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Griffiths AJF, Miller JH, Suzuki DT, et al. An Introduction to Genetic Analysis. 7th edition. New York: W. H. Freeman; 2000.

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An Introduction to Genetic Analysis. 7th edition.

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Genes as determinants of the inherent properties of species

What is the nature of genes, and how do they perform their biological roles? Three fundamental properties are required of genes and the DNA of which they are composed.

1.

Replication. Hereditary molecules must be capable of being copied at two key stages of the life cycle (Figure 1-2). The first stage is the production of the cell type that will ensure the continuation of a species from one generation to the next. In plants and animals, these cells are the gametes: egg and sperm. The other stage is when the first cell of a new organism undergoes multiple rounds of division to produce a multicellular organism. In plants and animals, this is the stage at which the fertilized egg, the zygote, divides repeatedly to produce the complex organismal appearance that we recognize.

2.

Generation of form. The working structures that make up an organism can be thought of as form or substance. Looked at in this way, DNA has essential “information”; in other words, “that which is needed to give form.”

3.

Mutation. A gene that has changed from one allelic form into another has undergone mutation – an event that happens rarely but regularly. Mutation is not only a basis for variation within a species, but, over the long term, also the raw material for evolution.

Figure 1-2. DNA replication is the basis of the perpetuation of life through time.

Figure 1-2

DNA replication is the basis of the perpetuation of life through time.

We will examine replication and the generation of form in this section and mutation in the next.

DNA and its replication

An organism's basic complement of DNA is called its genome. The body cells of most plants and animals contain two genomes (Figure 1-3). These organisms are diploid. The cells of most fungi, algae, and bacteria contain just one genome. These organisms are haploid. The genome itself is made up of one or more extremely long molecules of DNA that are organized into chromosomes. For instance, human body cells contain two sets of 23 chromosomes, for a total of 46. Genes are simply the functional regions of chromosomal DNA. Each chromosome in the genome carries a different array of genes. In diploid cells, each chromosome and its component genes are present twice. Two chromosomes with the same gene array are said to be homologous. When a cell divides, all the chromosomes (one or two genomes) are replicated; so each daughter cell contains the full complement. Therefore, the unit of replication is the chromosome; when a chromosome is replicated, all the genes of that chromosome are automatically replicated along with it.

Figure 1-3. Successive enlargements bringing the genetic material of an organism into sharper focus.

Figure 1-3

Successive enlargements bringing the genetic material of an organism into sharper focus.

To understand replication, we need to understand the basic nature of DNA. DNA is a linear, double-helical structure looking rather like a molecular spiral staircase. The double helix is composed of two intertwined chains of building blocks called nucleotides. Each nucleotide consists of a phosphate group, a deoxyribose sugar molecule, and one of four different nitrogenous bases either adenine, guanine, cytosine, or thymine. Each of the four nucleotides is usually designated by the first letter of the base that it contains: A, G, C, or T. The four nucleotides are shown in Figure 1-4a and b. The carbons in the deoxyribose sugar group are assigned numbers followed by a prime (1′, 2′, and so forth) to distinguish them from the numbering of the atoms in the bases. In DNA, the nucleotides are connected to each other at the 3′ and 5′ positions, as shown in Figure 1-4(c); hence each chain is said to have polarity, with one end having a 5′ phosphate group and the other a 3′ OH group. The connecting bonds between the repeating sugar and phosphate groups are called phosphodiester bonds.

Figure 1-4. The fundamental building blocks of DNA.

Figure 1-4

The fundamental building blocks of DNA. (a) Chemical structures of the four nucleotides (two with purine bases and two with pyrimidine bases). The sugar is called deoxyribose because it is a variation of a common sugar, ribose, which has one more oxygen (more...)

The polarities of the two intertwined nucleotide chains are in opposite directions; the chains are said to be antiparallel. The two nucleotide chains are held together by weak bonds called hydrogen bonds, between bases. Hydrogen bonding is very specific because of a “lock-and-key” fit between the shape and atomic charge of the bases. Adenine pairs only with thymine, and guanine pairs only with cytosine. The bases that form base pairs are said to be complementary. Hence a short segment of DNA drawn with arbitrary nucleotide sequence might be

Image ch1e1.jpg

The same structure is depicted in more detail in Figure 1-5. Although hydrogen bonds are weak individually, their combined bonding holds the two chains together in a stable manner. Furthermore, it is important that the bonds between the bases be relatively weak because, as we shall see, the two chains have to be pulled apart to allow the replication process to work. The base pairs, which run down the center of the double helix, are flat hydrophobic structures that have a tendency to stack owing to the exclusion of water molecules. This stacking draws the two intertwined strands of DNA into its helical structure (Figure 1-6).

Figure 1-5. The arrangement of the components of DNA in which a segment of the double helix has been unwound to show the structures more clearly.

Figure 1-5

The arrangement of the components of DNA in which a segment of the double helix has been unwound to show the structures more clearly. (a) An accurate chemical diagram showing the sugar-phosphate backbone in blue and the hydrogen bonding of bases in the (more...)

Figure 1-6. Ribbon representation of the DNA double helix.

Figure 1-6

Ribbon representation of the DNA double helix. Blue = sugar-phosphate backbone; brown = base pairs.

For replication to take place, the two strands of the double helix must unwind in one direction, rather like the opening of a zipper. The two exposed nucleotide chains then act as alignment guides, or templates, for the deposition of free nucleotides. These nucleotides have been synthesized inside the cell and arrive in the nucleus by diffusion. Their polymerization into a new strand is catalyzed by the enzyme DNA polymerase. This enzyme initially binds to double-helical DNA at a specific nucleotide sequence called the origin of replication and then moves along the DNA, polymerizing new chains as shown in Figure 1-7. The crucial point illustrated in Figure 1-7 is that, because of base complementarity, the two daughter DNA molecules are identical with each other and with the original molecule. However, note that each daughter molecule is half old and half newly polymerized. This method of replication is therefore called semiconservative.

Figure 1-7. Semiconservative replication in process.

Figure 1-7

Semiconservative replication in process.

MESSAGE

DNA is composed of two antiparallel nucleotide strands held together by complementary hydrogen bonding of A with T and G with C.

In the foregoing description of DNA and its replication, we see two principles that are the bases of most genetic transactions:

1.

Complementary bases bind to each other.

2.

Certain proteins (for example, DNA polymerase) act by binding to a specific base sequence in a nucleic acid.

We will encounter these two ideas numerous times throughout the book.

MESSAGE

Base complementarity and the binding of proteins to specific base sequences in a nucleic acid are two recurring mechanisms in genetics.

Generation of form

If DNA represents information, what constitutes form at the cellular level? The simple answer is “protein” because the great majority of structures in a cell are protein or have been made by protein. In this section, we trace the steps through which information becomes form.

Every functional gene is read by the cellular machinery to produce the product of that gene. For most genes, the product is a specific protein. The first step taken by the cell to make the protein is to copy, or transcribe, the information encoded in the DNA of the gene as a related but single-stranded molecule called ribonucleic acid (RNA). This RNA molecule represents a “working copy” of the gene. Indeed, a gene can be defined as a segment of DNA that specifies a functional RNA. Like DNA, RNA is composed of nucleotides, but these nucleotides contain the sugar ribose instead of deoxyribose. Furthermore, instead of thymine, RNA contains uracil (U), a base that has hydrogen-bonding properties identical with those of thymine. Hence the RNA bases are A, G, C, and U. The RNA copy made from the gene is called a transcript.

The polymerization of ribonucleotides to form RNA is catalyzed by the enzyme RNA polymerase. This enzyme binds to a specific sequence, the transcriptional start site, at one end of a gene. It separates the two strands of DNA. It moves along the gene, maintaining the separated “bubble,” and, as it proceeds, it uses only one of the separated strands as a template, synthesizing an ever-growing tail of polymerized nucleotides that eventually become the full-length transcript. The addition of ribonucleotides by RNA polymerase is always at the 3′ end of the growing chain. Transcription is represented diagrammatically in Figure 1-8. Note again the two powerful principles of macromolecular interactions: RNA polymerase binds to a specific initiation sequence on DNA and moves along the DNA, illustrating protein–nucleic acid binding; the action of the DNA template strand in aligning ribonucleotides is based on the principle of base complementarity, this time between DNA bases and RNA bases. Note that the RNA transcript has the same sequence as the nontemplate strand of the DNA (Figure 1-8).

Figure 1-8. Transcription process.

Figure 1-8

Transcription process.

MESSAGE

During transcription one of the DNA strands of a gene acts as a template; ribonucleotides are added at a 3′ growing tip, catalyzed by the enzyme RNA polymerase.

The biological role of most genes is to carry or encode information on the composition of proteins. This composition, together with the timing and amount of production of each protein, is an extremely important determinant of the structure and physiology of organisms. The primary structure of a protein is a linear chain of building blocks called amino acids. This primary chain is coiled and folded and, in some cases, associated with other chains — to form a functional protein. Proteins are important either as structural components — such as the proteins that constitute hair, skin, and — muscle or as active agents in cellular processes — for example, enzymes and active-transport proteins. Each gene is responsible for coding for one specific protein or a part of a protein. Let's look at how a gene is organized. For the purpose of this overview, we will focus on the protein-coding genes of eukaryotes. Eukaryotes are those organisms whose cells have a membrane-bound nucleus. Outside the nucleus of each cell are a complex array of membranous structures, including the endoplasmic reticulum and Golgi apparatus, and organelles such as mitochondria and chloroplasts. Animals, plants, algae, and fungi are eukaryotes.

Figure 1-9 shows the general structure of a eukaryotic gene. At one end, there is a regulatory region to which various proteins (such as RNA polymerase) bind, causing the gene to be transcribed at the right time and in the right amount. A region at the other end of the gene contains sequences encoding the termination of transcription. In the genes of many eukaryotes, the protein-encoding sequence is interrupted by segments (ranging in number from one to many) called introns. The origin and functions of introns are still unclear. They are excised from the primary transcript. The split-up coding sequences between the introns are called exons.

Figure 1-9. Generalized structure of a eukaryotic gene.

Figure 1-9

Generalized structure of a eukaryotic gene. This example has three introns and four exons.

Figure 1-10 illustrates the essentials of gene action in a generalized eukaryotic cell. The nucleus contains most of the DNA, but note that mitochondria and chloroplasts also contain small chromosomes.

Figure 1-10. Simplified view of gene action in a eukaryotic cell.

Figure 1-10

Simplified view of gene action in a eukaryotic cell. The basic flow of genetic information is from DNA to RNA to protein. Four types of genes are shown. Gene 1 responds to external regulatory signals and makes a protein for export; gene 2 responds to (more...)

Some protein-encoding genes are transcribed more or less constantly; they are the “housekeeping” genes that are always needed for basic reactions. Other genes may be rendered unreadable or readable to suit the functions of the organism at particular moments and under particular external conditions. The signal that masks or unmasks a gene may come from outside the cell; for example, from a steroid hormone or a nutrient. Or the signal may come from within the cell itself as the result of the reading of other genes. In either case, special regulatory sequences in the DNA are directly affected by the signal, and they in turn affect the transcription of the protein-encoding gene. The regulatory substances that are the signals bind to the regulatory DNA of the target genes to control the synthesis of transcripts.

When the introns have been cut out of the primary transcript, the remaining RNA sequence is called messenger RNA (mRNA). The mRNA molecules exit the nucleus through nuclear pores and enter the cytoplasm. The cytoplasm is where protein synthesis takes place. The nucleotide sequence of an mRNA molecule is “read” from the 5′ end to the 3′ end, in groups of three. These groups of three are called codons.

Image ch1e2.jpg

Because there are four nucleotides, there are 4 × 4 × 4 = 64 different codons, each one standing for an amino acid or a signal to terminate translation. For instance, AUU stands for isoleucine, CCG for proline, and UAG is a translation-termination (“stop”) codon.

Protein synthesis takes place on cytoplasmic organelles called ribosomes. A ribosome attaches to the 5′ end of an mRNA molecule and moves along the mRNA, catalyzing the assembly of the string of amino acids that will constitute the primary structure of the protein. This primary chain is called a polypeptide. Each amino acid is brought to the ribosome by a specific transfer RNA (tRNA) molecule that docks at a codon of the mRNA. Docking is by base pairing between a three-nucleotide tRNA segment called an anticodon and the codon:

Image ch1e3.jpg

Because this process of reading the mRNA sequence and converting it into an amino acid sequence is rather like converting one language into another, the process of protein synthesis is called translation. The process of translation is shown in Figure 1-11.

Figure 1-11. The addition of a single amino acid to the growing polypeptide chain in the translation of mRNA.

Figure 1-11

The addition of a single amino acid to the growing polypeptide chain in the translation of mRNA.

Trains of ribosomes pass along an mRNA molecule, each member of a train making the same type of polypeptide. At the end of the mRNA, a termination codon causes the ribosome to detach and recycle to another mRNA.

Let's pause to reconsider this amazing process in relation to the principles of macromolecular association. The alignment of tRNA anticodon to mRNA codon is by base complementarity. The attachment of the ribosome to the mRNA, its movement along the mRNA, and the binding of the tRNA to the ribosome are all examples of protein–nucleic acid bonding.

MESSAGE

The information in protein-coding genes is used by the cell in two steps of information transfer:

Image ch1e4.jpg

Each gene encodes a separate protein, each with specific functions either within the cell (for example, the purple-rectangle proteins in Figure 1-10) or for export to other parts of the organism (the purple-circle proteins). The synthesis of proteins for export (secretory proteins) takes place on ribosomes that are located on the surface of the rough endoplasmic reticulum, a system of large flattened vesicles. The completed amino acid chains are passed into the lumen of the endoplasmic reticulum, where they fold up spontaneously to take on their protein shape. The proteins may be modified at this stage, but they eventually enter the chambers of the Golgi apparatus and from there, the secretory vessels, which eventually fuse with the cell membrane and release their contents to the outside.

Proteins destined to function in the cytoplasm and most of the proteins that function in mitochondria and chloroplasts are synthesized in the cytosoplasm on ribosomes not bound to membranes. For example, proteins that function as enzymes in the glycolysis pathway follow this route. The proteins destined for organelles are specially tagged to target their insertion into specific organelles. In addition, mitochondria and chloroplasts have their own small circular DNA molecules. The synthesis of proteins encoded by genes on mitochondrial or chloroplast DNA takes place on ribosomes inside the organelles themselves. Therefore the proteins in mitochondria and chloroplasts are of two different origins: either encoded in the nucleus and imported into the organelle or encoded in the organelle and synthesized within the organelle compartment.

Prokaryotes are one-celled organisms such as bacteria, whose cellular structure is simpler than that of eukaryotes; there is no nucleus separated from the cytoplasm by a nuclear membrane. Protein synthesis in prokaryotes is generally similar to that in eukaryotes mRNA, tRNA, and ribosomes are used), but there are some important differences. For example, prokaryotic genes have no introns. Furthermore, there are no compartments bounded by membranes through which the RNA or protein must pass.

MESSAGE

The flow of information from DNA to RNA to protein is a central focus of modern biology.

By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.

Copyright © 2000, W. H. Freeman and Company.
Bookshelf ID: NBK22032

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