the division of somatic (nonsex) cells. Meiosis is the pairing and separation of replicated chromosomes during the division of sex cells to produce gametes (reproductive cells).

Genetic information is transferred from DNA to RNA to protein - Many genes encode traits by specifying the structure of proteins. Genetic information is first transcribed from DNA into RNA, and then RNA is translated into the amino acid sequence of a protein.

Mutations are permanent, heritable changes in genetic information - Gene mutations affect only the genetic information of a single gene; chromosome mutations alter the number or the structure of chromosomes and therefore usually affect many genes.

Some traits are affected by multiple factors - Some traits are influenced by multiple genes that interact in complex ways with environmental factors. Human height, for example, is affected by hundreds of genes as well as environmental factors such as nutrition.

Evolution is genetic change - Evolution can be viewed as a two-step process: first, genetic .variation arises and, second, some genetic variants increase in frequency, whereas other variants decrease in frequency.

Viruses are processed by RNA.

            Despite their tremendous diversity, all living organisms use the same genetic system. A complete set of genetic instructions for any organism is it’s Genome, and all genes are encoded in nucleic acids, either DNA or RNA.  Genetic instructions are in the same format, the same words are identical. The process by which genetic information is copied and decoded is remarkably similar for all forms of life.  All life on earth came from the same primordial ancestor that arose 3.5 to 4 billion years ago.

Cells are of two basic types: eukaryotic and prokaryotic

 

DNA consists of two polynucleotide chains that are antiparallel and complementary

RNA consists of a single nucleotide chain

  

Plant and Animal Cells, similar but different

 

     Most DNA is contained in the Nucleus              Synthesis of mRNA > cytoplasm > synthesis of Protein

            A few organelles , notably chloroplasts and mitochondrion , contain DNA.  Each human mitochondrion  contains about 15,000 nucleotides of DNA, encoding 37 genes. Compared with that of nuclear DNA, which contains some 3 billion nucleotides encoding perhaps 35,000 genes, the amount of mitochondrial DNA (mtDNA) is very small none the less mtDNA and chloroplast (cpDNA) (plant) genes encode some important characteristics. 

The first Genetic Code was probably RNA, not DNA

            In 1981 Thomas Cech and his colleagues discovered that RNA can serve as a biological catalyst. They found that RNA from the protozoan Tetrahymena hermophila can excise 400 nucleotides from its RNA in the absence of any protein.  Other examples of catalytic RNAs have now been discovered in different types of cells. Called ribozymes, these RNA molecules can cut out parts of their own sequences, connect some RNA molecules together, replicate others, and even catalysze the formation of peptide bonds between amino acids. The discovery of ribozymes complements other evidence suggesting that the original genetic material was RNA.

            Ribozymes that were self-replicating probably first arose between 3.5 billion and 4 billion years ago and may have begun the evolution of life on Earth. Early life was an RNA world, with RNA molecules serving both as carriers of genetic information and as catalysts that drove the chemical reactions needed to sustain and perpetuate life. These catalytic RNA’s may have acquired the ability to synthesize protein-based enzymes, which are more efficient catalysts; with enzymes taking over more and more of the catalytic functions, RNA probably became relegated to the role of information storage and transfer. DNA, with its chemical stability and faithful replication, eventually replaced RNA as the primary carrier of genetic information. In modern cells, RNA still plays a vital role in both DNA replication and protein synthesis.

 

 

Transcription is the synthesis of RNA molecules, with DNA as a template, and it is the first step in the transfer genetic information from genotype to phenotype. The process is complex, and requires a number of protein components. As we examine the stages of transcription, try to keep all the detail in perspective; focus on understanding how the details relate to the overall purpose of transcription -the selective synthesis of an RNA molecule.

 

 

 

 

 

Single chromosome                                                       set of chromosome

The gene is the fundamental unit of heredity ;Genes are located on chromosomes

 

Structure of a eukaryotic chromosome     Removal of the tubulin subunits from microtubules at the kinetochore, are responsible for the poleward movement of chromosomes during anaphase

 

Cell division is essential to Growth of the Living plants or animals

What was simple cell division for prokaryotic became more complicated for eukaryotic cells.

The number of chromosomes and DNA molecules changes in he course of the cell cycle

 

 

Meiosis I

Prophase I     Chromosomes condense, homologeus chromosomes synapse, crossing over takes place, nuclear envelope breaks down, and mitotic spindle forms.

Metaphase I   Homologous p;airs of chromosomes line up on the metaphase plate.

Anaphase I    The two chromosomes (each with two chromatids) of each homologous pair separate and move toward opposite poles.

Telophase I   Chromosomes arrive at the spindle poles.

Cytokinesis   The cytoplasm divides to produce two cells, each having half the original number of chromosomes.

Interkinesis   In some dells the spindle breaks down, choromo9s9jes relax, and a nuclear envelope reforms, but no DNA synthesis takes place.

Meiosis II

Prophae II    Chromosomes condense, the spindle forms, and the nuclear envelope disintegrates.

Metaap;hase II  Individual chromosomes line upon the metaphase plate.

Anaphanse II   Sister chromoatids separate and migrate as individual chromosomes toward the spindle poles.

Telophase II   Chromosomes arrive at the spindle poles; the spindle breaks down and a nuclear envelope reforms.

Cytokineses    The cytoplasim divides.

 

 

 

Comparison of mitosis and meiosis

 

Crossing over takes place in meiosis and is responsible for recombination

 

left: Male and female gametes (sperm and egg) differ in size

right: The X & Y chromosomes in humans differ in size and genetic content.

 

Inheritance of sex in organisms with X & Y chromosomes results in equal numbers of male & female offsprings

 

 

Powerful X-Rays can cause mutations

 

 

 

The Ancients knew nothing of this

 

 

Prokaryotes

The history of prokaryotic life is a success story spanning billions of years (Figure 15.8). Prokaryotes lived and evolved all alone on Earth for 2 billion years. They have continued to adapt and flourish on an evolving Earth and in turn have helped to change Earth.

They're Everywhere!

Today, prokaryotes are found wherever there is life, and they outnumber all eukaryotes combined. More prokaryotes inhabit a handful of fertile soil or the mouth or skin of a human than the total number of people who have ever lived. Prokaryotes also thrive in habitats too cold, too hot, too salty, too acidic, or too alkaline for any eukaryote. In 1999, biologists even discovered prokaryotes growing on the walls of a gold mine 2 miles below Earth's surface.

 

           Figure 15.8a               Figure 15.8b                                       Figure 14.27

Figure 15.8 Over 3 billion years of prokaryotes. (a) This microscopic fossil is a filamentous species consisting of a chain of prokaryotic cells. It is one of a diversity of prokaryotes found in western Australian rocks that are about 3.5 billion years old. (b) The orange rods are individual modern bacteria, each about 5 mm long, on the head of a pin. Most prokaryotic cells have diameters in the range of 1-10 mm, much smaller than most eukaryotic cells (typically 10-100 mm). This micrograph will help you understand why a pin prick can cause infection. And it will help you remember to flame the tip of a needle before using it to remover a splinter. The heat kills the bacteria.

Though individual prokaryotes are relatively small organisms, they are , giants in their collective impact on Earth and its life. We hear most about a few species that cause serious illness. During the fourteenth century, Black Death-bubonic plague, a bacterial disease-spread across Europe, killing an estimated 25% of the human population. Tuberculosis; cholera, many sexually transmissible diseases, and certain types of food poisoning are some other human diseases caused by bacteria.

However, prokaryoric life is no rogue’s gallery. Far more common than harmful bacteria are those that are benign or beneficial. Bacteria in our intestines provide us with important vitamins, and others living in our mouth prevent harmful fungi from growing there. Prokaryotes also recycle carbon and other vital chemical elements back and forth between organic matter and the soil and atmosphere. For example, there are prokaryotes that decompose dead organisms. Found in soil and at the bottom of lakes, rivers, and oceans, these decomposers return chemical elements to the environment in the form of inorganic compounds that can be used by plants, which in turn feed animals. If prokaryotic decomposers were to disappear, the chemical cycles that sustain life would come to a halt. All forms of eukaryotic life would also be doomed. In contrast, prokaryotic life would undoubtedly persist in the absence of eukaryotes, as it once did for 2 billion years.

The Two Main Branches of Prokaryotic Evolution: Bacteria and Archaea

Prokaryotes have a cellular organization fundamentally different from that of eukaryotes. Whereas eukaryotic cells have a membrane-enclosed nucleus and numerous other membrane-enclosed organelles, prokaryotic cells lack these structural features. The traditional five-kingdom classification scheme emphasizes this fundamental difference in cellular organization. Prokaryotes make up the kingdom Monera, separate from the four eukaryotic kingdoms (Protista, Plantae, Fungi, and Animalia). In the past two decades, however, researchers have learned that a single prokaryotic kingdom may not fit evolutionary history. By comparing genomes of diverse prokaryotes, biologists have identified two major branches of prokaryotic evolution: the bacteria and the archaea. Though they have prokaryotic cell organization in common, bacteria and cuchaea differ in many structural, biochemical, and physiological characteristics. And there is also evidence that archaea are more closely related to eukaryotes than they are to bacteria. It was these discoveries that prompted the three-domain classification- domains Bacteria, Archaea, and Eukarya - which you can review in Figure 14.27b. The majority of prokaryotes are bacteria, but the archaea are worth studying for their evolutionary and ecological significance.

The term archaea ("ancient") refers to the antiquity of the group's origin from the earliest cells. Even today, most species of archaea inhabit extreme environments, such as hot springs and salt ponds. Few other modem organisms (if any) can survive in these environments, which may resemble habitats on the early Earth.

Biologists refer to some archaea as "extremophiles:' meaning "lovers of the extreme:' There are extreme halophiles ("salt lovers"), archaea that thrive in such environments as Utah's Great Salt Lake and seawater-evaporating ponds used to produce salt (Figure 15.9) .There are also extreme thermophiles ("heat lovers") that live in very hot water; some even populate the deep-ocean vents that gush superheated water hotter than 100°C, the boiling point of water at sea level. And then there are the methanogens, archathat live in anaerobic environments and give off methane as a waste product. They are abundant in the anaerobic mud at the bottom of lakes and swamps. You may have seen methane, also called marsh gas, bubbling up from a swamp. Great numbers of methanogens also inhabit the digestive tracts of animals. In humans, intestinal gas is largely the result of their metabolism. More importantly, methanogens aid digestion in cattle, deer, and other animals that depend heavily on cellulose for their nutrition. Normally, bloating does not occur because these animals regularly belch out large volumes of gas produced by the methanogens and other microorganisms that enable them to utilize cellulose. And that may be more than you wanted to know about these gas-producing microbes.

 

Figure 15.9                                       Figure 4.5   Prokaryote

Figure 15.9 Extreme halophiles (“salt-loving” archaea). These are seawater-evaporating ponds at the edge San Francisco Bay. The colors of the ponds result from dense growth of the prokaryotes that thrive when the salinity of the water reaches 15-20% (before evaporation, seawater has a salt concentration of about 3%). The ponds are used for commercial salt production; the halophilic archaea are harmless.

          

Figure 15.10                                                          Figure 15.11

Figure 15.11 Some examples of bacterial diversity  (a) This prokaryotic organism, called an actinomycete, is a mass of branching chains of rod-shaped cells. These bacteria are very common in soil, where they break down organic substances. The filaments enable the organism to bridge dry gaps between soil particles. Most species secrete antibiotics, which inhibit the growth of competing bacteria. Pharmaceutical companies use various species of actinomycetes to produce antibiotic drugs, including streptomycin. (b) This filamentous prokaryote belongs to a photosynthetic group called the cyanobacteria. Many species are truly multicellular in having a division of labor among specialized cells. The box on this micrograph highlights a cell that converts atmospheric nitrogen to ammonia, which can then be incorporated into amino acids and other organic compounds. (c) There are actually some prokaryotic cells that are gigantic, even by eukaryoti standards. The bright ball in this photo is a marine bacterium discovered in 1997 (the two smaller spheres above it are dead cells) This prokaryotic cell is over half a millimeter in diameter, about the size of a fruit fly's head.

The Structure, Function, and Reproduction of Prokaryotes

You can use Figure 4.5 to review the general structure of prokaryotic cells. Note again the absence of a true nucleus and the other membrane-enclosed organelles characteristic of the much more complex eukaryotic cells. Another feature to note in prokaryotes is that nearly all species have cell walls exterior to their plasma membranes. These walls are chemically different from the cellulose walls of plant cells. Some antibiotics, including the penicillins, kill certain bacteria by incapacitating an enzyme the microbes use to make their walls. Determining cell shape by microscopic examination is an important step in identifying prokaryotes (Figure 15.10). Spherical species are called cocci (singular, coccus), from the Greek word for "berries." Cocci that occur in clusters are called staphylococci ("cluster of grapes"), or staph for short (as in "staph infections"). Other cocci occur in chains; they are called I streptococci ("twisted grapes"). The bacterium that causes strep throat in humans is a streptococcus. Rod-shaped prokaryotes are called bacilli (singular, bacillus). A third group of prokaryotes are curved or spiral-shaped. The largest spiral-shaped prokaryotes are called spirochetes. The bacterium that causes syphilis, for example, is a spirochete. The culprit that causes Lyme disease is also a spirochete. Most prokaryotes are unicellular and very small, but there are exceptions to both of these generalizations. Some species tend to aggregate transiently into groups of two or more cells, such as the streptococci already mentioned. Others form true colonies, which are permanent aggregates of identical cells (Figure 15.11a). And some species even exhibit a simple multi cellular organization, with a division of labor between specialized types of cells (Figure 15.11 b ). Among unicellular species, there are some giants that actually dwarf most eukaryotic cells (Figure 15.11 c).

 

Figure 15.12                                                          Figure 15.13

Figure 15.12 Prokaryotic flagella. These locomotor appendages are entirely different in structure and mechanics from the eukaryotic flagella discussed in Chapter 4. At the base of the prokaryotic version is a motor and set of rings embedded in the plasma membrane and cell wall. This machinery actually spins like a wheel, rotating the filament of the flagellum.

Figure 15.13 An anthrax endospore. This prokaryote is Bacillus anthracis, the notorious bacterium that produces the deadly disease called anthrax in cattle, sheep, and humans. There are actually two cells here, one inside the other. The outer cell produced the specialized inner cell, called an endospore. The endospore has a thick, protective coat. Its cytoplasm is dehydrated, and the cell does not metabolize. Under harsh conditions, the outer cell may disintegrate, but the endospore survives all sorts of trauma, including lack of water and nutrients, extreme heat or cold, and most poisons. When the environment becomes more hospitable, the endospore absorbs water and resumes growth. In late 2001, one or more bioterrorists disseminated anthrax spores through the U.S. postal system.

About half of all prokaryotic species are motile. Many of those travelers have one or more flagella that propel the cells away from unfavorable places or toward more favorable places, such as nutrient-rich locales (Figure 15.12).

Although few bacteria can thrive in the extreme environments favored by many archaea, some bacteria can survive extended periods of very harsh conditions by forming specialized "resting" cells, or endospores (Figure 15.13) .Some endospores can remain dormant for centuries. Not even boiling water kills most of these resistant cells.  To sterilize laboratory equipment, microbiologists use an appliance called an autoclave, a pressure cooker that kills endospores by heating to a temperature of 121°C (250°F) with high-pressure steam. The food-canning industry uses similar methods to kill endospores of dangerous soil bacteria such as Clostridium botulinum, which produces a toxin that causes the potentially fatal disease botulism.

Most prokaryotes can reproduce at a phenomenal rate if conditions are favorable. The cells copy their DNA almost continuously and divide again and again by the process called binary fission. To understand how this makes explosive population growth possible, flash back to that childhood numbers game: "Would you rather have a million dollars or start out with just a penny and have it doubled every day for a month?" If you opt for the penny, you feel like a loser at midmonth, when you have only a few hundred dollars. But by the end of the month, you've bagged about 10 million bucks. This is the exponential growth that repeated doublings make possible. Now apply that concept to bacterial reproduction, except double the number every 20 minutes. That's the rate at which some bacteria can divide if there is plenty of food and space. In just 24 hours, a single tiny cell could give rise to a bacterial colony equivalent in mass to about 15,000 humans! Fortunately, few bacterial populations can sustain exponential growth for long. Environments are usually limiting in resources such as food and space. The bacteria also produce metabolic waste products that may eventually pollute the colony's environment. Still, you can understand why certain bacteria can make you sick so soon after just a few cells infect you - or why food can spoil so rapidly. Refrigeration retards food spoilage not because the cold kills the bacteria on food but because most microorganisms reproduce only very slowly at such low temperatures.

The Nutritional Diversity of Prokaryotes

             Prokaryotic evolution "invented" every type of nutrition we observe through out life, plus some nutritional modes unique to prokaryotes. Nutrition refers here to how an organism obtains two resources for synthesizing organic compounds: energy and a source of carbon. Species that use light energy are termed phototrophs. Chemotrophs obtain their energy from chemicals taken from the environment. If an organism needs only the inorganic compound carbon dioxide (CO2) as a carbon source, it is called an autotroph. Heterotrophs require at least one organic nutrient - the sugar glucose, for instance - as a source of carbon for making other organic compounds.  We can combine the phototroph-versus-cheniotroph (energy source) and autotroph-versus-heterotroph (carbon source) criteria to group organisms according to four major modes of nutrition:

1.  Photoautotrophs are photosynthetic organisms that harness light energy to drive the synthesis of organic compounds from CO2. Among the diverse groups of photosynthetic prokaryotes are the cyanobacteria, such as the species in Figure 15.11 b. All photosynthetic eukaryotes-plants and algae-also fit into this nutritional. category.

2.  Chemoautotrophs need only CO2 as a carbon source. However, instead of using light for energy, these prokaryotes extract energy from certain inorganic substances, such as hydrogen sulfide (H2S) or ammonia (NH3). This mode of nutrition is unique to certain prokaryotes. For example, prokaryotic species living around the hot-water vents deep in the seas are the main food producers in those bizarre ecosystems.

3.  Photoheterotrophs can use light to generate ATP but must obtain their carbon in organic form. This mode of nutrition is restricted to certain prokaryotes.

4. Chemoheterotrophs must consume organic molecules for both energy and carbon. This nutritional mode is found widely among prokaryotes, certain protists, and even some plants. And all fungi and animals are chemoheterotrophs.

Table 15.1 reviews the four major modes of nutrition.

Table 15.1

Nutritional Classification of Organisms

Nutritional Type

Energy Source

Carbon Source

Photoautotroph (photosynthesizer)

Sunlight

CO2

Chemoautotroph

Inorganic chemicals,

CO2

Photoheterotroph

Sunlight

Organic compounds

Chemoheterotroph

Organic compounds

Organic  compounds

Figure 15.14 Really bad bacteria. The yellow rods are Haemophilus influenzae bacteria on skin cells lining the interior of a human nose. These pathogens are transmitted through the air. H. influenzae, not to be confused with influenza (flu) viruses, causes pneumonia and other lung infections that kill about 4 million people worldwide per year. Most victims are children in developing countries, where malnutrition lowers resistance to all pathogens.

The Ecological Impact of Prokaryotes

Organisms as pervasive, abundant, and diverse as prokaryotes are guaranteed to have tremendous impact on Earth and all its inhabitants. Here we survey just a few examples of prokaryotic clout.

Bacteria That Cause Disease We are constantly exposed to bacteria, some of which are potentially harmful (Figure 15.14). Bacteria and other microorganisms that cause disease are called pathogens. Most of us are healthy most of the time only because our body defenses check the growth of pathogens. Occasionally, the balance shifts in favor of a pathogen, and we become ill. Even some of the bacteria that are normal residents of the human body can make us sick when our defenses have been weakened by poor nutrition or by a viral infection.

            Most pathogenic bacteria cause disease by producing poisons. There are two classes of these poisons: exotoxins and endotoxins. Exotoxins are poisonous proteins secreted by bacterial cells. A single gram of the exotoxin that causes botulism could kill a million people. Another exotoxin producer is Staphylococcus aureus (abbreviated S. aureus). It is a common, usually harmless resident of our skin surface. However, if S. aureus enters the body through a cut or other wound or is swallowed in contaminated food, it can cause serious diseases. One type of S. aureus produces exotoxins that cause layers of skin to slough off; another can cause vomiting and severe diarrhea; yet another can produce the potentially deadly toxic shock syndrome. In contrast to exotoxins, endotoxins are not cell secretions but are chemical components of the cell walls of certain bacteria. All endotoxins induce the same general symptoms: fever, aches, and sometimes a dangerous drop in blood pressure (shock). The severity of symptoms varies with the host's condition and with the bacterium. Different species of Salmonella, for example, produce endotoxins that cause food poisoning and typhoid fever.

            During the last 100 years, following the nineteenth-century discovery that "germs" cause disease, the incidence of bacterial infections has declined, particularly in developed nations. Sanitation is generally the most effective way to prevent bacterial disease. The installation of water treatment and sewage systems continues to be a public health priority through-out the world. Antibiotics have been discovered that can cure most bacterial diseases. However, resistance to widely used antibiotics has evolved in many of these pathogens.

In addition to sanitation and antibiotics, a third defense against bacterial disease is education. A case in point is Lyme disease, currently the most widespread pest-carried disease in the United States. The disease is caused by a spirochete bacterium carried by ticks that live on deer and field mice (Figure 15.15) .Lyme disease usually starts as a red rash shaped like a bull's-eye around a tick bite. Antibiotics can cure the disease if administered within about a month after exposure. If untreated, Lyme disease can cause debilitating arthritis, heart disease, and nervous disorders. A vaccine is now available, but it does not give full protection. The best defense is public education about avoiding tick bites and the importance of seeking treatment if a rash develops. When walking through brush, using insect repellent and wearing light-colored clothing can reduce contact with ticks.

Pathogenic bacteria are in the minority among prokaryotes. Far more common are species that are essential to our well-being, either directly or indirectly. Let's turn our attention now to the vital role that prokaryotes play in sustaining the biosphere.

Prokaryotes and Chemical Recycling Not too long ago, in geologic  terms, the atoms of the organic molecules in your body were parts of the in-organic compounds of soil, air, and water, as they will be again. Life depends on the recycling of chemical elements between the biological and physical components of ecosystems. Prokaryotes play essential roles in these chemical cycles. For example, cyanobacteria not only restore oxygen to the atmosphere; some of them also convert nitrogen gas (N2) in the atmosphere to nitrogen compounds that plants can absorb from soil and water (see Figure 15.11 b ). Other prokaryotes, including bacteria living within the roots of bean plants and other legumes, also contribute large amounts of nitrogen compounds to soil. In fact, all the nitrogen that plants use to make proteins and nucleic acids comes from prokaryotic metabolism in the soil, In turn, animals get their nitrogen compounds from plants.

Another vital function of prokaryotes is the breakdown of organic waste and dead organisms. Prokaryotes decompose organic matter and, in the process, return elements to the environment in inorganic forms that can be used by other organisms. If it were not for such decomposers, carbon, nitrogen, and other elements essential to life would become locked in the organic molecules of corpses and waste products.

Prokaryotes and Bioremediation Humans have put the metabolically divers prokaryotes to work in cleaning up the environment. The use of organisms to remove pollutants from water, air, and soil is called bioremediation. The most familiar example of bioremediation is the use of prokaryotic decomposers to treat our sewage. Raw sewage is first passed through a series of screens and shredders, and solid matter is allowed to settle out from the liquid waste. This solid matter, called sludge, is then gradually added to a culture of anaerobic prokaryotes, including both bacteria and archaea.  The microbes decompose the organic matter in the sludge, converting it to material that can be used as landfill or fertilizer after chemical sterilization. Liquid wastes are treated separately from the sludge Figure 15.16).

We are just beginning to explore the great potential that prokaryotes offer for bioremediation. Certain bacteria that occur naturally on ocean beaches can decompose petroleum and are useful in cleaning up oil spills (Figure 15.17). Genetically engineered bacteria may be able to degrade oil more rapidly than the naturally occurring oil-eaters. Bacteria may also help us clean up old mining sites.  The water that drains from mines is highly acidic and is also laced with poisons-often compounds of arsenic, copper, zinc, and the heavy metals lead, mercury, and cadmium. Contamination of our soils and groundwater by these toxic substances poses a widespread threat, and cleaning up the mess is extremely expensive. Although there are no simple solutions to the problem, prokaryotes may be able to help. Bacteria called Thiobacillus thrive in the acidic waters that drain from mines. Some mining companies use these microbes to extract copper and other valuable metals from low-grade ores. While obtaining energy by oxidizing sulfur or sulfur- containing compounds, the bacteria also accumulate metals from the mine waters. Unfortunately, their use in cleaning up mine wastes is limited be- cause their metabolism also adds sulfuric acid to the water. If this problem is solved, perhaps through genetic engineering, Thiobacillus and other prokaryotes may help us overcome some environmental dilemmas that seem intractable today. One current research focus is a bacterium that tolerates radiation doses thousands of times stronger than those that would kill people. This species may help clean up toxic dump sites that include radioactive wastes.

  

                                                     Figure 15.16                                                 Figure 15.17

Figure 15.16 Putting prokaryotes to work in sewage treatment facilities. This is a trickling filter system, one type of mechanism for treating liquid wastes after sludge is removed. The long horizontal pipes rotate slowly, spraying liquid wastes through the air onto a thick bed of rocks. Bacteria and fungi growing on the rocks remove much of the organic material dissolved in the waste. Outflow from the rock bed is sterilized and then released, usually into a river or ocean.

Figure 15.17 Treatment of an oil spill in Alaska.  The workers are spraying fertilizers onto an oil-soaked beach. The fertilizers stimulate growth of naturally occurring bacteria that initiate the breakdown of the oil. This technique is the fastest and least expensive way yet devised to clean up spills on beaches. Of course, it would be much better to keep oil off the beaches in the first place!

It is the nutritional diversity of prokaryotes that makes such benefits as chemical recycling and bioremediation possible. 'The various modes of nutrition and metabolic pathways we find throughout life are all variations on themes that prokaryotes "invented" during their long reign as Earth's exclusive inhabitants. Prokaryotes are at the foundation of life in both the ecological sense and the evolutionary sense. The subsequent breakthroughs in evolution were mostly structural, including the origin of the eukaryotic cell and the diversification of the organisms we call protists.

 

 

 

Eukayotes

            First Eukayotes: 1.7 billion years ago  Eukayotic cells came into being.  These big cells by comparison seem to have captured the small cells with special capability and enslaved them, and eventually encompass them as an integral part of the bacterial cell colony encased in a membrane. This cleaver membrane is a double layer of molecule soldiers, one layer opens and closes before the other layer opens and closes, thus letting waste out and bringing food in.  

 

Prior to the electron microscope, humans were oblivious to the existence of small things.

 

 Perimeter “storm door” cell walls

Protists

            “No more pleasant sight has met my eye than this of so many thousands of creatures in one small drop of water” wrote Anton van Leeuwenhoek after his discovery of the microbial world more than three centuries ago. It a world every biology student should have the opportunity to rediscover by peering through a microscope into a droplet of pond water filled with diverse creatures we call protists.              Protists are eukaryotic, and thus even the simplest are much more complex than the prokaryotes. The first eukaryotes to evolve from prokaryotic ancestors were protists. The very word implies great antiquity (from the Greek protos, first) .The primal eukaryotes were not only the predecessors of the great variety of modern protists, but were also ancestral to all other eukaryotes-plants, fungi, and animals. Two of the most significant chapters in the history of life-the origin of the eukaryotic cell and the subsequent emergence of multicellular eukaryotes-unfolded during the evolution of protists.

The Origin of Eukaryotic Cells .

            The many differences between prokaryotic and eukaryotic cells far outnumber the differences between plant and animal cells. The fossil record indicates that eukaryotes evolved from prokaryotes more than 1.7 billion years ago. One of biology's most engaging questions is how this happened-in particular, how the membrane-enclosed organelles of eukaryotic cells arose. A widely accepted theory is that eukaryotic cells evolved through a combination of two processes. In one process, the eukaryotic cell's endomembrane system-all the membrane-enclosed organelles except mitochondria and chloroplasts evolved from inward folds of the plasma membrane of a prokaryotic cell (1>2)  A second, very different process, called endosymbiosis, generated mitochondria and chloroplasts.(3>4 & 5>6)

Figure 15.18  How did eukaryote cells evolve? 

            Symbiosis is a close association between organisms of two or more species. The word symbiosis is from the Greek for "living together” and endosymbiosis refers to one species living within another, called the host. chloroplasts and mitochondria evolved from small symbiotic prokaryotes that established residence within other, larger host prokaryotes (Figure 15.18b ). The ancestors of mitochondria may have been aerobic bacteria that were able to use oxygen to release large amounts of energy from organic molecules by cellular respiration. At some point, such a prokaryote might have been an internal parasite of a larger heterotroph, or an ancestral host cell may have ingested some of these aerobic cells for food. If some of the smaller cells were indigestible, they might have remained alive and continued to perform respiration in the host cell. In a similar way, photosynthetic bacteria ancestral to chloroplasts may have come to live inside a larger host cell. Because almost all eukaryotes have mitochondria but only some have chloroplasts, it is likely that mitochondria evolved first.

            By whatever means the relationships began, it is not hard to imagine the symbiosis eventually becoming mutually beneficial. In a world that was becoming increasingly aerobic, a cell that was itself an anaerobe would have benefited from aerobic endosymbionts that turned the oxygen to advantage. And a heterotrophic host could derive nourishment from photosynthetic endosymbionts In the process of becoming more interdependent, the host and endosymbionts would have become a single organism, its parts inseparable.

            Developed most extensively by Lynn Margulis, the endosymbiosis theory is supported by extensive evidence. Present-day mitochondria and chloroplasts are similar to prokaryotic cells in a number of ways. For example, both types of organelles contain small amounts of DNA, RNA, and ribosomes that resemble prokaryotic versions more than eukaryotic ones. These components enable cWoroplasts and mitochondria to exhibit some autonomy in their activities. The organelles transcribe and translate their DNA into polypeptides, contributing to some of their own enzymes. They also replicate their own DNA and reproduce within the cell by a process resembling the binary fission of prokaryotes.

            The origin of the eukaryotic cell made more complex organisms possible, and a vast variety of protists evolved.

The Diversity of Protists

            All protists are eukaryotes, but they are so diverse that few other general characteristics can be cited. In fact, protists vary in structure and function more than any other group of organisms. Most protists are unicellular, but there are some colonial and multicellular species. Because most protists are unicellular, they are justifiably considered the simplest eukaryotic organisms. But at the cellular level, many protists are exceedingly complex-the most elaborate of all cells. We should expect this of organisms that must carry out within the boundaries of a single cell, all the basic functions performed by the collective of specialized cells that make up the bodies of plants and animals. Each unicellular protist is not at all analogous to a single cell from a human, but is itself an organism as complete as any whole animal or plant.

            For our survey of these diverse organisms, we'll look at four major categories of protists, grouped-more by lifestyle than by their evolutionary relationships: protozoans, slime molds, unicellular algae, and seaweeds.

            Protozoans Protists that live primarily by ingesting food, a mode of nutrition that is animal-Iike, are called protozoans ("first animal"). Protozoans thrive in all types of aquatic environments, including wet soil and the watery environment inside animals. Most species eat bacteria or other protozoans, but some can absorb nutrients dissolved in the water. Protozoans that live as parasites in animals, though in the minority, cause some of the world's most harmful human diseases. We'll examine five groups of protozoans: flagellates, amoebas, forams, apicomplexans, and ciliates.

            Flagellates are protozoans that move by means of one or more flagella. Most species are free-Iiving (nonparasitic). However, there are also some nasty parasites that make humans sick. An example is Giardia, a flagellate that infects the human intestine and can cause abdominal cramps and severe diarrhea. People become infected mainly by drinking water contaminated with feces from infected animals. Giardia can ruin a camping trip. Another group of dangerous flagellates are the trypanosomes, including a species that causes sleeping sickness, a serious illness prevalent in tropical Africa and transmitted by the tsetse fly (Figure 15.19a)

Figure 15.19 Examples of protozoans.(a) Trypanosomes are flagellates that live as parasites in the bloodstream of vertebrate animals. The squiggles among these human red blood cells are trypanosomes that cause sleeping sickness, a debilitating disease common in parts of Africa.  Trypanosomes escape being killed by their host's defenses by being quick-change artists. They alter the molecular structure of their coats frequently, thus preventing immunity from developing in the host. (b)  This amoeba is ingesting a smaller protozoan as food. The amoeba's pseuilopodia arch around the prey and engulf it into a food vacuole (also see Chapter 5). (c) Forams are almost all marine. The foram cell secretes a porous, multichambered shell made of organic material hardened with calcium carbonate, the same mineral that makes up limestone. Thin strands of cytoplasm (pseudopodia) extend through the pores, functioning in swimming, shell formation, and feeding. The shells of fossilized forams are major components of the limestone rocks that are now land formations. (d) Plasmodium, the apicomplexan that causes malaria, uses its apical complex to enter red blood cells of its human host. The parasite feeds on the host cell from within, eventually destroying it. (e) The ciliate Paramecium uses its cilia to move through pond water. Cilia also line an indentation called the oral groove, and their beating keeps a current of water containing bacteria and small protists moving toward the cell "mouth" at the base of the groove.

            Amoebas are characterized by great flexibility and the absence of permanent locomotor organelles. Most species move and feed by means of pseudopodia ( singular, pseudopodium )', temporary extensions of the cell (Figure 15.19b) .Amoebas can assume virtually any shape as they creep  over rocks, sticks, or mud at the bottoII1 of a pond or ocean. Other protoroans with pseudopodia include the forams (Figure 15.19c).

            Apicomplexans are all parasitic, and some cause serious human diseases. Theyare named for an apparatus at their apex that is specialized for penetrating host cells and tissues. This protozoan group includes Plasmodium, dIe parasite that causes malaria (Figure 15.19d). Spread by mosquitoes, malaria is one of the most debilitating and widespread human diseases. Each year in the tropics, more than 200 million people become infected, and at least a million die in Africa alone. As part of the effort to combat malaria, scientists determined the complete sequence of the Plasmodium genome in 2002.

            Ciliates are protozoans that use locomotor structures called cilia to move and feed. Nearlyall ciliates are free-living (nonparasitic). The best known example is the freshwater ciliate Paramecium (Figure 15.19e) .

            Slime Molds These protists are more attractive than their name. Slime molds resemble fungi in appearance and lifestyle, but the similarities are due to convergent evolution; slime molds and fungi are not at all closely related. The filamentous body of a slime mold, like that of a fungus, is an adaptation that increases exposure to the environment. This suits the role of these organisms as decomposers. The two main groups of these protists are plasmodial slime molds and cellular slime molds.

            Plasmodial slime molds are named for the feeding stage in their life cycle, an amoeboid mass called a plasmodium (not to be confused with Plasmodium, the parasite that causes malaria). You can find plasmodial slime molds among the leaf littler and other decaying material on a forest floor, and you won't need a microscope to see them. A plasmodium can measure several centimeters across, with its network of fine filaments taking in bacteria and bits of dead organic matter amoeboid style. Large as it is, the plasmodium is actually a single cell with many nuclei (Figure 15.20).

            Cellular slime molds pose a semantic question about what it means to be an individual organism. The feeding stage in the life cycle of a cellular slime mold consists of solitary amoeboid cells. They function individually, using their pseudopodia to feed on decaying organic matter. But when food is depleted, the cells aggregate to form a slug-like colony that moves and functions as a single unit (Figure 15.21 ).

            Unicellular Algae Photosynthetic protists are called algae (singular, alga). Their chloroplasts support food chains in freshwater and marine ecosystems. Many unicellular algae are components of plankton (from the Greek planktos, wandering), the communities of organisms, mostly microscopic, that drift or swim weakly near the surfaces of ponds, lakes, and oceans. More specifically, planktonic algae are referred to as phytoplankton. We'll look at three groups of unicellular algae: dinoflagellates, diatoms, and green algae (a group that also includes colonial and truly multicellular species).

  

Left: Figure 15.20 A plasmodial slime mold. Pseudopodia of the huge cell engulf small food particles in mulch or moist soil. The web-like form is an adaptation that enlarges the organism's surface area, increasing its contact with food, water, and oxygen. Within the fine channels of the plasmodium, cytoplasm streams first one way and then the other, in pulses that are beautiful to watch with a microscope. The cytoplasmic streaming helps distribute nutrients and oxygen within the giant cell.

Right: Figure 15.21 Life cycle of a cellular slime mold. Most of the time, cellular slime molds live as solitary amoeboid cells, using their pseudopodia to creep through compost and engulf bacteria. When food is in short supply, the amoeboid cells swarm together, forming a colony that looks and moves like a slug. After wandering around for a short time, the colony extends a stalk and develops into a multicellular reproductive structure.

   

Figure 15.22 Unicellular and colonial algae. (a) A dinoflagellate, with its wall of protective plates. (b) A sample of diverse diatoms, which have glassy walls. (c) Chlamydomonas, a unicellular green alga with a pair of flagella. (d) Volvox, a colonial green alga.

            Dinoflagellates are abundant in the vast aquatic pastures of phytoplankton. Each dinoflagellate species has a characteristic shape reinforced by external plates made of cellulose (Figure 15.22a). The beating of two flagella in perpendicular grooves produces the spinning movement for which these organisms are named (from the Greek dinos, whirling). Dinoflagellate blooms-population explosions-sometimes cause warm coastal waters to turn pinkish orange, a phenomenon known as a red tide. Toxins produced by some red-tide dinoflagellates have caused massive fish kills, especially in the tropics, and are poisonous to humans as well.

            Diatoms have glassy cell walls containing silica, the mineral used to make glass (Figure 15.22b) .The cell wall consists of two halves that fit together like the bottom and lid of a shoe box. Diatoms store their food , reserves in the form of an oil that provides buoyancy, keeping diatoms floating as phytoplankton near the sunlit surface. Massive accumulations of fossilized diatoms make up thick sediments known as diatomaceous earth, which is mined for its use as both a filtering material and an abrasive. Green algae are named for their grass-green chloroplasts. Unicellular green algae flourish in most freshwater lakes and ponds. Some species are flagellated (Figure 15.11c). The green algal group also includes colonial forms, such as the Volvox in Figure 15.11d. Each Volvox colony is a ball of flagellated cells ( the small green dots in the photo) that are very similar to certain unicellular green algae. The balls within the balls in Figure 15.22d are "daughter" colonies that will be released when the parent colonies rupture. Of all photosynthetic protists, green algae are the most closely related to true plants.

Figure 15.23 The three major groups of seaweeds. (a) Green algae. This sea lettuce is an edible species that inhabits the intertidal lone. In addition to seaweeds, the green algal group includes unicellular and colonial species, such as those in Figures 15.22c and d. (b) Red algae. These seaweeds are most abundant in the warm coastal waters of the tropics. Of all the seaweeds, red algae can generally live in the deepest water. Their chloroplasts have special pigments that absorb the blue and green light that penetrates best through

water. The species in this photo is an example of corraline algae, which contribute to the architecture of some coral reefs. The cell walls are hardened bya mineral. (c) Brown algae. This group includes the largest seaweeds, known as kelp, which grow as marine "forests" in relatively deep water beyond the intertidal lone. Some species grow to a length of over 60 m in a single season, the fastest linear growth of any organism. Kelp is a renewable resource reaped by special boats that cut and collect the tops of the algae. More importantly, kelp forests provide habitat for many animals, including a great diversity of fishes. If you have walked on a beach covered with kelp that has washed ashore after a storm, you may have noticed the organs called floats, which keep the photosynthetic blades of the kelp in the light near the water's surface. Maybe you even picked up and popped some of those floats, the way you do those irresistible packing-material bubbles. 

            Seaweeds Defined as large, multicellular marine algae, seaweeds grow on rocky shores and just offshore beyond the zone of the pounding surf. Their cell walls have slimy and rubbery substances that cushion their bodies against the agitation of the waves. Some seaweeds are as large and complex as many plants. Even the word seaweed implies plantlike appearance, but the similarities between these algae and true plants are a consequence of convergent evolution. In fact, the closest relatives of seaweeds are certain unicellular algae, which is why many biologists include seaweeds with the protists. Seaweeds are classified into three different groups, based partly on the types of pigments present in their chloroplasts: green algae, red algae, and brown algae (Figure 15.23) .

            Coastal people, particularly in Asia, harvest seaweeds for food. For example, in Japan and Korea, some seaweed species are ingredients in soups. Other seaweeds are used to wrap sushi. Marine algae are rich in iodine and other essential minerals. However, much of their organic material consists of unusual polysaccharides that humans cannot digest, which prevents seaweeds from becoming staple food. They are ingested mostly for their rich tastes and unusual textures. The gel-forming substances in the cell walls of seaweeds are widely used as thickeners or such processed foods as puddings, ice cream, and salad dressing. And the seaweed extract called agar provides the gel forming base for the media microbiologists use to culture bacteria in Petri dishes.

Evolution Connection

The Origin of Multicellular Life

            An orchestra can playa greater variety of musical compositions than a violin soloist can. Put simply, increased complexity makes more variations possible. Thus, the origin of the eukaryotic cell led to an evolutionary radiation of new forms of life. Unicellular protists, which are organized on the complex eukaryotic plan, are much more diverse in form than the simpler prokaryotes. The evolution of multicellular bodies broke through another threshold in structural organization.

Figure 15.24 A model for the evolution of multicellular organisms from unicellular protists.

(1) An ancestral colony may have formed, as colonial protests do today, when a cell divided and its offspring remained attached to one another. (2) The cells in the colony may have become somewhat specialized and interdependent, with different cell types becoming more and more efficient at performing specific, limited tasks. Cells that retained a flagellum may have become specialized for locomotion, while others that lost their flagellum could have assumed functions such as ingesting or synthesizing food. (3) Additional specialization among the cells in the colony may have led to distinctions between sex cells (gametes) and non-reproductive cells (somatic cells).

            Multicellular organisms are fundamentally different from unicellular ones. In a unicellular organism, all of life's activities occur within a single cell. In contrast, a multicellular organism has various specialized cells that perform different functions and are dependent on each other. For example, some cells procure food, while others transport materials or provide movement.

            The evolutionary links between unicellular and multicellular life were probably colonial forms, in which unicellular protists stuck together as loose federations of independent cells (Figure 15.2.4). The gradual transition from colonies to truly multicellular organisms involved the cells becoming increasingly interdependent as a division of labor evolved. We can see one level of specialization and cooperation in the colonial green alga Volvox (see Figure 15.22d). Volvox produces gametes (sperm and ova), which depend on nonreproductive cells, or somatic cells, while developing. Cells in truly multicellular organisms are specialized for many more nonreproductive functions, including feeding, waste disposal, gas exchange, and protection, to name a few.

            Multicellularity evolved many times among the ancestral stock of protists, leading to new waves of biological diversification. The diverse seaweeds are examples of the descendants, and so are plants, fungi, and animals. In the next chapter, we II trace the long evolutionary movement of plants and fungi onto land.

 

 

Plants

Colonizing Land

Plants are terrestrial (land-dwelling) organisms. True, some, such as water lilies, have returned to the water, but they evolved secondarily from terrestrial ancestors (as did several species of aquatic animals, such as porpoises).

            A plant is a multicellular eukaryote that makes organic molecules by photosynthesis. Photosynthesis distinguishes plants from the animal and fungal kingdoms. Large algae  are also multicellular, eukaryotic, and photosynthetic. The following are terrestrial adaptations that distinguishes plants from algae.

Figure 16.2 Contrasting environments for algae and plants

Terrestrial Adaptations of Plants

Structural Adaptations Living on land poses very different problems from living in water (Figure 16.2). In terrestrial habitats, the resources that a photosynthetic organism needs are found in two very different places. Light and carbon dioxide are mainly available above-ground, while water and mineral nutrients are found mainly in the soil. Thus, the complex bodies of plants show varying degrees of structural specialization into subterranean and aerial organs-roots and leaf-bearing shoots, respectively.

            Most plants have symbiotic fungi associated with their roots. These root-fungus combinations are called mycorrhizae ("fungus root"). For their part, the fungi absorb water and essential minerals from the soil and provide these materials to the plant. The sugars produced by the plant nourish the fungi. Mycorrhizae are evident on some of the oldest plant fossils. They are key adaptations that made it possible to live on land (Figure 16.3).

            Leaves are the main photosynthetic organs of most plants. Exchange of carbon dioxide and oxygen between the atmosphere and the photosynethic interior of a leaf occurs via stomata, the microscopic pores through the leafs surface (see Figure 7.3). A waxy layer called the cuticle coats the leaves and other aerial parts of most plants, helping the plant body retain its water. (Think of the waxy surface of a cucumber or unpolished apple.)

            Differentiation of the plant body into root and shoot systems solved one problem but created new ones. For the shoot system to stand up straight in the air, it must have support. This is not a problem in the water: Huge seaweeds need no skeletons because the surrounding water buoys them. An important terrestrial adaptation of plants is lignin, a chemical that hardens the cell walls. Imagine what would happen to you if your skeleton were to disappear or suddenly turn mushy. A tree would also collapse if it were not for its "skeleton”, its framework of lignin-rich cell walls.

 

Figure 16.3 Mycorrhizae: symbiotic associations of fungi and roots. The finely branched filaments of the fungus provide an extensive surface area for absorption of water and minerals from the soil. The fungus provides some of those materials to the plant and benefits in turn by receiving sugars and other organic products of the plant's photosynthesis.

Figure 16.4 Network of veins in a leaf. The vascular tissue of the veins delivers water and minerals absorbed by the roots and carries away the sugars produced in the leaves.

            Specialization of the plant body into roots and shoots also introduced the problem of transporting vital materials between the distant organs. The terrestrial equipment of most plants includes vascular tissue, a system of tube-shaped cells that branch throughout the plant (Figure 16.4). The vascular tissue actually has two types of tissues specialized for transport: xylem, consisting of dead cells with tubular cavities for transporting water and minerals from roots to leaves; and phloem, consisting of living cells that distribute sugars from the leaves to the roots and other nonphotosynthetic parts of the plant.

Reprodudive Adaptations Adapting to land also required a new mode of reproduction. For algae, the surrounding water ensures that gametes (sperm and eggs) and developing offspring stay moist. The aquatic environment also provides a means of dispersing the gametes and offspring. Plants, however, must keep their gametes and developing offspring from drying out in the air. Plants (and some algae) produce their gametes in protective structures called gametangia (singular, gametangium). A gametangium has a jacket of protective cells surrounding a moist chamber where gametes can develop without dehydrating.

            In most plants, sperm reach the eggs by traveling within pollen, which is carried by wind or animals. The egg remains within tissues of the mother plant and is fertilized there. In plants, but not algae, the zygote (fertilized egg) develops into an embryo while still contained within the female parent, which protects the embryo and keeps it from dehydrating (Figure 16.5). Most plants rely on wind or animals, such as fruit-eating birds or mammals, to disperse their offspring, which are in the form of embryos contained in seeds.

            The reproductive "strategy" of plants is analogous to how mammals manage to reproduce on land. As in plants, mammalian fertilization is internal ( within the mother's body). And in most mammals, embryonic development also occurs within the mother's body, as it does in plants.

The Origin of Plants from Green Algae

The move onto land and the spread of plants to diverse terrestrial environments was incremental. It paralleled the gradual accumulation of terrestrial adaptations, beginning with populations that descended from algae. Green algae are the protists most closely related to plants. More specifically, molecular comparisons and other evidence place a group of multicellular green algae called charophyceans closest to plants (Figure 16.6).

            The evolutionary "walk" onto land was more like adaptive baby steps. Many species of modern charophyceans are found in shallow water around the edges of ponds and lakes. Some of the ancient charophyceans that lived about the time that land was first colonized may have inhabited shallow-water habitats subject to occasional drying. Natural selection would have favored individual algae that could survive through periods when they were not submerged. The protection of developing gametes and embryos within jacketed organs (gametangia) on the parent is one adaptation to living in shallow water that would also prove essential on land. We know that by about 475 million years ago, the vintage of the oldest plant fossils, an accumulation of adaptations allowed permanent residency above water. The plants that color our world today diversified from those early descendants of green algae.

 

Figure 16.5  The protected embryo of a plant. Internal fertilization with sperm and egg combining without a moist chamber on the mother plant, is an adaptation for living on land. This female parent continues to nurture and protect the plant embryo which develops from the zygote. 

Figure 16.6 Charophyceans, closest algai relative to plants. (a) Chara is a particularly elaborate green alga. (b) Coleochaete though less plantlike than Chara in appearance, is actually more closely related to plants.

Highlights of Plant Evolution

The fossil record chronicles four major periods of plant evolution, which are also evident in the diversity of modern plants (Figure 16.7) .Each stage is marked by the evolution of structures that opened new opportunities on land.

            The first period of evolution was the origin of plants from their aquatic ancestors, the green algae called charophyceans. The first terrestrial adaptations included gametangia, which protected gametes and embryos. This made it possible for the plants known as bryophytes, including the mosses, to diversify from early plants. Vascular tissue also evolved relatively early in plant history. However, most bryophytes lack vascular tissue, which is why they are categorized as nonvascular plants.

            The second period of plant evolution was the diversification of vascular plants (plants with vascular tissue that conducts water and nutrients). The earliest vascular plants lacked seeds. Today, this seedless condition is retained by ferns and a few other groups of vascular plants.

            The third major period of plant evolution began with the origin of the seed. Seeds advanced the colonization of land by further protecting plant embryos from desiccation ( drying) and other hazards. A seed consists of an embryo packaged along with a store of food within a protective covering. The seeds of early seed plants were not enclosed in any specialized chambers. These plants gave rise to many types of gymnosperms ("naked seed"). Today, the most widespread and diverse gymnosperms are the conifers, which are the pines and other plants with cones.

            The fourth major episode in the evolutionary history of plants was the emergence of flowering plants, or angiosperms ("seed container"). The flower is a complex reproductive structure that bears seeds within protective chambers (containers) called ovaries. This contrasts with the bearing of naked seeds by gymnosperms. The great majority of modern-day plants are angiosperms.

            There are four major groups of modern plants: obryophytes, ferns, gymnosperms, and angiosperms. Bryophytes

            The most familiar bryophytes are mosses. A mat of moss actually consists of many plants growing in is a tight pack, helping to hold one another up (Figure 16.8). The mat has a spongy quality that enables it to absorb and retain water.

            Mosses are not totally liberated from their ancestral aquatic habi!at. They do display two of the key terrestrial adaptations that made the move onto land possible: a waxy .cuticle that helps prevent dehydration; and the retention of developing embryos within the mother plant's gametangium. However, mosses need water to reproduce. Their sperm are flagellated, like those of most green algae. These sperm must swim through water to reach eggs. (A film of rainwater or dew is often enough moisture for the sperm to travel.) In addition, most mosses have no vascular tissue to carry water from soil to aerial parts of the plant. This explains why damp, shady places are the most common habitats of mosses. These plants also lack lignin, the wall-hardening material that enables other plants to stand tall. Mosses may sprawl as mats over acres, but they always have a low profile.

Figure 16.7 Highlights of plant evolution.  Modern representatives of the major evolutionary branches are illustrated at the top of this phylogenetic tree. As we survey the diversity of plants. Miniature versions of this tree will help you place each plant group in its evolutionary context.

            If you look closely at some moss growing in your vicinity, you may actually see two distinct versions of the plant. The greener, spongelike plant that is the more obvious is called the gametophyte. You may see the other version of the moss, called a sporophyte. growing out of a gametophyte as a stalk with a capsule at its tip (Figure 16.9) .The cells of the gametophyte are haploid (one set of chromosomes). In contrast, the sporophyte is made up of diploid cells (two chromosome sets), These two different stages of the plant life cycle are named for the types of reproductive cells they produce. Gametophytes produce gametes (sperm and eggs), while sporophytes produce spores. As reproductive cells, spores differ from gametes in two ways: A spore can develop into a new organism without fusing with another cell ( two gametes must fuse to form a zygote) ; and spores usually have tough coats that enable them to resist harsh environments.

 

Figure 16.8 A peat moss bog in Norway. Although mosses are short in stature, their collective impact on Earth is huge. For example, peat mosses, or Sphagnum, carpet at least 3% of Earth's terrestrial surface, with greatest density in high northern latitudes. The accumulation of "peat," the thick mat of living and dead plants in wetlands, ties up an enormous amount of organic carbon because peat has an abundance of chemical materials that are not easily degraded by microbes. That explains why peat makes an excellent fuel as an alternative to coal and wood. More importantly, the carbon storage by peat bogs plays an important role in stabilizing Earth's atmospheric carbon dioxide concentrations, and hence climatr, through the CO2-related greenhouse effect (see Chapter 7).

Figure 16.9  The two forms of moss:  The feathery plant we generally know is a gametophyte. The stalk of the capsule at it’s tip is the sporophyte. This photo shows the capsule releasing it’s spores, reproductive cells that can develop into a new gamotype.

Figure 16.10 Alternation of generations. Plants have life cycles very different from ours. Each of us is a diploid individual; the only haploid stages in the human life cycle, as for nearly all animals, are sperm and eggs. By contrast, plants have alternating generations: Diploid (2n) individuals (sporophytes) and haploid (nj individuals (gametophytes) generate each other in the life cycle. In the case of mosses, the gametophyte is the dominant stage. In fact, the moss sporophyte remains attached to the gametophyte, depending on its parent for water and nutrients. In other plant groups, this balance is reversed, with the sporophyte being the more developed of the two generations.

            The gametophyte and sporophyte are alternating generations that take turns producing each other. Gametophytes produce gametes that unite to form zygotes, which develop into new sporophytes. And sporophytes produce spores that give rise to new gametophytes. This type of life cycle, called alternation of generations. occurs only in plants and certain algae (Figure 16.10). Among plants, mosses and other bryophytes are unique in having the gametophyte as the dominant generation - the larger, more obvious plant. We see an increasing dominance of the sporophyte as the more highly developed generation.

Ferns took terrestrial adaptation to the next level with the evolution of vascular tissue. However, the sperm of ferns, like those of mosses, are flagellated and must swim through a film of water to fertilize eggs. Ferns are also seedless, which helps explain why they do not dominate most modern terrestrial landscapes. However, of all seedless vascular plants, ferns are by far the most diverse today with more than 12,000 species. Most of those species inhabit the tropics, although many species are found in temperate forests, such as most woodlands of the United States (Figure 16.11 ).

During the Carboniferous period, about 290-360 million years ago, ancient ferns were among a much greater diversity of seedless plants that formed vast, swampy forests that covered much of what is now Eurasia and North America (Figure 16.11). At that time, these continents were close to the equator and had tropical climates. The tropic swamp forests of the Carboniferous period generated great quantities of organic matter. As the plants died, they fell into stagnant wetlands and did not decay completely. Their remains formed thick deposits of organic rubble, or peat. Later, seawater flooded the swamps, marine sediments covered the peat, and pressure and heat gradually converted the peat to coal. Coal is black sedimentary rock made up of fossilize plant material. It formed during several geological periods, but the most extensive coal beds are derived from Carboniferous deposits. (The name Carboniferous comes from the Latin carbo, coal and fer-bearing). Coal, oil, and natural gas are fossil fuels - fuels formed from the remains of extinct organisms. Fossil fuels are burned to generate much of our electricity. As we deplete our oil and gas reserves, the use of coal is likely to increase.

 

Figure 16.11 Ferns (seedless vascular plants) This species grows on the forest floor in the eastern United States. The "fiddleheads" in the inset on the right are young fonds (leaves) ready to unfurl. The fern generation familiar to us is this sporophyte generation. The inset on the left is the underside of a soiriphyte leaf specialized for reproduction. The yellow dots consists of spore capsules that can release numerous tiny spores. The spores develop into gametophytes. However, you would have to crawl on the forest floor and explore with careful hands and sharp eyes to find fern gametophytes, tiny plants growing on or just below the surface.

Figure 16.12 A "coal forest” of the Carboniferous period.  This painting, based on fossil evidence, reconstructs one of the great seedless forests. Most of the large trees with straight trunks are seedless plants called Iycophytes. On the left, the tree with numerous feathery branches is another type of seedless plant called a horsetail. The plants near the base of the trees are ferns. Note the giant bird-sized dragonfly, which would have made quite a buzz.

“Coal forests” dominated the North American and Eurasian landscapes until near the end of the Carboniferous period. At that time, global climate, turned drier and colder, and the vast swamps began to disappear. This climatic change provided an opportunity for seed plants, which can complete their life cycles on dry land and withstand long, harsh winters

            Of the earliest seed plants, the most successful were the gym nosperms, and several kinds grew along with the seedless plants in the Carboniferous swamps. Their descendants include the conifers, or cone-bearing plants. Conifers Perhaps you have had the fun of hiking or skiing through a forest of conifers, the most common gymnosperms. Pines, firs, spruces, junipers, cedars, and redwoods are all conifers. A broad band of coniferous forests covers much of northern Eurasia and North America and extends southward in mountainous regions.

            Conifers are among the tallest, largest, and oldest organisms on Earth. Redwoods, found only in a narrow coastal strip of northern California, grow to heights of more than 110 m; only certain eucalyptus trees in Australia are taller. The largest (most massive) organisms alive are the giant sequoias, relatives of redwoods that grow in the Sierra Nevada mountains of California. One, known as the General Sherman tree, has a trunk with a circumference of 26 m and weighs more than the combined weight of a dozen space shuttles. Bristlecone pines, another species of California conifer, are among the, oldest organisms alive. One bristlecone, named Methuselah, is more than 4,600 years old; it was a young tree when humans invented writing. Nearly all conifers are evergreens, meaning they retain leaves throughout the year. Even during winter, a limited amount of photosynthesis occurs on sunny days. And when spring comes, conifers already have fully developed leaves that can take advantage of the sunnier days. The needle-shaped leaves of pines and firs are Key also adapted to survive dry seasons.  A thick cuticle covers the leaf, and the stomata are located in pits, further .reducing water loss.

            We get most of our lumber and paper pulp from the wood of conifers. What we call wood is actually an accumulation of vascular tissue with lignin, which gives the tree structural support.

            Terrestrial Adaptations of Seed Plants Compared to ferns, conifers and most other gymnosperms have three additional adaptations that make survival in diverse terrestrial habitats possible: (1) further reduction of the gametophyte; (2) the evolution of pollen; and ( 3) the advent of the seed.

            The first adaptation is an even greater development of the diploid sporophyte compared to the haploid gametophyte generation (Figure 16.14).

            A pine tree or other conifer is actually a sporophyte with tiny gametophytes living in cones (Figure 16.15). The gametophytes, though multicellular, are totally dependent on and protected by the tissues of the parent sporophyte. Some plant biologists speculate that the shift toward diploidy in land plants was related to the harmful impact of the sun's ionizing radiation, which causes mutations. This damaging radiation is more intense on land than in aquatic habitats, where organisms are somewhat protected by the light-filtering properties of water. Of the two generations of land plants, the diploid form (sporophyte) may cope better with mutagenic radiation. A diploid organism homozygous for a particular essential allele has a "spare tire" in the sense that one copy of the allele may be sufficient for survival if the other is damaged.

 

Figure 16.13  Coniferous forest near Peyto lake in the Canadian Rockies

Figure 16.15 A pine tree, a conifer. The tree bears two types of cones. The hard, woody ones we usually notice are female cones. Each scale of the female cone (upper left inset) is actually a modified leaf bearing a pair of structures called ovules on its upper surface. An ovule contains the egg-producing female gametophyte. The smaller male cones (lower right inset) produce the male gametophytes, which are pollen grains. Mature male cones release clouds of millions of pollen grains. You may have seen yellowish conifer pollen covering car tops or floating on ponds in the spring. Some of the windblown pollen manages to land on female cones on trees of the same species. The female cones generally develop on the higher branches, where they are unlikely to be dusted with pollen from the same tree. Sperm released by pollen fertilizes eggs in the ovules of the female cones. The ovules eventually develop into seeds.

            A second adaptation of seed plants to dry land was the evolution of pollen. A pollen grain is actually the much-reduced male gametophyte. It houses cells that will develop into sperm. In the case of conifers, wind carries the pollen from male to female cones, where eggs develop within female garnetophytes (see Figure 16.15). This mechanism for sperm transfer contrasts with the swimming sperm of mosses and ferns. In seed plants, this use of resistant, airborne pollen to bring gametes together is a terrestrial adaptation that led to even greater success and diversity of plants on land.

            The third important terrestrial adaptation of seed plants is, of course, the seed itself. A seed consists of a plant embryo packaged along with a food supply within a protective coat. Seeds develop from structures called ovules (Figure 16.16). In conifers, the ovules are locate on the scales of female cones. Conifers and other gymnosperms, lacking ovaries, bear their seeds "naked" on the cone scales ( though the seeds do have protective coats, of course). Once released from the parent plant, the resistant seed can remain dormant for days, months, or even years. Under favorable conditions, the seed can then germinate, its embryo emerging through the seed coat as a seedling. Some seeds drop close to their parents. Others are carried far by the wind or animals.

Figure 16.16 From ovule to seed. (a) The sporophyte produces spores within a tissue surrounded by a protective laver called integuments. (b) The spore develops into a female gametophyte, which produces one or more eggs. If a pollen grain enters the ovule through a special pore in the integuments, it discharges sperm cells that fertilize eggs. (c) Fertilization initiates the transformation of ovule to seed. The fertilized egg (zvgote) develops into an embryo; the rest of the gametophyte forms a tissue that stockpiles food; and the integuments of the ovule harden to become the seed coat.

The photograph of the coniferous forest in Figure 16.13 could give us a somewhat distorted view of today's plant life. Conifers do cover much land in the northern parts of the globe, but it is the angiosperms, or flowering plants, that dominate most other regions. There are about 250,000 angiosperm species versus about 700 species of conifers and other gymnosperms. Whereas gymnosperms supply most of our lumber and paper, angiosperms supply nearly all our food and much of our fiber for textiles. Cereal grains, including wheat, corn, oats, and barley, are flowering plants, as are citrus and other fruit trees, garden vegetables, cotton, and flax. Fine hardwoods from flowering plants such as oak, cherry, and walnut trees supplement the lumber we get from conifers.

            Several unique adaptations account for the success of angiosperms. For example, refinements in vascular tissue make water transport even more efficient in angiosperms than in gymnosperms. Of all terrestrial adaptations, however, it is the flower that accounts for the unparalleled success of the angiosperms.

            Flowers. Fruits. and the Angiosperm Life Cycle No organisms make a showier display of their sex lives than angiosperms. From roses to dandelions, flowers display a plant's male and female parts. For most angiosperms, insects and other animals transfer pollen from the male parts of one flower to the female sex organs of another flower. This targets the pollen rather than relying on the capricious winds to blow the pollen between plants of the same species.

            A flower is actually a short stem with four whorls of modified leaves: sepals, petals, stamens, and carpels (Figure 16.17). At the bottom of the flower are the sepals, which are usually green. They enclose the flower before it opens (think of a rosebud). Above the sepals are the petals, which are usually the most striking part of the flower and are often important in attracting insects and other pollinators. The actual reproductive structures are multiple stamens and one or more carpels. Each stamen consists of a stalk bearing a sac called an anther, the male organ in which pollen grains develop. The carpel consists of a stalk, the style, with an ovary at the base and a sticky tip known as the stigma, which traps pollen. The ovary is a protective chamber t containing one or more ovules, in which the eggs develop.

            Figure 16.18 highlights key stages in the angiosperm life cycle. The plant familiar to us is the sporophyte. As in gymnosperms, the pollen grain is the male gametophyte of angiosperms. The female gametophyte is located within an ovule, which in turn resides within a chamber of the ovary. Pollen that lands on the sticky stigma of a carpel extends a tube down to an ovule and deposits two sperm nuclei within the female gametophyte. This double fertilization is an angiosperm characteristic. One sperm cell fertilizes an egg in the female gametophyte. This produces a zygote, which develops into an embryo. The second sperm cell fertilizes another female gametophyte cell, which then develops into a nutrient-storing tissue called endosperm. Double fertilization thus synchronizes the development of the embryo and food reserves within an ovule. The whole ovule develops into a seed. The seed's enclosure within an ovary is what distinguishes angiosperms from the naked-seed condition of gymnosperms.

            A fruit is the ripened ovary of a flower. As seeds are developing from ovules, the ovary wall thickens, forming the fruit that encloses the seeds.  A pea pod is an example of a fruit, with seeds (mature ovules, the peas) encased in the ripened ovary (the pod). Fruits protect and help disperse seeds, As Figure 16.19 demonstrates, many angiosperms depend on animals to disperse seeds. Conversely, most land animals, including humans, rely on angiosperms as a food source.

            Angiosperms and Agriculture Flowering plants provide nearly all our food. Al1 of our fruit and vegetable crops are angiosperms. Corn, rice, wheat, and the other grains are grass fruits. Grains are also the main food source for domesticated animals, such as cows and chickens. We also grow angiosperms for fiber, medications, perfumes, and decoration.

            Like other animals, early humans probably collected wild seeds and fruits, Agriculture was gradually invented as humans began sowing seeds and cultivating plants to have a more dependable food source. As they domesticated certain plants, humans began to intervene in plant evolution by selective breeding designed to improve the quantity and quality of the foods. Agriculture is a unique kind of evolutionary relationship between plants and animals,

 

Plant Diversity as a Nonrenewable Resource

            The exploding human population, with its demand for space and natural resources, is extinguishing plant species at an unprecedented rate. The problem is especially critical in the tropics, where more than half the human population lives and population growth is fastest. Tropical rain forests are being destroyed at a frightening pace. The most common cause of this destruction is slash-and-burn clearing of the forest for agricultural use. Fifty million acres, an area about the size of the state of Washington, are cleared each year, a rate that would completely eliminate Earth's tropical forests within 25 years. As the forest disappears, so do thousands of plant species insects and other animals that depend on these plants are also vanishing.  In all researchers estimate that the destruction of habitat In the rain forest and other ecosystems is claiming

Biology and Society

The Balancing Act of Forest Conservation

            With a soft floor underfoot and the scent of pine needles in the air, few places are as pleasing to the senses as coniferous forests filled with cone-bearing plants such as pines, firs, spruces, and redwoods. Today, about 190 million acres of coniferous forests in the United States, mostly in the western states and Alaska, are designated national forests. Some of these areas are set aside as unspoiled wilderness and wildlife habitats. But most national forests are working forests, managed by the U.S. Forest Service for harvesting lumber, grazing, mining, and public recreation.

            Coniferous forests are highly productive; you probably use products harvested there every day. For example, conifers provide much of our lumber for building and wood pulp for paper production. Currently, our demand for wood and paper is so great-the average U.S. citizen consumes about 50 times more paper than the average person in less developed nations-that clear-cut areas have become commonplace (Figure 16.1 ). In many areas, only about 10% of the original forest remains intact. Some forests have been replanted but the rate of cutting often exceeds the rate at which new trees can grow. Moreover, many scientists predict that an increase in global temperatures, which now seems to be occurring, poses an additional threat to coniferous forests.

            The loss of coniferous forests threatens more than just the trees themselves. The original forests of North America were more biologically diverse than the forests that are now regrowing. Balancing the uses of coniferous forests while simultaneously trying to sustain them for future generations is a formidable challenge. What can you do? Reducing paper waste, increasing recycling, and expanding the use of electronic media can all help. The trees that fill coniferous forests are just one of several major types of vegetation that share the planet with us.

Fungi

            The word fungus often evokes some unpleasant images. Fungi rot timbers, spoil food, and afflict humans with athlete's foot and worse maladies. However, ecosystems would collapse without fungi to decompose dead organisms, fallen leaves, feces, and other organic materials, thus reCycling vital chemical elements back to the environment in forms other organisms can assimilate. And you have already learned that nearly all plants have mycorrhizae, fungus-root associations that absorb minerals and water from the soil. In addition to these ecological roles, fungi have been used by humans in various ways for centuries. We eat some fungi (mushrooms and truffles, for instance), culture fungi to produce antibiotics and other drugs, add them to dough to make bread rise, culture them in milk to produce a variety of cheeses, and use them to ferment beer and wine.

            Fungi are eukaryotes, and most are multicellular. They were once grouped with plants. But in fact molecular studies indicate that fungi and animals probably arose from a common ancestor. In other words, a mushroom is probably more closely relate to you than it is to any plant! However, fungi are actually a form of life so distinctive that they are accorded their own kingdom, the kingdom Fungi (Figure 16.20).

Characteristics of Fungi

            Fungal Nutrition Fungi are heterotrophs that acquire their nutrients byabsorption. In this mode of nutrition, small organic molecules are absorbed from the surrounding medium. A fungus digests food outside its body by secreting powerful hydrolytic enzymes into the food. The enzymes decompose complex molecules to the simpler compounds that the fungus can absorb. For example, fungi that are decomposers absorb nutrients from nonliving organic material, such as fallen logs, animal corpses, or the wastes of live organisms. Parasitic fungi absorb nutrients from the cells or body fluids of living hosts. Some of these fungi, such as certain species infecting the lungs of humans, are pathogenic. In other cases, such as mycorrhizae, the relationships between fungi and their hosts are mutually beneficial.

Figure 16.20 A gallery of diverse fungi. (a) These mushrooms are the reproductive structures of a fungus that absorbs nutrients as it decomposes compost on a forest floor. (b) Some mushroom-producing fungi poke up "fairy rings," which can appear on a lawn overnight. The legendary explanation of these circles is that mushrooms spring up where fairies have danced in a ring on moonlit nights. Attervvard, the tired fairies sit down on some of the mushrooms, but toads use other mushrooms as stools; hence the name toadstools. Biology offers an alternative explanation. A ring develops at the edge of the main body of the fungus, which consists of an underground mass of tiny filaments within the ring. The filaments secrete enzymes that digest soil compost. As the underground fungal mass grows outward from its center, the diameter of the fairy rings produced at its expanding perimeter increases annually. Ic) This fungus, Pilobolus, decomposes animal dung. The bulbs at the tips of the stalks are sacs of spores, which are reproductive cells. Pilobolus can actually aim these spore sacs. The stalks bend toward light, where grass is likely to be growing, and then shoot their spore sacs like cannonballs. Grazing animals eat the spore sacs and scatter the spores in feces, where the spores grow into new fungi. Id) The fungi we call molds grow rapidly on their food sources, often on our food sources. The mold on this orange reproduces asexually by producing chains of microscopic spores (inset) that are dispersed via air currents. (e) This predatory fungus traps and feeds on tiny roundworms in the soil. The fungus is equipped with hoops that can constrict around a worm in less than a second. (f) Yeasts are unicellular fungi. This yeast cell is reproducing asexually by a process called budding. For centuries, humans have domesticated yeasts and put their metabolism to work in breweries and bakeries.

            Fungal Structure Fungi are structurally adapted for their absorptive nutrition. The bodies of most fungi are constructed of structures called hyphae (singular, hypha). Hyphae are minute threads composed of tubular , walls surrounding plasma membranes and cytoplasm. The hyphae form an interwoven mat called a rnyceliurn (plural, mycelia), which is the feeding network of a fungus (Figure 16.21 ). Fungal mycelia can be huge, although they usually escape our notice because they are often subterranean.  In 2000, scientists discovered the mycelium of one humongous fungus in Oregon that is 5.5 km (3.4 miles) in diameter and spreads through 2,200 acres of forest (equivalent to over 1,600 football fields). This fungus is at least 2,400 years old and hundreds of tons in weight, qualifying it among Earth's oldest and largest organisms.

            Most fungi are multicellular, with hyphae divided into cells by cross-walls. The cross-walls generally have pores large enough to allow ribosomes, mitochondria, and even nuclei to flow from cell to cell. The cell walls of fungi differ from the cellulose walls of plants. Most fungi build their cell  walls mainly of chitin, a strong but flexible polysaccharide similar to the chitin found in the external skeletons of insects.

            Mingling with the organic matter it is decomposing and absorbing, a mycelium maximizes contact with its food source. Ten cubic centimeters of rich organic soil may contain as much as a kilometer of hyphae. And a fungal mycelium grows rapidly, adding as much as a kilometer of hyphae each day as it branches within its food. Fungi are nonmotile organisms; they cannot run, swim, or fly in search of food. But the mycelium makes up for the lack of mobility by swiftly extending the tips of its hyphae into new territory.

            Fungal Reproduction Fungi reproduce by releasing spores that are produced either sexually or asexually. The output of spores is mind-boggling. For example, puffballs, which are the reproductive structures of certain fungi, can puff out clouds containing trillions of spores (see Figure 13.14). Carried by wind or water, spores germinate to produce mycelia  if they land in a moist place where there is food. Spores thus function in dispersal and account for the wide geographic distribution of many species of fungi. The airborne spores of fungi have been found more than 160 km ( 100 miles) above Earth. Closer to home, try leaving a slice of bread out for a week or two and you will observe the furry mycelia that grow from the invisible spores raining down from the surrounding air. It's a good thing those particular molds cannot grow in our lungs.

The Ecological Impact of Fungi

            Fungi have been major players in terrestrial communities ever since they moved onto land in the company of plants.

Fungi as Decomposers Fungi and bacteria are the principal decomposers that keep ecosystems stocked with the inorganic nutrients essential ; for plant growth. Without decomposers, carbon, nitrogen, and other elements would accumulate in organic matter. Plants and the animals they feed would starve because elements taken from the soil would not be returned.

 

Figure 16.21 The fungal mycelium  The mushroom we see is like an iceberg. It is a reproductive structure consisting of tightly packed hyphae that extend upward from a much more massive mycelium of hyphae growing underground. The photos show mushrooms and the mycelium of cottony threads that decompose organic litter.

Figure 16.22 Parasitic fungi that cause plant disease. (a) This photo shows American elm trees after the arrival of the parasitic fungus that causes Dutch elm disease. The fungus evolved with European species of elm trees, and it is relatively harmless to them. But it is deadly to American elms. The fungus was accidentally introduced into the United States on logs sent from Europe to pay World War I debts. Insects called bark beetles carried the fungus from tree to tree. Since then, the disease has destroyed elm trees all across North America. (b) The seeds of some kinds of grain, including rye, wheat, and oats, are sometimes infected with fungal growths. called ergots, the dark structures on this seed head of rye. Consumption of flour made from ergot-infested grain can cause gangrene, nervous spasms, burning sensations, hallucinations, temporary insanity, and death. One epidemic in Europe in the year A.D. 944 killed more than 40,000 people. During the Middle Ages, the disease (ergotism) became known as Saint Anthony's fire because many of its victims were cared for by a Catholic nursing order dedicated to Saint Anthony. Several kinds of toxins have been isolated from ergots. One called lysergic acid is the raw material from which the hallucinogenic drug LSD is made. Certain other chemical extracts are medicinal in small doses. One ergot compound is useful in treating high blood pressure, for example.

Fungi are well adapted as decomposers of organic refuse. Their invasive hyphae enter the tissues and cells of dead organic matter and hydrolyze polymers, including tile cellulose of plant cell walls. A succession of fungi, in concert with bacteria and, in some environments, invertebrate animals, is responsible for the complete breakdown of organic litter. The air is so loaded with fungal spores that as soon as a leaf falls or an insect dies, it is covered with spores and is soon infiltrated by fungal hyphae.

We may applaud fungi that decompose forest litter or dung, but it is a different story when molds attack our fruit or our shower curtains. Between 100/0 and 50% of the world's fruit harvest is lost each year to fungal attack. And a wood-digesting fungus does not distinguish between a fallen oak limb and the oak planks of a boat. During the Revolutionary War, the British lost more ships to fungal rot than to enemy attack. What's more, soldiers stationed in the tropics during World War II watched as their tents, clothing, boots, and binoculars were destroyed by molds. Some fungi can even decompose certain plastics.

            Parasitic Fungi Of the 100,000 known species of fungi, about 30% make their living as parasites, mostly on or in plants. In some cases, fungi that infect plants have literally changed landscapes. One species, for example, has eliminated most American elm trees (Figure 16.22a). Fungi are also serous agricultural pests. Some species infect grain crops and cause tremtmendous economic losses each year (Figure 16.22b).

            Animals are much less susceptible to parasitic fungi than are plants Only about 50 species of fungi are known to be parasitic in humans and other animals. However, their effects are significant enough to make us take them seriously. Among the diseases that fungi cause in humans are yeast infections of the lungs, some of which can be fatal, and vaginal yeast infections. Other fungal parasites produce a skin disease called ringworm, so named because it appears as circular red areas on the skin. The ringworm fungi can infect virtually any skin surface. Most commonly, they attack the feet and cause intense itching and sometimes blisters. This condition, known as athlete's foot, is highly contagious but can be treated with various fungicidal preparations.

            Commercial Uses of Fungi It would not be fair to fungi to end our discussion with an account of diseases. In addition to their positive global impact as decomposers, fungi also have a number of practical uses for humans.

 

Figure 16.23 Feeding on fungi. (a) Truffles (the fungal kind, not the chocolates) are the reproductive structures of fungi that grow with tree roots as mycorrhizae. Truffles release strong odors that attract mammals and insects that excavate the fungi and disperse their spores. In some cases, the odors mimic sex attractants of certain mammals. Truffle hunters traditionally used pigs to locate their prizes. However, dogs are now more commonly used because they have the nose for the scent without the fondness for the flavor. Gourmets describe the complex flavors of truffles as nutty, musky, cheesy, or some combination of those tastes. At about $400 per pound for truffles, you probably won't get a chance to do a taste test of your own in the campus cafeteria. (b) The turquoise streaks in blue cheese and Roquefort are the mycelia of a specific fungus.

Figure 16.24 Fungal production of an antibiotic. The first antibiotic discovered was penicillin, which is made by the common mold called Penicillium. In this petridish, the clear area between the mold and the bacterial colony is where the antibiotic produced by Penicillium inhibits the growth of the bacteria, a species of Staphylococcus.

            Most of us have eaten mushrooms, although we may not have realized that we were ingesting the reproductive extensions of subterranean fungi. Mushrooms are often cultivated commercially in artificial caves in which cow manure is piled (be sure to wash your store-bought mushrooms thoroughly). Edible mushrooms also grow wild in fields, forests, and backyards but so do poisonous ones. There are no simple rules to help the novice distinguish edible from deadly mushrooms. Only experts in mushroom taxonamy should dare to collect the fungi for eating.

            Mushrooms are not the only fungi we eat. The fungi called truffles are highly prized by gourmets (Figure 16.23a). And the distinctive flavors of certain kinds of cheeses come from the fungi used to ripen them (Figure 16.23b). Particularly important in food production are unicellular fungi, the yeasts. Yeasts are used in baking, brewing, and winemaking.

            Fungi are medically valuable as well. Some fungi produce antibiotics that are used to treat bacterial diseases. In fact, the first antibiotic discovered was penicillin, which is made by the common mold called Penicillium (Figure 16.24).

            As sources of antibiotics and food, as decomposers, and as partners with plants in mycorrhizae, fungi play vital roles in life on Earth.

Mutual Symbiosis

            Evolution is not just and adaptation of individual species. Relationships between species are also an evolutionary product. Symbiosis is the term used to describe ecological relationships between organisms of different specie. that are in direct contact Parasitism; a symbiotic relationship in which one species, the parasite, benefits while harming its host in the process. The focus here is on mutualism, symbiosis that benefits both specie.

            Eukaryotic cells evolved from mutual symbiosis among prokaryotes And today, bacteria living in the roots of certain plants provide nitrogen compounds to their host and receive food in exchange. We have our own mutually symbiotic bacteria that help keep our skin healthy and produce certain vitamins in our intestines. Particularly relevant is the symbiotic association of fungi and plant roots--mycorrhizaeo--which made life’s move onto land possible.

            Lichens, symbiotic association. of fungi and algae, are striking examples of how two species can become so merged that the cooperative is essential1ya new life-form. At a distance, it is easy to mistake lichens for mosses or other simple plants growing on rocks, rotting logs, trees, roofs, or gravestones (Figure 16.25). In fact, lichens are not mosses or any kind of plant, nor are they even individual organisms. A lichen is a symbiotic association of millions of tiny algae embraced by a mesh of fungal hyphae The photosynthetic algae feed the fungi The fungal mycelium, in turn, provides a suitable habitat for the algae, helping to absorb and retain water and minerals. The mutual1stic merger of partners is so complete that lichens are actual1y named as species, as though they are individual organisms. Mutualisms such as lichens and mycorrhizae showcase the web of life that has evolved on Earth.

Figure 16.25 Lichens: symbiotic associations of fungi and algae. lichens generally grow very slowly, sometimes in spurts of less than a millimeter per year. You can date the oldest lichens you see here by the engraving on the gravestone. Elsewhere, there are lichens that are thousands of years old, rivaling the oldest plants as Earth's elders. The close relationship between the fungal and algal partners is evident in the microscopic blowup of a lichen.

 

 

Evolution of Animals

Origin of Animal Diversity

Animal life began in Precambrian seas with the evolution of multiceluar creatures that ate other organisms. We are among their descendants.

What is an Animal?

            Animals are eukaryotic, multicellular, heterotrophic organisms that obtain nutrients by ingestion -- ingestion means eating food. This mode of nutrition contrasts animals with fungi, which obtain nutrients by absorption after digesting the food outside the body. Animals digest their food within their bodies after ingesting other organisms, dead or alive, whole or by the piece (Figure 17.2).

            Most animals reproduce sexually. The zygote (fertilized egg) develops into an early embryonic stage called a blastula, which is usually hollow ball of cells (Figure 17.3). The next embryonic stage in most animals is a gastrula, which has layers of cells that will eventually form the adult body parts. The gastrula also has a primitive gut, which will develop into the animal's digestive compartment. Continued development, growth, and maturation transform some animals directly from the embryo into an adult. However many animals include larval stages. A larva is a sexually immature form of an animal. It is anatomically distinct from the adult form, usually eats different foods, and may even have a different habitat. Think how different a frog is from its larval form, which we calla tadpole. A change of body form, called metamorphosis, eventually remodels the larva into the adult form.

  

Figure 17.2 Nutrition by ingestion, the animal way of life. Most animals ingest relatively large pieces of food, though rarely as large as the prey in this case. In this amazing scene, a rock python is beginning to ingest a gazelle. The snake will spend two weeks or more in a quiet place digesting its meal.

Figure 17.3 Life cycle of a sea star as an example of animal development. (1) Male and female adult animals produce haploid gametes (eggs and sperm) by meiosis. (2) An egg and a sperm fuse to produce a diploid zygote. (3) Early mitotic divisions lead to an embryonic stage called a blastula, common to all animals. Typically, the blastula consists of a ball of cells surrounding a hollow cavity. (4) Later, in the sea star and many other animals, one side of the blastula cups inward, forming an embryonic stage called a gastrula. (5) The gastrula develops into a saclike embryo with a two-layered wall and an opening at one end. Eventually, the outer layer (ectoderm) develops into the animal's epidermis (skin) and nervous system. The inner layer (endoderm) forms the digestive tract. Still later in development, in most animals, a third layer (mesoderm) forms between the other two and develops into most of the other internal organs (not shown in the figure). (6) Following the gastrula, many animals continue to develop and then mature directly into adults. But others, including the sea star, develop into one or more larval stages first. (7) The larva undergoes a major change of body form, called metamorphosis, in becoming an adult-a mature animal capable of reproducing sexually.

            Most animals have muscle cells, as well as nerve cells that control the muscles. The evolution of this equipment for coordinated movement enhanced feeding, even enabling some animals to search for or chase their food. The most complex animals, of course, can use their muscular and nervous systems for many functions other than eating. Some species even use massive networks of nerve cells called brains to think.

Figure 17.4 One hypothesis for a sequence of stages in the origin of animals from a colonial protist. (1) The earliest colonies may have consisted of only a few cells, all of which were flagellated and basically identical. (2) Some of the later colonies may have been hollow spheres-floating aggregates of heterotrophic cells-that ingested organic nutrients from the water. (3) Eventually, cells in the colony may have specialized, with some cells adapted for reproduction and others for somatic (non-reproductive) functions, such as locomotion and feeding. (4) A simple multicellular organism with cell layers may have evolved from a hollow colony, with cells on one side of the colony cupping inward, the way they do in the gastrula of an animal embryo (see Figure 17.3). (5) A layered body plan would have enabled further division of labor among the cells. The outer flagellated cells would have provided locomotion and some protection, while the inner cells could have specialized in reproduction or feeding. With its specialized cells and a simple digestive compartment, the proto-animal shown here could have fed on organic matter on the sea floor.

Figure 17.5 A Cambrian seascape. drawing based on fossils collected at a site called Burgess Shale in British Columbia, Canada.

Early Animals and the Cambrian Explosion

Animals probably evolved from a colonial, flagellated protist that lived in Precambrian seas (Figure 17.4) .By the late Precambrian, about 600-700 million years ago, a diversity of animals had already evolved. Then came the Cambrian explosion. At the beginning of the Cambrian period, 545 million years ago, animals underwent a relatively rapid diversification. During a span of only about 10 million years, all the major animal body plans we see today evolved. It is an evolutionary episode so boldly marked in the fossil record that geologists use the dawn of the Cambrian period as the beginning of the Paleozoic era. Many of the Cambrian animals seem bizarre compared to the versions we see today, but most zoologists now agree that the Cambrian fossils can be classified as ancient representatives of contemporary animal phyla (Figure 17.5).

            What ignited the Cambrian explosion? Hypotheses abound. Most researchers now believe that the Cambrian explosion simply extended animal diversification that was already well under way during the late Precambrian. But what caused the radiation of animal forms to accelerate so dramatically during the early Cambrian? One hypothesis emphasizes increasingly complex predator-prey relationships that led to diverse adaptations for feeding, motility, and protection. This would help explain why most Cambrian animals had shells or hard outer skeletons, in contrast to Precambrian animals, which were mostly soft-bodied. Another hypothesis focuses on the evolution of genes that control the development of animal form, such as the placement of body parts in embryos. At least some of these genes are common to diverse animal phyla. However, variation in how, when, and where these genes are expressed in an embryo can produce some of the major differences in body form that distinguish the phyla. Perhaps this developmental plasticity was partly responsible for the relatively rapid diversification of animals during the early Cambrian.  In the last half billion years, animal evolution has mainly generated new variations of old "designs" that originated in the Cambrian seas.

Animal Phylogeny

            Because animals diversified so rapidly on the scale of geologic time, it is difficult, using only the fossil record, to sort out the sequence of branching in animal phylogeny. To reconstruct the evolutionary history of animal phyla, researchers must depend mainly on clues from comparative anatomy and embryology. Molecular methods are now providing additional tools for testing hypotheses about animal phylogeny. Figure 17.6 represents one set of hypotheses about the evolutionary relationships     among nine major animal phyla. The circled numbers on the tree highlight four key evolutionary branch points, and these numbers are keyed to the following discussion.

(1) The first branch point distinguishes sponges from all other animals based on structural complexity. Sponges, though multicellular, lack the true tissues, such as epithelial (skin) tissue, that characterize more complex animals.

(2)  The second major evolutionary split is based partly on body symmetry: radial versus bilateral. To understand this difference, imagine a pail and shovel. The pail has radial symmetry. identical all around a central axis. The shovel has bilateral symmetry, which means there's only one way to split it into two equal halves-right down the midline. Figure 17.7 contrasts a radial animal with a bilateral one.

            The symmetry of an animal generally fits its lifestyle. Many radial animals are sessile forms (attached to a substratum) or plankton (drifting or weakly swimming aquatic forms). Their symmetry equips them to meet the environment equally well from all sides. Most animals that move actively from place to place are bilateral. A bilateral animal has a definite "head end" that encounters food, danger, and other stimuli first when the animal is traveling. In most bilateral animals, a nerve center in the form of a brain is at the head end, near a concentration of sense organs such as eyes. Thus, bilateral symmetry is an adaptation for movement, such as crawling, burrowing, or swimming.

Figure 17.7 Body symmetry. (a) The parts of a radial animal, such as this sea anemone, radiate from the center. Any imaginary slice through the central axis would divide the animal into mirror images. (b) A bilateral animal, such as this lobster, has a left and right side. Only one imaginary cut would divide the animal into mirror-image halves.

  

Figure 17.8 Body plans of bilateral animals. The various organ systems of these animals develop from the three tissue layers that form in the embryo. (a) Flatworms are examples of animals that lack a body cavity. (b) Roundworms have a pseudocoelom, a body cavity only partially lined by mesoderm, the middle tissue layer. (c) Earthworms and other annelids are examples of animals with a true coelom. Acoelom is a body cavity completely lined by mesoderm. Mesenteries, also derived from mesoderm, suspend the organs in the fluid-filled coelom.

(3)  The evolution of body cavities led to more complex animals. A body cavity is a fluid-filled space separating the digestive tract from the outer body wall. A body cavity has many functions. Its fluid cushions the suspended organs, helping to prevent internal injury. The cavity also enables the internal organs to grow and move independently of the outer body wall. If it were not for your body cavity, exercise would be very hard on your internal organs. And every beat of your heart or ripple of your intestine would deform your body surface. It would be a scary sight. In soft-bodied animals such as earth worms, the noncompressible fluid of the body cavity is under pressure and functions as a hydrostatic skeleton against which muscles can work. In fact, body cavities may have first evolved as adaptations for burrowing.

            Among animals with a body cavity, there are differences in how the cavity develops. In all cases, the cavity is at least partly lined by a middle layer of tissue, called mesoderm, which develops between the inner ( endoderm) and outer ( ectoderm) layers of the gastrula embryo. If the body cavity is not completely lined by tissue derived from mesoderm, it is termed a pseudocoelom (Figure 17.8) .A true coelom. the type of body cavity humans and many other animals have, is completely lined by tissue derived from mesoderm.

(4)  Among animals with a true coelom. there are two main evolutionary branches. They differ in several details of embryonic development. Including the mechanism of coelom formation. One branch includes mollusks (such as clams, snails, and squids). annelids (such as earthworms), and arthropods (such as crustaceans, spiders. and insects). The two major phyla of the other branch are echInoderms (such as sea stars and sea urchIns) and chordates (including humans and other vertebrates).

Major Invertebrate Phyla

Living as we do on land, our sense of animal diversity is biased in favor of vertebrates, which are animals with a backbone. Vertebrates are well represented on land in the form of such animals as reptiles, birds, and mammals. However, vertebrates make up only one subphylum within the phylum Chordata, or less than 5% of all animal species. If we were to sample the animals in an aquatic habitat, such as a pond, tide pool, or coral reef, we would find ourselves in the realm of invertebrates. These are the animals without backbones. It is traditional to divide the animal kingdom into vertebrates and invertebrates, but this makes about as much zoological sense as sorting animals into flatworms and nonflatworms. We give special attention to the vertebrates only because we humans are among the backboned ones. However, by exploring the other 95% of the animal kingdom-the invertebrates-we'll discover an astonishing diversity of beautiful creatures that too often escape our notice.

Sponges

            Sponges (phylum Porifera) are sessile animals that appear so sedate to the human eye that the ancient Greeks believed them to be plants (Figure 17.9). The simplest of all animals, sponges probably evolved very early from colonial protists. Sponges range in height from about 1 cm to 2 m. Sponges have no nerves or muscles, but the individual cells can sense and react to changes in the environment. The cell layers of sponges are loose federations of cells, not really tissues, because the cells are relatively unspecialized. Of the 9,000 or so species of sponges, only about 100 live in fresh water; the rest are marine.

 

Figure 17.9  Sponge

Figure 17.10 Anatomy of a sponge. Feeding cells called choanocytes have flagella that sweep water through the sponge's body. Choanocytes trap bacteria and other food particles, and amoebocytes distribute the food to other cells. To obtain enough food to grow by 100 g (about 3 ounces), a sponge must filter 1,000 kg (about 275 gallons) of seawater.

            The body of a sponge resembles a sac perforated with holes (the name of the sponge phylum, Porifera, means "pore bearer"). Water is drawn through the pores into a central cavity, then flows out of the sponge through a larger opening (Figure 17.10). Most sponges feed by collecting bacteria from the water that streams through their porous bodies. Flagellated cells called choanocytes trap bacteria in mucus and then engulf the food by phagocytosis. Cells called arnoebocytes pick up food from the choanocytes, digest it, and carry the nutrients to other cells. Amoebocytes are the "do-all" cells of sponges. Moving about by means of pseudopodia, they digest and distribute food, transport oxygen, and dispose of wastes. Amoebocytes also manufacture the fibers that make up a sponge's skeleton. In some sponges, these fibers are sharp and spur-like. Other sponges have softer, more flexible skeletons; we use these pliant, honey-combed skeletons as bathroom sponges.

Cnidarians

            Cnidarians (phylum Cnidaria) are characterized by radial symmetry and tentacles with stinging cells. Jellies, sea anemones, hydras, and coral animals are all cnidarians. Most of the 10,000 cnidarian species are marine.

            The basic body plan of a cnidarian is a sac with a central digestive compartment, the gastrovascular cavity. A single opening to this cavity functions as both mouth and anus. This basic body plan has two variations: the sessile polyp and the floating medusa (Figure 17.11 ). Polyps adhere to the substratum and extend their tentacles, waiting for prey. Examples of the polyp form are hydras, sea anemones, and coral animals (Figure 17.12) .A medusa is a flattened, mouth-down version of the polyp. It moves freely in the water by a combination of passive drifting and contractions of its bell-shaped body. The animals we generally call jellies are medusas (jellyfish is another common name, though these animals are not really fishes, which are vertebrates). Some cnidarians exist only as polyps, others only as medusas, and still others pass sequentially through both a medusa stage and a polyp stage in their life cycle.

  

Figure 17.11 Polyp and medusa forms of cnidarians. Note that cnidarians have two tissue layers, distinguished in the diagrams by blue and yellow. The gastrovascular cavity is a digestive sac, meaning that it has only one opening, which functions as both mouth and anus. {a) Sea anemones are examples of the polyp form of the basic cnidarian body plan. {b) Jellies are examples of the medusa form.

 

Figure 17.12 Coral animals. Each polyp in this colony is about 3 mm in diameter. Coral animals secrete hard external skeletons of calcium carbonate (limestone). Each polyp builds on the skeletal remains of earlier generations to construct the "rocks" we call coral. Though individual coral animals are small, their collective construction accounts for such biological wonders as Australia's Great Barrier Reef, which Apollo astronauts were able to identify from the moon. Tropical coral reefs are home to an enormous variety of invertebrates and fishes.

Figure 17.13 Cnidocyte action. Each cnidocyte contains a fine thread coiled within a capsule. When a trigger is stimulated by touch, the thread shoots out. Some cnidocyte threads entangle prey, while others puncture the prey and inject a poison.

            Cnidarians are carnivores that use tentacles arranged in a ring around the mouth to capture prey and push the food into the gastrovascular cavity, where digestion begins. The undigested remains are eliminated through the mouth/anus. The tentacles are armed with batteries of cnidocytes ("stinging cells"), unique structures that function in defense and in the capture of prey (Figure 17.13). The phylum Cnidaria is named for these stinging cells.

Flatworms

            Flatworms (phylum Platyhelminthes) are [ the simplest bilateral animals. True to their name, these worms are leaf-like or ribbon-like, ranging from about 1 mm to about 20 m in length. There are about 20,000 species of flatworms living in marine, fresh water, and damp terrestrial habitats. Planarians are examples of free-living (nonparasitic) flatworms (Figure 17.14) .The phylum also includes many parasitic species, such as flukes and tapeworms.

            Parasitic flatworms called blood flukes are a huge health problem in the tropics. These worms have suckers that attach to the inside of the blood vessels near the human host's intestines. This causes a long-lasting disease with such symptoms as severe abdominal pain, anemia, and dysentery. About 250 million people in 70 countries suffer from blood fluke disease. Flukes generally have complex life cycles that require more than one host species. People are most commonly exposed to blood flukes while working in irrigated fields contaminated with human feces. Blood flukes living in a human host reproduce sexually, and fertilized eggs pass out in the host's feces. If an egg lands in a pond or stream, a motile larva hatches. This larva can enter a snail, the next host. Asexual reproduction in the snail eventually produces other larvae that can infect humans. A person becomes infected when these larvae penetrate the skin.

            Tapeworms parasitize many vertebrates, including humans. In contrast to planarians and flukes, most tapeworms have a very long, ribbon like body with repeated parts (Figure 17.15) .They also differ from other flatworms in not having any digestive tract at all. Living in partially digested food in the intestines of their hosts, tapeworms simply absorb nutrients across their body surface. Like parasitic flukes, tapeworms have a complex life cycle, usually involving more than one host.  Humans can become infected with tapeworms by eating rare beef containing the worm's larvae. The larvae are microscopic, but the adults can reach lengths of 20 m in the human intestine. Such large tapeworms can cause intestinal blockage and rob enough nutrients from the human host to cause nutritional deficiencies. An orally administered drug called niclosamide kills the adult worms.

Roundworms

            Roundworms (phylum Nematoda) get their common name from their cylindrical body, which is usually tapered at both ends (Figure 17.16a).Roundworms are among the most diverse (in species number) and widespread of all animals. About 90,000 species of roundworms are known, and perhaps ten times that number actually exist. Round worms range in length from about a millimeter to a meter. They are found in most aquatic habitats, in wet soil, and as parasites in the body fluids and tissues of plants and animals. Free living roundworms in the soil are important decomposers. Other species are major agricultural pests that attack the roots of plants, Humans host at least 50 parasitic roundworm species, including pinworms, hookworms, and the parasite that causes trichinosis (Figure 17.16b).

 

Figure 17.14 Anatomy of a planarian. This free-living flatworm has a head with two light-detecting eye-spots and a flap at each side that detects certain chemicals in the water. Dense clusters of nervous tissue form a simple brain. The digestive tract is highly branched, providing an extensive surface area for the absorption of nutrients. When the animal feeds, a muscular tube projects through the mouth and sucks food in. The digestive tract, like that of cnidarians, is a gastrovascular cavity (a single opening functions as both mouth and anus). Planarians live on the undersurfaces of rocks in freshwater ponds and streams.

Figure 17.15 Anatomy of a tapeworm. Humans acquire larvae of these parasites by eating undercooked meat that is infected. The head of a tapeworm is armed with suckers and menacing hooks that lock the worm to the intestinal lining of the host. Behind the head is a long ribbon of units that are little more than sacs of sex organs. At the back of the worm, mature units containing thousands of eggs break off and leave the host's body with the feces.

            Roundworms exhibit two evolutionary innovations not found in flat-worms. First, roundworms have a complete digestive tract, which is a digestive tube with two openings, a mouth and an anus. This anatomy contrasts with the digestive sac, or gastrovascular cavity, of cnidarians and flatworms, which uses a single opening as both mouth and anus. All the remaining animals in our survey of animal phyla have a complete digestive tract. A complete digestive tract can process food and absorb nutrients as a meal moves in one direction from one specialized digestive organ to the next. In humans, for example, the mouth, stomach, and intestines are examples of digestive organs. A second evolutionary innovation we see for the first time in roundworms is a body cavity, which in this case is a pseudo coelom (see Figure 17.8).

Mollusks

            Snails and slugs, oysters and clams, and octopuses and squids are all mollusks (phylum Mollusca). Mollusks are soft-bodied animals, but most are protected by a hard shell.  Slugs, squids, and octopuses have reduced shells, most of which are internal, or they have lost their she»s completely during their evolution. Many mollusks feed by using a strap-like rasping organ called a radula to scrape up food. Garden snails use their radulas like tiny saws to cut pieces out of leaves. Most of the 150,000 known species of mollusks are marine, though some inhabit fresh water, and there are land-dwelling mollusks in the form of snails and slugs.

            Despite their apparent differences, all mollusks have a similar body plan (Figure 17.17) .The body has three main parts: a muscular foot, usually used for movement; a visceral mass containing most of the internal organs; and a fold of tissue called the mantle. The mantle drapes over the visceral mass and secretes the shell (if one is present).

            The three major classes of mollusks are gastropods (including snails and slugs), bivalves (including clams and oysters), and cephalopods (including squids and octopuses). Most gastropods are protected by a single, spiraled shell into which the animal can retreat when threatened (Figure 17.18a). Many gastropods have a distinct head with eyes at the tips of tentacles (think of a garden snail). Bivalves, including numerous species of clams, oysters, mussels, and scallops, have shells divided into two halves hinged together (Figure 17.18b). Most bivalves are sedentary, living in sand or mud in marine and freshwater environments. They use their muscular foot for digging and anchoring. Cephalopods generally differ from gastropods and sedentary bivalves in being built for speed and agility. A few cephalopods have large, heavy shells, but in most the shell is small and internal (as in squids) or missing altogether (as in octopuses). Cephalopods are marine predators that use beaklike jaws and a radula to crush or rip prey apart. The cephalopod mouth is at the base of the foot, which is drawn out into several long tentacles for catching and holding prey (Figure 17.18c).

 

Figure 17.16 Roundworms. (a) This species has the classic roundworm shape: cylindrical with tapered ends. You can see the mouth at the end that is more blunt. Not visible is the anus at the other end of a complete digestive tract. This worm looks like it's wearing a corduroy coat, but the ridges actually indicate muscles that run the length of the body. (b) The disease called trichinosis is caused by these roundworms, encysted here in human muscle tissue. Humans acquire the parasite by eating undercooked pork or other meat that is infected. The worms then burrow into the human intestine and eventually travel to other parts of the body, encysting in muscles and other organs.

Annelids

            Annelids (phylum Annelida) are worms with body segmentation, which is the division of the body along its length into a series of repeated segments that look like a set of fused rings. Look closely at an earthworm, an annelid you have all encountered, and you'll see why these creatures are also called segmented worms (Figure 17.19).  In all, there are about 15,000 annelid species, ranging in length from less than 1 mm to the 3-m giant Australian earthworm. Annelids live in the sea, most freshwater habitats, and damp soil. The three main classes of annelids are the earthworms and their relatives, the polychaetes, and the leeches.

Figure 17.17 The general body plan of a mollusk. Note the body cavity (a true coelom, though a small one) and the complete digestive tract, with both mouth and anus.

            Earthworms eat their way through the soil, extracting nutrients as the soil passes through the digestive tube (Figure 17.208). Undigested material, mixed with mucus secreted into the digestive tract, is eliminated as castings through the anus. Farmers value earthworms because the animals till the earth, and the castings improve the texture of the soil. Charles Darwin estimated that each acre of British farmland had about 50,000 earthworms that produced 18 tons of castings per year.

            In contrast to earthworms, most polychaetes are marine, mainly crawling or burrowing in the seafloor. Segmental appendages with hard bristles help the worm wriggle about in search of small invertebrates to eat. The appendages als-o increase the animal's surface area for taking up oxygen and disposing of metabolic wastes, including carbon dioxide (Figure 17.20b ).

            The third group of annelids, leeches, are notorious for the bloodsucking habits of some species. However, most species are free-living carnivores that eat small invertebrates such as snails and ins~cts. The majority of leeches live in fresh water, but a few terrestrial species inhabit moist vegetation in the tropics. Until the twentieth century, bloodsucking leeches were frequently used by physicians for bloodletting, the removal of what was considered "bad blood" from sick patients. Some leeches have razorlike jaws that cut through the skin, and they secrete saliva containing a strong anesthetic and an anticoagulant into the wound. The anesthetic makes the bite virtually painless, and the anticoagulant keeps the blood from clotting. Leech anticoagulant is now being produced commercially by genetic engineering and may find wide use in human medicine. Tests show that it prevents blood clots that can cause heart attacks. Leeches are also still occasionally used to remove blood from bruised tissues and to help relieve swelling in fingers or toes that have been sewn back on after accidents (Figure 17.20c). Blood tends to accumulate and cause swelling in a reattached finger or toe until small veins have a chance to grow back int9 it. Leeches are applied to remove the excess blood.

Arthropods

            Arthropods (phylum Arthropoda) are named for their Jointed appendages. {such as crabs and lobsters), arachnids (such as spiders and scorpions), and insects are all examples of arthropods. Zoologists estimate that the total arthropod population of Earth numbers about a billion billion (1018) individuals. Researchers have identified about a million arthropod species, mostly insects. In fact, two out of every three species of life that have been described are arthropods.  And arthropods are represented in nearlyall habitats of the biosphere. On the criteria of species diversity, distribution, and sheer numbers, arthropods must be regarded as the most successful of all animal phyla.

  

Figure 17.18 Mollusks. (a) Shell collectors are delighted by the variety of gastropods. (b) This scallop, a bivalve, has many eyes peering out between the two halves of the hinged shell. (c) An octopus is a cephalopod without a shell. All cephalopods have large brains and sophisticated sense organs, which contribute to the success of these animals as mobile predators. This octopus lives on the seafloor, where it scurries about in search of crabs and other food. Its brain is larger and more complex, proportionate to body size, than that of any other invertebrate. Octopuses are very intelligent and have shown remarkable learning abilities in laboratory experiments.

General Characteristics of Arthropods

 Arthopods are segmented animals. In contrast to the matching segments of annelids, however, arthropod segments and their appendages have become specialized for a great variety of functions. This evolutionary flexibility contributed to the great diversification of arthropods. Specialization of segments, or fused groups of segments, also provides for an efficient division of labor among body regions. For example, the appendages of different segments are variously modified (for walking, feeding, sensory reception, copulation, and defense (Figure 17.21).

 

Figure 17.19 Segmented anatomy of an earthworm. Annelids are segmented both externally and internally. Many of the internal structures are repeated, segment by segment. The coelom (body cavity) is partitioned by walls (only two segment walls are fully shown here). The nervous system (yellow) includes a nerve cord with a cluster of nerve cells in each segment. Excretory organs (green), which dispose of fluid wastes, are also repeated in each segment. The digestive tract, however, is not segmented; it passes through the segment walls from the mouth to the anus. Segmental blood vessels connect continuous vessels that run along the top (dorsallocation) and bottom (ventral location) of the worm. The segmental vessels include five pairs of accessory hearts. The main heart is simply an enlarged region of the dorsal blood vessel near the head end of the worm.

Figure 17.21 Arthropod characteristics of a lobster. The whole body, including the appendages, is covered by an exoskeleton. The two distinct regions of the body are the cephalothorax (consisting of the head and thorax) and the abdomen. The head bears a pair of eyes, each situated on a movable stalk. The body is segmented, but this characteristic is only obvious in the abdomen. The animal has a tool kit of specialized appendages, including pincers, walking legs, swimming appendages, and two pairs of sensory antennae. Even the multiple mouthparts are modified legs, which is why they work form side to side rather than up and down (as our jaws do).

            The body of an arthropod is completely covered by an exoskeleton (external skeleton). This coat is constructed from layers of protein and a polysaccharide called chitin. The exoskeleton can be a thick, hard armor over some parts, of the body yet paper-thin and flexible in other locations, such as the joints. The exoskeleton protects the animal and provides points of attachment for the muscles that move the appendages. There are, of course, advantages to wearing hard parts on the outside. Our own skeleton is interior to most of our soft tissues, an arrangement that doesn't provide much protection from injury. But our skeleton does offer the advantage of being able to grow along with the rest of our body. In contrast, a growing arthropod must occasionally shed its old exoskeleton and secrete a larger one. This process, called molting, leaves the animal temporarily vulnerable to predators and other dangers.

      

Figure 17.20 Annelids. (a) Giant Australian earthworms are bigger than most snakes. Perhaps you've slipped on slimy worms, but imagine actually tripping over one. (b) Polychaetes have segmental appendages that function in movement and as gills. On the left is a sandworm. The beautiful polychaete on the right is an example of a fan worm, which lives in a tube it constructs by mixing mucus with bits of sand and broken shells. Fan worms use their feathery head-dresses as gills and to extract food particles from the seawater. This species is called a Christmas tree worm. (c) A nurse applied this medicinal leech (Hirudo medicinalisl to a patient's sore thumb to drain blood from a hematoma (abnormal accumulation of blood around an internal injury).

            Arthropod Diversity The four main groups of arthropods are the arachnids, the crustaceans, the millipedes and centipedes, and the insects. Most arachnids live on land. Scorpions, spiders, ticks, and mites are examples (Figure 17.22). Arachnids usually have four pairs of walking legs and a specialized pair of feeding appendages. In spiders, these feeding appendages are fanglike and equipped with poison glands. As a spider uses these appendages to immobilize and chew its prey, it spills digestive juices onto the torn tissues and sucks up its liquid meal.

            Crustaceans are nearly all aquatic. Crabs, lobsters, crayfish, shrimps, and barnacles are all crustaceans (Figure 17.23). They all exhibit the crustacean hallmark of multiple pairs of specialized appendages (see Figure 17.21). One group of crustaceans, the isopods, is represented on land by pill bugs, which you have probably found on the undersides of moist leaves and other organic debris.

Figure 17.22 Arachnids. (a) Scorpions are nocturnal hunters. Their ancestors were among the first terrestrial carnivores, preying on herbivorous arthropods that fed on the early land plants. Scorpions have a pair of appendages modified as large pincers that function in defense and food capture. The tip of the tail bears a poisonous stinger. Scorpions eat mainly insects and spiders. They will sting people only when prodded or stepped on. (If you camp in the desert and leave your shoes on the ground when you go to bed, make sure there are no scorpions in those shoes before putting them on in the morning.) (b) Spiders are usually most active during the daytime, hunting insects or trapping them in webs. Spiders spin their webs of liquid silk, which solidifies as it comes out of specialized glands. Each spider engineers a style of web that is characteristic of its species, getting the web right on the very first try. Besides building their webs of silk, spiders use the fibers in many other ways: as droplines for rapid escape; as cloth that covers eggs; and even as "gift wrapping" for food that certain male spiders offer to seduce females. (c) This magnified house dust mite is a ubiquitous scavenger in our homes. Each square inch of carpet and every one of those dust balls under a bed s are like cities to thousands of dust mites. Unlike some mites that carry pathogenic bacteria, dust mites are harmless except to people who are allergic to the mites' feces.

  

                             (a) A shrimp                             (b)  Barnacles                     Figure 17.24 A millipede

Figure 17.23 Crustaceans. (a) A grass shrimp. (b) Easily confused with bivalve mollusks, barnacles are actually sessile crustaceans with exoskeletons hardened into shells by calcium carbonate (lime). The jointed appendages projecting from the shell capture small plankton.

            Millipedes and centipedes have similar segments over most of the body and superficially resemble annelids, but their jointed legs give them away as arthropods. Millipedes are landlubbers that eat decaying plant matter (Figure 17.24) .They have two pairs of short legs per body segment. Centipedes are terrestrial carnivores, with a pair of poison claws used in defense and to paralyze prey, such as cockroaches and flies. Each of their body segments bears a single pair of long legs.

            In species diversity, insects outnumber all other forms of life combined. They live in almost every terrestrial habitat and in fresh water, and flying insects fill the air. Insects are rare, though not absent, in the seas, where crustaceans are the dominant arthropods. There is a whole big branch of biology, called entomology. that specializes in the study of insects.

            The oldest insect fossils date back to about 400 million years ago, during the Paleozoic era (see Table 14.1). Later, the evolution of flight sparked an explosion in insect variety (Figure 17.25). Like the grasshopper in Figure 17.25, most insects have a three-part body: head, thorax, and abdomen. The head usually bears a pair of sensory antennae and a pair of eyes. Several pairs of mouthparts are adapted for particular kinds of eating-for example, for biting and chewing-plant material in grasshoppers; for lapping up fluids in houseflies; and for piercing skin and sucking blood in ! mosquitoes and other biting flies. Most adult insects have three pairs of legs and one or two pairs of wings, all borne on the thorax.

            Flight is obviously one key to the great success of insects. An animal that can fly can escape many predators, find food and mates, and disperse to new habitats much faster than an animal that must crawl about on the ground. Because their wings are extensions of the exoskeleton and not true appendages, insects can fly without sacrificing any walking legs. By contrast, the flying vertebrates-birds and bats-have one of their two pairs of wa1king legs modified for wings, which explains why these vertebrates are generally not very swift on the ground.

  

Figure 17.25  A small sample of insect diversity

Figure 17.26  Metamorphosis of a monarch butterfly. (a) The larva (caterpillar) spends its time eating and growing, molting as it grows. (b) After several molts, the larva encases itself in a cocoon and becomes a pupa. (c) Within the pupa, the larval organs break down and adult organs develop from cells that were dormant in the larva. (d) Finally, the adult emerges from the cocoon. (e) The butterfly flies off and reproduces, nourished mainly from the calories it stored when it was a caterpillar.

            Many insects undergo metamorphosis in their development. In the case of grasshoppers and some other insect groups, the young resemble adults but are smaller and have different body proportions. The animal goes through a series of molts, each time looking more like an adult, until it reaches full size. In other cases, insects have distinctive larval stages specialized for eating and growing that are known by such names as maggots, grubs, or caterpillars. The larval stage looks entirely different from the adult stage, which is specialized for dispersal and reproduction. Metamorphosis from the larva to the adult occurs during a pupal stage (Figure 17.26).

            Animals so numerous, diverse, and widespread as insects are bound to affect the lives of all other terrestrial organisms, including humans. On one hand, we depend on bees, flies, and many other insects to pollinate our crops and orchards. On the other hand, insects are carriers of the micro-organisms that cause many diseases, including malaria and African sleeping sickness. Insects also compete with humans for food. In parts of Africa, for instance, insects claim about 75% of the crops. Trying to minimize their losses, farmers in the United States spend billions of dollars each year on pesticides, spraying crops with massive doses of some of the deadliest poisons ever invented. Try as they may, not even humans have challenged the preeminence of insects and their arthropod kin. As Cornell University's Thomas Eisner puts it: "Bugs are not going to inherit the Earth. They own it now. So we might as well make peace with the landlord:

Echinoderms

            The echinoderms .(phylum Echinodermata) are named for their spiny surfaces. Sea urchins, the porcupines of the invertebrates, are certainly echinoderms that live up to the phylum name. Among the other echmoderms are sea stars, sand dollars, and sea cucumbers (Figure 17.27).  Echinoderms are all marine. Most are sessile or slow moving. Echinoderms lack body segments, and most have radial symmetry as adults. Both the external and the internal parts of a sea star, for instance, radiate from the center like spokes of a wheel. In contrast to the adult, the larval stage of echinoderms is bilaterally symmetrical. This supports other evidence that echinoderms are not closely related to cnidarians or other radial animals that never show bilateral symmetry. Most echinoderms have an endoskeleton (interior skeleton) constructed from hard plates just beneath the skin. Bumps and spines of this endoskeleton account for the animal's rough or prickly surface. Unique to echinoderms is the water vascular system, a network of water-filled canals that circulate water throughout the echinoderm's body, facilitating gas exchange and waste disposal. The water vascular system also branches into extensions called tube feet. A sea star or sea urchin pulls itself slowly over the seafloor using its suction- cup-like tube feet. Sea stars also use their tube feet to grip prey during feeding (see Figure 17.27a).

            Looking at sea stars and other adult echinoderms, you may think they .have little in common with humans and other vertebrates. But if you return to Figure 17.6, you'll see that echinoderms share an evolutionary branch with chordates, the phylum that includes vertebrates. Analysis of embryonic development reveals this relationship. The mechanism of coelom formation and many other details of embryology differentiate the echinoderms and chordates from the evolutionary branch that includes mollusks, annelids, and arthropods. With this phylogenetic context, we're now ready to make the transition from invertebrates to vertebrates.

Figure 17.27 Echinoderms. (a) The mouth of a sea star, not visible here, is located in the center of the undersurface. The inset shows how the tube feet function in feeding. When a sea star encounters an oyster or clam, its favorite foods, it grips the mollusk's shell with its tube feet and positions its mouth next to the narrow opening between the two halves of the prey's shell. The sea star then pushes its stomach out through its mouth and through the crack in the mollusk's shell. The predator then digests the soft tissue of its prey. (b) In contrast to sea stars, sea urchins are spherical and have no arms. If you look closely, you can see the long tube feet projecting among the spines. Unlike sea stars, which are mostly carnivorous, sea urchins mainly graze on seaweed and other algae. (c) On casual inspection, sea cucumbers do not look much like other echinoderms. Sea cucumbers lack spines, and the hard endoskeleton is much reduced. However, closer inspection reveals many echinoderm traits, including five rows of tube feet.

The vertebrate Genealogy

Most of us are curious about our genealogy. On the personal level, we wonder about our family ancestry. As biology students, we are interested in tracing human ancestry within the broader scope of the entire animal kingdom. In this quest, we ask three questions: What were our ancestors like? How are we related to other animals? and What are our closest relatives? 

  

Figure 17.28 Backbone, extra long. Vertebrates are named for their backbone, which consists of a series of vertebrae. The vertebrate hallmark is apparent in this snake skeleton. You can also see the skull, the bony case protecting the brain. The backbone and skull are parts of an endoskeleton, a skeleton inside the animal rather than covering it.

Figure 17.29 Invertebrate chordates. (a) lancelets owe their name to their bladelike shape. Marine animals only a few centimeters long, lancelets wiggle backward into sand, leaving only their head exposed. The animal filters tiny food particles from the seawater. (b) This adult tunicate, or sea squirt, is a sessile filter feeder that bears little resemblance to other chordates. However, a tunicate goes through a larval stage that is unmistakably chordate.

Figure 17.30  Cordate characteristics

In this section, we trace the evolution of the vertebrates, the group that includes humans and their closest relatives. Mammals, birds, reptiles, amphibians, and the various classes of fishes are all classified as vertebrates. Among the unique vertebrate features are the cranium and backbone, a series of vertebrae for which the group is named (Figure 17.28). Our first step in tracing the vertebrate genealogy is to determine where vertebrates fit in the animal kingdom.

Characteristics of Chordates

            Vertebrates make up one subphylum of the phylum Chordata. Our phylum also includes two subphyla of invertebrates, animals lacking a backbone: lancelets and tunicates (Figure 17.29). These invertebrate chordates and vertebrates all share four key features that appear in the embryo and sometimes in the adult. These four chordate hallmarks are ( 1) a dorsal, hollow nerve cord ( the chordate brain and spinal cord); (2) a notochord, which is a flexible, longitudinal rod located between the digestive tract and the nerve cord; ( 3) pharyngeal slits, which are gill structures in the pharynx, the region of the digestive tube just behind the mouth; and ( 4) a post -anal tail, which is a tail to the rear of the anus (Figure 17.30). Though these chordate characteristics are often difficult to recognize in the adult animal, they are always present in chordate embryos. For example, the notochord, for which our phylum is named, persists in adult humans only in the form of the cartilage disks that function as cushions between the vertebrae. (Back injuries described as "ruptured disks" or "slipped disks" refer to these structures. )

            Body segmentation is another chordate characteristic, though not a unique one. The chordate version of segmentation probably evolved independently of the segmentation we observe in annelids and arthropods. Chordate segmentation is apparent in the backbone of vertebrates (see Figure 17.28) and in the segmental muscles of all chordates (see the chevron-shaped- »» -muscles in the lancelet of Figure 17.29a). Segmental musculature is not so obvious in adult humans unless one is motivated enough to sculpture those washboard "abs of steel."

            Vertebrates retain the basic chordate characteristics, but have additional features that are unique, including, of course, the backbone (see Figure 17.28). Figure 17.31 is an overview of chordate and vertebrate evolution that will provide a context for our survey of the vertebrate classes.

Fishes

            The first vertebrates probably evolved during the early Cambrian period about 540 million years ago. These early vertebrates, the agnathans, lacked jaws. Agnathans are represented today by vertebrates called lampreys (see Figure 17.31). Some lampreys are parasites that use their jawless mouths as suckers to attach to the sides of large fishes and draw blood. In contrast, most vertebrates have jaws, which are hinged skeletons that work the mouth. We know from the fossil record that the first jawed vertebrates

were fishes that replaced most agnathans by about 400 million years ago. In addition to jaws, these fishes had two pairs of fins, which made them maneuverable swimmers. Some of those fishes were more than 10 m long. Sporting jaws and fins, some of the early fishes were active predators that could chase prey and bite off chunks of flesh. Even today, most fishes are carnivores. The two major groups of living fishes are the class Chondrichthyes ( cartilaginous fishes-the sharks and rays) and the class Osteichthyes (the bony fishes, including such familiar groups as tuna, trout, and goldfish).

            Cartilaginous fishes have a flexible skeleton made of cartilage. Most sharks are adept predators-fast swimmers with streamlined bodies, acute senses, and powerful jaws (Figure 17.]2a). A shark does not have keen eyesight, but its sense of smell is very sharp. In addition, special electrosensors on the head can detect minute electrical fields produced by muscle contractions in nearby animals. Sharks also have a lateral line system. a row of sensory organs running along each side of the body. Sensitive to changes in water pressure, the lateral line system enables a shark to detect minor vibrations caused by animals swimming in its neighborhood. There are fewer than 1,000 living species of cartilaginous fishes, nearly all of them marine.

            Bony fishes (Figure 17.]2b) have a skeleton reinforced by hard calcium salts. They also have a lateral line system, a keen sense of smell, and excellent eyesight. On each side of the head, a protective flap called the operculwn (plural, opercula) covers a chamber housing the gills. Movement of the operculum allows the fish to breathe without swimming. (By contrast, sharks lack opercula and must swim to pass water over their gills. ) Bony fishes also have a specialized organ that helps keep them buoyant-the swim bladder. a gasfilled sac. Thus, many bony fishes can conserve energy by remaining almost motionless, in contrast to sharks, which sink to the bottom if they stop swimming. Some bony fishes have a connection between the swim bladder and the digestive tract that enables them to gulp air and extract oxygen from it when the dissolved oxygen level in the water gets too low. In fact, swim bladders evolved from simple lungs that augmented gills in absorbing oxygen from the water of stagnant swamps, where the first bony fishes lived.

 

Figure 17.32 Two classes of fishes. (a) A member of the class Chondrichthyes, the cartilaginous (b) A member of the class Osteichthyes, the bony fishes.

            The largest class of vertebrates { about 30,000 species ), bony fishes are common in the seas and in freshwater habitats. Most bony fishes, including trout, bass, perch, and tuna, are ray-finned fishes. Their fins are supported by thin, flexible skeletal rays (see Figure 17 .32b). A second evolutionary branch of bony fishes includes the lungfishes and lobe-finned fishes. Lung-fishes live today in the Southern Hemisphere. They inhabit stagnant ponds and swamps, surfacing to gulp air into their lungs. The lobe-fins are named for their muscular fins supported by stout bones. Lobe-fins are extinct except for one species, a deep-sea dweller that may use its fins to waddle along the seafloor. Ancient freshwater lobe-finned fishes with lungs played a key role in the evolution of amphibians, the first terrestrial vertebrates.

Amphibians

            In Greek, the, word amphibios means "living a double life. Most members of the class Amphibia exhibit a mixture of aquatic and terrestrial adaptations. Most species are tied to water because their eggs, lacking shells, dry out quickly in the air; The frog in Figure 17.33 spends much of its time on land, but it lays its eggs in water. An egg develops into a larva called a tadpole, a legless, aquatic algae-eater with gills, a lateral line system resembling that of fishes, and a long finned tail. In changing into a frog, the tadpole undergoes a radical metamorphosis. When a young frog crawls onto shore and begins life as a terrestrial insect -eater, it has four legs, air-breathing lungs instead of gills, a pair of external eardrums, and no lateral line system. Because of metamorphosis, many amphibians truly live a double life. But even as adults, amphibians are most abundant in damp habitats, such as swamps and rain forests. This is partly because amphibians depend on their moist skin to supplement lung function in exchanging gases with the environment. Thus, even those frogs that are adapted to relatively dry habitats spend much of their time in humid burrows or under piles of moist leaves. The amphibians of today, including frogs and salamanders, account for only about 8% of all living vertebrates, or about 4,000 species.

  

Figure 17.33 The uduallifeu of an amphibian. Though not all amphibians have aquatic larval stages. this class of vertebrates is named for the familiar tadpole-to-frog metamorphosis of many species

Figure 17.34 The origin of tetrapods. Fossils of some lobe-finned fishes have skeletal supports extending into their fins Early amphibians left fossilized limb skeletons that probably functioned in movement on land

            Amphibians were the first vertebrates to colonize land. They descended from fishes that liad lungs and fins with muscles and skeletal supports strong enough to enable some movement, however clumsy, on land (Figure 17.34). The fossil record chronicles the evolution of four-limbed amphibians from fishlike ancestors. Terrestrial vertebrates-amphibians, reptiles, birds, and mammals-are collectively called tetrapods, which means "four legs:' Had our amphibian ancestors had three pairs of legs on their undersides instead of just two, we might be hexapods. This image seems silly, but serves to reinforce the point that evolution, as descent with modification, is constrained by history.

Reptiles

            Class Reptilia includes snakes, lizards, turtles, crocodiles, and alligators. The evolution of reptiles from an amphibian ancestor paralleled many additional adaptations for living on land. Scales containing a protein called keratin waterproof the skin of a reptile, helping to prevent dehydration in dry air. Reptiles cannot breathe through their dry skin and obtain most of their oxygen with their lungs. Another breakthrough for living on land that evolved in reptiles is the amniotic egg, a water-containing egg enclosed in a shell (Figure 17.35). The amniotic egg functions as a "self -contained pond" that enables reptiles to complete their life cycle on land. With adaptations such as waterproof skin and amniotic eggs, reptiles broke their ancestral ties to aquatic habitats. There are about 6,500 species of reptiles alive today.

            Reptiles are sometimes labeled "cold-blooded" animals because they do not use their metabolism extensively to control body temperature. But reptiles do regulate body temperature through behavioral adaptations. For example, many lizards regulate their internal temperature by basking in the sun when the air is cool and seeking shade when the air is too warm. Because they absorb external heat rather than generating much of their own, reptiles are said to be ectotherms, a term more accurate than cold-blooded. By heating directly with solar energy rather than through the metabolic breakdown of food, a reptile can survive on less than 10% of the calories required by a mammal of equivalent size.

            As successful as reptiles are today, they were far more widespread, numerous, and diverse during the Mesozoic era, which ,is sometimes called the "age of reptiles:' Reptiles diversified extensively during that era, producing a dynasty that lasted until the end of the Mesozoic, about 65 million years ago. Dinosaurs, the most diverse group, included the largest animals ever to inhabit land. Some were gentle giants that lumbered about while browsing vegetation. Others were voracious carnivores that chased their larger prey on two legs (Figure 17.36).

 

Figure 17.35 Terrestrial equipment of reptiles. This bull snake displays two reptilian adaptations to living on land: a waterproof skin with keratinized scales; and amniotic eggs, with shells that protect a watery, nutritious internal environment where the embryo can develop on land. Snakes evolved from lizards that adapted to a burrowing lifestyle.

Figure 17.36 A Mesozoic feeding frenzy.  Hunting in packs, Deinonychus (meaning "terrible claw") probably used its sickle-shaped claws to slash at larger prey.

 

Figure 17.37 A bald eagle in flight. Bird wings are airfoils, which have shapes that create lift by altering air currents. Air passing over a wing must travel farther in the same amount of time than air passing under the wing. This expands the air above the wing relative to the-air below the wing. And this makes the air pressure pushing upward against the lower wing surface greater than the pressure of the expanded air pushing downward on the wing. The wings of birds and airplanes owe their "lift" to this pressure differential.

The age of reptiles began to wane about 70 million years ago. During the Cretaceous, the last period of the Mesozoic era, global climate became cooler and more variable. This was a period of mass extinctions that claimed all the dinosaurs by about 65 million years ago, except for one lineage. That lone surviving lineage is represented today by birds.

Birds

            Birds (class Aves)evolved during the great reptilian radiation of the Mesozoic era.  Amniotic eggs and scales on the legs are  just two of the reptilian features we see in birds. But modern birds look quite different from modern reptiles because of their feathers and other distinctive flight equipment. Almost all of the 8,600 living bird species are airborne. The few flightless species, including the ostrich, evolved from flying ancestors. Appreciating the avian world is all about understanding flight.

            Almost every element of bird anatomy is modified in some way that enhances flight. The bones have a honeycombed structure that makes them strong but light ( the wings of airplanes have the same basic construction).  For example, a huge seagoing species called the frigate bird has a wingspan of more than 2 m, but its whole skeleton weighs only about 113 g (4 ounces). Another adaptation that reduces the weight of birds is the absence of some internal organs found in other vertebrates. Female birds, for instance, have only one ovary instead of a pair. Also, modern birds are toothless, an adaptation that trims the weight of the head (no uncontrolled nosedives). Birds do not chew food in the mouth but grind it in the gizzard, a chamber of the digestive tract near the stomach.

            Flying requires a great expenditure of energy and an active metabolism. In contrast to the ectothermic reptiles, birds are endotherms. That means they use their own metabolic heat to maintain a warm, constant body temperature. A bird's most obvious flight equipment is its wings. Bird wings are air-foils that illustrate the same principles of aerodynamics as the wings of an airplane (Figure 17.37). A bird's flight motors are its powerful breast muscles, which are anchored to a keel-like breastbone. It is mainly these flight muscles that we call "white meat" on a turkey or chicken. Some birds, such as eagles and hawks, have wings adapted for soaring on air currents and flap their wings only occasionally. Other birds, including hummingbirds, excel at maneuvering but must flap continuously to stay aloft. In either case, it is the shape and arrangement of the feathers that form the wing into an air-foil. Feathers are made of keratin, the same protein that forms our hair and fingernails as well as the scales of reptiles. Feathers may have functioned first as insulation, helping birds retain body heat, only later being co-opted as flight gear.

            In tracing the ancestry of birds back to the Mesozoic era, we must search for the oldest fossils with feathered wings that could have the functioned in flight. Fossils of an ancient bird named Archaeopteryx have been found in Bavarian limestone in Germany and date back some 150 million years into the dinosaurs, birds, and Jurassic period (see Figure 14.15). Archaeopteryx is not considered the ancestor of modern birds, and paleontologists place it on a side branch of the avian linage Nonetheless, Archaeopteryx probably was derived from ancestral forms that also gave rise to modern birds. Its skeletal anatomy indicates that it was a weak flyer, perhaps mainly a tree-dwelling glider. A combination of gliding downward and jumping into the air from the ground may have been the earliest mode of flying in the bird lineage.

  

Figure 17.38 The three major groups of mammals. (a) Monotremes, such as this echidna, are the only mammals that lay eggs (inset). (b) The young of marsupials, such as this brushtail opossum, are born very early in their development. They finish their growth while nursing from a nipple in their mother's pouch. (c) In eutherians (placentals), such as these zebras, young develop within the uterus of the mother. There they are nurtured by the flow of blood though the dense network of vessels in the placenta. The reddish portion of the afterbirth clinging to the newborn zebra in this photograph is the placenta. (see prior)

Mammals

            Mammals (class Mammalia) evolved from reptiles about 225 million years ago, long before there were any dinosaurs. During the peak of the age of reptiles, there were a number of mouse-sized, nocturnal mammals that lived on a diet of insects. Mammals became much more diverse after the downfall of the dinosaurs. Most mammals are terrestrial. However, there are nearly 1,000 species of winged mammals, the bats. And about 80 species of dolphins, porpoises, and whales are totally aquatic. The blue whale, an endangered species that grows to lengths of nearly 30 m, is the largest animal that has ever existed.

            Two features-hair and mammary glands that produce milk that nourishes the young-are mammalian hallmarks. The main function of hair is to insulate the body and help maintain a warm, constant internal temperature; mammals, like birds, are endotherms. There are three major groups of mammals: the monotremes, the marsupials, and theeutherians. The duck-billed platypus is one of only threeexisting species of monotremes, the egg-laying mammals. The platypus lives along rivers in eastern Australia and on the nearby island of Tasmania. It eats mainly small shrimps and aquatic insects. The female usually lays two eggs and incubates them in a leaf nest. After hatching, the young nurse by licking up milk secreted onto the mother's fur. The animals called echidnas are also monotremes (Figure 17.38a).

            Most mammals are born rather than hatched. During gestation in marsupials and eutherians, the embryos are nurtured inside the mother by an organ called the placenta. Consisting of both embryonic and maternal tissues, the placenta joins the embryo to the mother within the uterus. The embryo is nurtured by maternal blood that flows close to the embryonic blood system in the placenta. The embryo is bathed in fluid contained by an amniotic sac, which is homologous to the fluid compartment within the amniotic eggs of reptiles.

            Marsupials are the so-called pouched mammals, including kangaroos and koalas. These mammals have a brief gestation and give birth to tiny, embryonic offspring that complete development while attached to the mother's nipples. The nursing young are usually housed in an external pouch, called the marsupium, on the mother's abdomen (Figure 17.38b ). Nearly all marsupials live in Australia, New Zealand, and Central and South America. Australia has been a marsupial sanctuary for much of the past 60 million years. Australian marsupials have diversified extensively, filling terrestrial habitats that on other continents are occupied by eutherian mammals.

            Eutherians are also called placental mammals because their placentas provide more intimate and long-lasting association between the mother and her developing young than do marsupial placentas (Figure 17.38c ) .Eutherians make up almost 95% of the 4,500 species of living mammals. Dogs, cats, cows, rodents, rabbits, bats, and whales are all examples of eutherian mammals. One of the eutherian groups is the order Primates, includes monkeys, apes, and humans.

Figure 17.39 The arboreal athleticism of primates. This orangutan displays primate adaptations for living in the trees: limber shoulder joints, manual dexterity, and stereo vision due to eyes on the front of the face.

The Human Ancestry

We have now traced the animal genealogy to the mammalian group that includes Homo sapiens and its closest kin. We are primates. To understand .what that means, we must trace our ancestry back to the trees, where some of our most treasured traits originated as arboreal adaptations.

The Evolution of Primates

Primate evolution provides a context for understanding human origins. The fossil record supports the hypothesis that primates evolved from insect-eating mammals during the late Cretaceous period, about 65 million years ago. Those early primates were small, arboreal { tree-dwelling) mammals.  Thus, the order Primates was first distinguished by characteristics that were shaped, through natural selection, by the demands of living in the trees.  For example, primates have limber shoulder joints, which make it possible to brachiate {swing from one branch to another). The dexterous hands of primates can hang on to branches and manipulate food. Nails have replaced claws in many primate species, and the fingers are very sensitive. The eyes of primates are close together on the front of the face. The overlapping fields of vision of the two eyes enhance depth perception, an obvious advantage when brachiating. Excellent eye-hand coordination is also important for arboreal maneuvering {Figure 17.39). Parental care is essential for young animals in the trees. Mammals devote more energy to caring for their young than most other vertebrates, and primates are among the most attentive parents of all mammals. Most primates have single births and nurture their offspring for a long time. Though humans do not live in trees, we retain in modified form many of the traits that originated there.

Taxonomists divide the primates into twp main groups: prosimians and anthropoids. The oldest primate fossils are prosimians. Modern prosimians include the lemurs of Madagascar and the lorises, pottos, and tarsiers that live in tropical Africa and southern Asia (Figure 17.40a). Anthropoids include monkeys, apes, and humans. All monkeys in the New World ( the Americas) are arboreal and are distinguished by prehensile tails that function as an extra appendage for brachiating (Figure 17.40b). (If you see a monkey in a zoo swinging by its tail, you know it's from the New World. ) Although some Old World monkeys are also arboreal, their tails are not prehensile. And many Old World monkeys, including baboons, macaques, and mandrills, are mainly ground-dwellers (Figure 17.40c).

   

 

    

Figure 17.40  Primate diversity (a) A prosimian. (b) – (c) Monkeys (d) – (g) Apes  (h) human

            Our closest anthropoid relatives are the apes: gibbons, orangutans, gorillas, and chimpanzees (Figure 17.40d-g). Modern apes live only in tropical regions of the Old World. With the exception of some gibbons, apes are larger than monkeys, with relatively long arms and short legs and no tail. Although  all the apes are capable of brachiation, only gibbons and orangutans are primarily arboreal. Gorillas and chimpanzees are highly social. Apes have larger brains proportionate to body size than monkeys, an their behavior is consequently more adaptable.

The Emergence of Humankind

Humanity is one very young twig on the vertebrate branch, just one of many branches on the tree of life. In the continuum of life spanning 3.5 billion years, humans and apes have shared a common ancestry for all but the last 5-7 million years (Figure 17.41 ). Put another way, if we compressed the history of life to a year, humans and chimpanzees diverged from a common ancestor less than 18 hours ago. The fossil record and molecular systematics concur in that vintage for the human lineage. Paleoanthropology, the study of human evolution, focuses on this very thin slice of biological history. Some Common Misconceptions Certain misconceptions about human evolution that were generated during the early part of the twentieth century still persist today in the minds of many, long after these myths have been debunked by the fossil evidence.

Figure 17.41  Primary Phylogeny

            Let's first dispose of the myth that our ancestors were chimpanzees or any other modern apes. Chimpanzees and humans represent two divergent branches of the anthropoid tree that evolved from a common, less specialized ancestor. Chimps are not our parent species, but more like our phylogenetic siblings or cousins.

            Another misconception envisions human evolution as a ladder with a series of steps leading directly from an ancestral anthropoid to Homo sapiens. This is often illustrated as a parade of fossil hominids (members of the human family) becoming progressively more modern as they march across the page. If human evolution is a parade, then it is a disorderly one, with many splinter groups having traveled down dead ends. At times in hominid history, several different human species coexisted (Figure 17.42). Human phylogeny is more like a multibranched bush than a ladder, with our species being the tip of the only twig that still lives.

            One more myth we must bury is the notion that various human characteristics, such as upright posture and an enlarged brain, evolved in unison. A popular image is of early humans as half-stooped, half-witted cave-dwellers.  In fact, we know from the fossil record that different human features evolved at different rates, with erect posture, or bipedalism, leading the way. Our pedigree includes ancestors who walked upright but had ape-sized brains. After dismissing some of the folklore on human evolution, however, we must admit that many questions about our ancestry have not yet been

resolved.

Figure 17.42 A timeline of human evolution.  Notice that there have been times when two or more hominid species coexisted. The skulls are all drawn to the same scale enable you to compare the sizes of craniums and hence brain

  

Figure 17.43 The antiquity of upright posture. (a) Lucy, a 3.18-million-year-old skeleton, represents the hominid species Australopithecus afarensis. Fragments of the pelvis and skull put A. afarensis on two feet. (b) Some 3.7 million years ago, several bipedal (upright-walking) hominids left footprints in damp volcanic ash in what is now Tanzania in East Africa. The prints fossilized and were discovered by British anthropologist Mary Leakey in 1978. The footprints are part of the strong evidence that bipedalism is a vefry old human trait. (c)  This A afarensis skull, 3.9 million years old, articulated with a vertical back bone. The upright posture of humans is a least that old. 

            Australopithecus and the Antiquity of Bipedalism Before there was Homo, several hominid species of the genus Australopithecus walked the African savanna (grasslands with clumps of trees ). Paleoanthropologists have focused much of their attention on A. afarensis, an early species of Australopithecus. Fossil evidence now pushes bipedalism in A. afarensis back to at least 4 million years ago (Figure 17.43) .Doubt remains whether an even older hominid, Ardipithecus ramidus, which dates back at least 4.4 million years, was bipedal.

            One of the most complete fossil skeletons of A. afarensis dates to about 3.2 million years ago in East Africa. Nicknamed Lucy by her discoverers, the individual was a female, only about 3 feet tall, with a head about the size of a softball (see Figure 17.43a). Lucy and her kind lived in savanna areas and may have subsisted on nuts and seeds, bird eggs, and whatever animals they could catch or scavenge from kills made by more efficient predators such as large cats and dogs.

            All Australopithecus species were extinct by about 1.4 million years ago. Some of the later species overlapped in time with early species of our own genus, Homo ( see Figure 17.42 ) .Much debate centers on the evolutionary relationships of the Australopithecus species to each other and to Homo. Were the Australopithecus species all evolutionary side branches? Or were some of them ancestors to later humans? Either way, these early hominids show us that th~ fundamental human trait ofbipedalism evolved millions of years before the other major human trait-an enlarged brain. As evolutionary biologist Stephen Jay Gould put it, "Mankind stood up first and got smart later”.

            Homo habilis and the Evolution of Inventive Minds Enlargement of the human brain is first evident in fossils from East Africa dating to the latter part of the era of Australopithecus, about 2.5 million years ago. Anthropologists have found skulls with brain capacities intermediate in size between those of the latest Australopithecus species and those of Homo sapiens. Simple handmade stone tools are sometimes found with the larger-brained fossils, which have been dubbed Homo habilis ("handy man"). After walking upright for about 2 million years, humans were finally beginning to use their manual dexterity and big brains to invent tools that enhanced their hunting, gathering, and scavenging on the African savanna.

Homo erectus and the Global Dispersal of Humanity The first species to extend humanity's range from its birthplace in Africa to other continents was Homo erectus, perhaps a descendant of H. habilis. The global dispersal began about 1.8 million years ago. But don't picture this migration as a mad dash for new territory or even as a casual stroll. If H. erectus simply expanded its range from Africa by about a mile per year, it would take only about 12,000 years to populate many regions of Asia and Europe. The gradual spread of humanity may have been associated with a change in diet to include a larger proportion of meat. In general, animals that hunt require more geographic territory than animals that feed mainly on vegetation.

            Homo erectus was taller than H. habilis and had a larger brain capacity. During the 1.5 million years the species existed, the H. erectus brain increased to as large as 1,200 cubic centimeters ( cm3), a brain capacity that overlaps the normal range for modern humans. Intelligence enabled humans to continue succeeding in Africa and also to survive in the colder climates of the north. Homo erectus resided in huts or caves, built fires, made clothes from animal skins, and designed stone tools that were more refined than the tools of H. habilis. In anatomical and physiological adaptations, H. erectus was poorly equipped for life outside the tropics but made up for the deficiencies with cleverness and social cooperation.

            Some African, Asian, European, and Australasian ( from Indonesia, New Guinea, and Australia) populations of H. erectus gave rise to regionally diverse descendants that had even larger brains. Among these descendants of H. erectus were the Neanderthals, who lived in Europe, the Middle East, and parts of Asia from about 130,000 years ago to about 35,000 years ago. (They are named Neanderthals because their fossils were first found in the Neander Valley of Germany. ) Compared with us, Neanderthals had slightly heavier browridges and less pronounced chins, but their brains, on average, were slightly larger than ours. Neanderthals were skilled toolmakers, and they participated in burials and other rituals that required abstract thought. Much current research on the Neanderthal skull addresses an intriguing question: Did Neanderthals have the anatomical equipment necessary for speech?

The Origin of Homo sapiens The oldest known post-H. erectus fossils, dating back over 300,000 years, are found in Africa. Many paleoanthropologists group these African fossils along with Neanderthals and various Asian and Australasian fossils as the earliest forms of our species, Homo sapiens. These regionally diverse descendants of H. erectus are sometimes referred to as "archaic Homo sapiens." The oldest fully modern fossils of H. sapiens-skulls and human evolution. other bones that look essentially like those of today's humans-are about 100,000 years old and are located in Africa. Similar fossils almost as ancient have also been discovered in caves in Israel. The famous fossils of modern humans from the Cro-Magnon caves of France date back about 35,000 years.

            The relationship of the Cro-Magnons and other modern humans to archaic Homo sapiens is a question that will continue to engage paleoanthropologists for decades. What was the fate of the various descendants of Homo erectus who populated different parts of the world! In the view of some anthropologists, these archaic H. sapiens populations gave rise to modern humans. According to this hypothesis, called the multiregional hypothesis, modern humans evolved simultaneously in different parts of the world (Figure 17.44a). If this view is correct, then the geographic diversity of humans originated relatively early, when H. erectus spread from Africa into the other continents between 1 and 2 million years ago. This hypothesis accounts for the great genetic similarity of all modern people by pointing out that interbreeding among neighboring populations has always provided corridors for gene flow throughout the entire geographic range of humanity.

            In sharp contrast to the multiregional hypothesis is a hypothesis that modern H. sapiens arose from a single ardlaic group in Africa. According to this "Out of Africa" hypothesis ( also called the replacement hypothesis) the Neanderthals and other archaic peoples outside Africa were evolutionary dead ends (Figure 17.44b). Proponents of this hypothesis argue that modern humans spread out of Africa about 100,000 years ago and completely replaced the archaic H. sapiens in other regions. So far, genetic evidence mostly; supports the replacement hypothesis. Based on comparisons of mitochondrial DNA (mtDNA) and of Y chromosomes between samples from various human populations, today's global human population seems to be very genetically uniform. Supporters of the replacement hypothesis argue that such uniformity could only stem from a single ancestral stock, not from diverse, geographically isolated populations. Proponents of the multiregional model counter that interbreeding between populations can explain our great genetic similarity. Debate about which hypothesis is correct-a multiregional or an "Out of Africa" origin of modem humans--centers mainly on differences in interpreting the fossil record and molecular data. As research continues, perhaps anthropologists will come closer to a consensus on our origins.

Figure 17.44 "Cut of Africa"-but when? Two hypotheses for the origin of modern Homo

sapiens. There is no question that Africa is the cradle of humanity; we can all trace our ancestry back to that continent. But how recently was the ancestor common to all the world's modern humans still in Africa? (a) According to the multiregional hypothesis, modern humans throughout the world evolved from the Homo erectus populations that spread to different regions beginning almost 2 million years ago. Interbreeding between populations (dashed line in the diagram) kept humans very similar genetically. (b) In contrast, the "Out of Africa" hypothesis postulates that all regional descendants of H. erectus became extinct except in Africa. And according to this model, it was a second dispersal out of Africa, just 100,000 years ago, that populated the world with modern humans, which had evolved from H. erectus in Africa.

Cultural Evolution An erect stance was the most radical anatomical change in our evolution; it required major remodeling of the foot, pelvis, and vertebral column. Enlargement of the brain was a secondary alteration made possible by prolonging the growth period of the skull and its contents (see Figure 14.17). The primate brain continues to grow after birth, and the period of growth is longer for a human than for any other primate. The extended period of human development also lengthens the time parents care for their offspring, which contributes to the child's ability to benefit from the experiences of earlier generations. This is the basis of culture—the transmission of accumulated knowledge over generations. The major means of this transmission is language, written and spoken.

            Cultural evolution is continuous, but there have been three major stages. The first stage began with nomads who hunted and gathered food on the African grasslands 2 million years ago. They made tools, organized communal activities, and divided labor. Beautiful ancient art is just one example of our cultural roots in these early societies (Figure 17.45) .The second main stage of cultural evolution came with the development of agriculture in Africa, Eurasia, and the Americas about 10,000 to 15,000 years ago. Along with agriculture came permanent settlements and the first cities. The third major stage in our cultural evolution was the Industrial Revolution, which began in the eighteenth century. Since then, new technology has escalated exponentially; a single generation spanned the flight of the Wright brothers and Neil Armstrong's walk on the moon. It took less than a decade for the World-Wide Web to transform commerce, communication, and education. Through all this cultural evolution, from simple hunter-gatherers to high-tech societies, we have not changed biologically in any significant way. We are probably no more intelligent than our cave-dwelling ancestors. The same toolmaker who chipped away at stones now designs microchips and software. The know-how to build. skyscrapers, computers, and spaceships is stored not in our genes but in the cumulative product of hundreds of generations of human experience, passed along by parents, teachers, books, and electronic media.

    

European Bison                        Rhinocerous                Human hand      Horses                          Owl

Figure 17.45  Art History goes way back, and so does our fascination with and dependence on animal diversity.  Cro-Magnon wildlife artists created these remarkable paintings beginning  about 30,000 years ago. Three cave explorers found this prehistoric art gallery on Christmas eve 1994, when they ventured into a cavern near Vllon –Pont d’Arc in southern France. 

 

Summary

Early Animals and the Cambrian Explosion Animals probably evolved from a colonial, flagellated protist more than 700 million years ago. At the beginning of the Cambrian period, 545 million years ago, animal diversity exploded.

.Animal Phylogeny Major branches of animal evolution are defined by four key evolutionary differences: the presence or absence of true tissues; radial versus bilateral body symmetry; presence or absence of a body cavity at least partly lined by mesoderm; and details of embryonic development.

.Sponges Sponges (phylum Porifera) are sessile animals with porous bodies and choanocytes but no true tissues. They filter-feed by drawing water through pores in the sides of the body.

.Cnidarians Cnidarians (phylum Cnidaria) have radial symmetry, a gas-trovascular cavity, and tentacles with cnidocytes. The body is either a sessile polyp or floating medusa.

.Flatworms Flatworms (phylum Platyhelminthes) are the simplest bilatera! animals. They may be free-living or parasitic in or on plants and animals.

.Roundworms Roundworms (phylum Nematoda) are unsegmented and cylindrical with tapered ends. They have a complete digestive tract and a pseudocoelom. They may be free-living or parasitic in plants and animals.

.Mollusks Mollusks (phylum Mollusca) are soft-bodied animals often protected by a hard shell. The body has three main parts: a muscular foot, a visceral mass, and a fold of tissue called the mantle-

.Annelids Annelids (phylum Annelida) are segmented worms. They may be free-living or parasitic on other animals.

.Arthropods Arthropods (phylum Arthropoda) are segmented animals with an exoskeleton and specialized, jointed appendages. Arthropods consist of four main groups: Arachnids, crustaceans, millipedes and centipedes, and insects. In species diversity, insects outnumber all other forms of life combined.

.Echinoderms Echinoderms (phylum Echinodermata) are sessile or slow-moving marine animals that lack body segments and possess a unique water vascular system. Bilaterally symmetrical larvae usually change to radially symmetrical adults. .

.Characteristics of Chordates Chordates (phylum Chordata) are defined by a dorsal, hollow nerve cord; a flexible notochord; pharyngeal slits; and a post-anal tail. Tunicates and lancelets are invertebrate chordates. All other chordates are vertebrates, possessing a cranium and backbone.

.Fishes Agnathans are jawless vertebrates. Cartilaginous fishes ( class Chondrichthyes), such as sharks, are mostly predators with powerful jaws and a flexible skeleton made of cartilage. Bony fishes ( class Osteichthyes) have a stiff skeleton reinforced by hard calcium salts. Bony fishes are further classified into ray-finned fishes, lungfishes, and lobe-finned fishes-

.Amphibians Amphibians ( class Amphibia) are tetrapod vertebrates that usually deposit their eggs (lacking shells) in water. Aquatic larvae typically undergo a radical metamorphosis into the adult stage. Their moist skin requires that amphibians spend much of their adult life in moist environments.

.Reptiles Reptiles (class Reptilia) are terrestrial ectotherms with lungs and waterproof skin covered by scales. Their amniotic eggs enhanced reproduction on land.

.Birds Birds ( class Aves ) are endothermic vertebrates with amniotic eggs, wings, feathers, and other adaptations for flight.

.Mammals Mammals ( class Mammalia) are endothermic vertebrates with hair and mammary glands. There are three major groups: Monotremes lay eggs; marsupials use a placenta but give birth to tiny offspring that usually complete development while attached to nipples inside the mother's pouch; and eutherians, or placental mammals, use their placenta in a longer-lasting association between the mother and her developing young.

 

Homo Sapiens (modern humans) originated in Africa about 250,000 and emerged from Africa about 100,000.  By 30,000 they are in Siberia, by 14,000 in Americas and by 1,600 in remote Pacific islands.

Earth’s New Crisis

Of the many crises in the history of life, the impact of one species, Homo sapiens, is the latest and potentially the most devastating.

            Evolution of the human brain may have been anatomically simpler than acquiring an upright stance, but the global consequences of cerebral expansion have been enormous. Cultural evolution made Homo sapiens a new force in the history of life-a species that could defy its physical limitations and shortcut biological evolution. We do not have to wait to adapt to an environment through natural selection; we simply change the environment to meet our needs. We are the most numerous and widespread of all large animals, and everywhere we go, we bring environmental change. There is nothing new about environmental change. The history of life is the story of biological evolution on a changing planet. But it is unlikely that change has ever been as rapid as in the age of humans. Cultural evolution outpaces biological evolution by orders of magnitude. We are changing the world faster than many species can adapt; the rate of extinctions in the twentieth century was 50 times greater than the average for the past 100,000 years.

            This rapid rate of extinction is mainly a result of habitat destruction, which is a function of human cultural changes and overpopulation. Feeding, clothing, and housing 6 billion people imposes an enormous strain on Earth's capacity to sustain life. If all these people suddenly assumed the high standard of living enjoyed by many people in developed nations, It is likely that Earths support systems would be overwhelmed. Already, for example, current rates of fossil-fuel consumption, mainly by developed nations, are so great that waste carbon dioxide may be causing the temperature of the atmosphere to increase enough to alter world climates. Today, it is not just individual species that are endangered, but entire ecosystems, the global atmosphere, and the oceans. Tropical rain forests, which playa vital role in moderating global weather, are being cut down at a startling rate. Scientists have hardly begun to study these ecosystems, and many species in them may become extinct before they are even discovered.