MODERN BOTANY - P. RAVEN - 1990

SECTION III. GENETICS

CHAPTER 8. CHEMISTRY AND HEREDITY

How Do Genes Work?

Watson and Crick uncovered the Chemical Nature of the Gene and proposed a model for its Replication. However, one question remained unanswered: how does the information contained in a DNA molecule influence Structure or function through The formation of specific Proteins? For example, how does DNA "make" a harmless pneumococcus virulent, determine the shape of a leaf or the scent of a flower, or why are your eyes the same color as your mother's?

Molecules of Heredity

Cellular Structure and function depend almost entirely on the composition of cellular proteins, Enzymes in particular. Therefore, the processes byซึ่ง specific proteins are formed using the Genetic information of DNA are of special interest, as a specific linear sequence of bases is "translated" into a corresponding linear sequence of Amino Acids (the Primary Cell/13.html">Protein Structure, which is essential for determining its shape and function). At certain Stages of Protein Synthesis, DNA-like molecules—ribonucleic acid (RNA) molecules—participate. Their involvement had been hypothesized long ago, since Cells synthesizing large amounts of protein also contain abundant RNA.

RNA differs somewhat from DNA (see Chapter 3): the sugar component in an RNA molecule is ribose rather than the deoxyribose of DNA; furthermore, RNA contains the pyrimidine uracil (U) instead of the thymine found in DNA. RNA is rarely double-stranded; thus, its properties and activity differ from those of DNA. There are three principal classes of RNA: messenger, transfer, and ribosomal.

Messenger RNA (mRNA) is a large molecule ranging in size from several hundred to 10,000 NUCLEOTIDES. It is synthesized on a DNA template following the same principle of complementarity used in the synthesis of a daughter DNA strand. The presence of adenine in the parent DNA strand dictates the incorporation of uracil into the growing mRNA strand. Each sequence of three bases in an mRNA molecule corresponds to a single amino acid during translation (i.e., Protein Synthesis on an RNA template); such a sequence is called a codon.

Transfer RNA (tRNA). It is sometimes referred to as the "dictionary of the language of life." There are several Different types of tRNA, apparently one specific type for each codon of the Genetic Code—that is, the code by which The base sequence in DNA determines the Amino Acid Sequence in the resulting protein (Fig. 8-7). METABOLISM/28.html">The Genetic Code is universal among all organisms, save for very minor exceptions. This is one of the most remarkable discoveries in molecular biology. Bacterial genes can function perfectly well (under appropriate conditions) in mammalian cells. Plant genes can be introduced into Bacteria, where they will direct the synthesis of their own products. These findings not only support the common ancestry of All living organisms but also form the basis for The Development of Introduction/32.html">Genetic Engineering techniques, which hold such great promise for human progress (see Chapter 30).

Class="center">Fig. 8-7. The genetic code, consisting of 64 codons (base triplets) and their corresponding amino acids (see Fig. 3-14). Of the 64 codons, only 61 are used to encode amino acids. The remaining three codons serve as "stop signals" for the termination of protein synthesis. Since 61 triplets encode 20 amino acids, there must obviously be "synonyms"—different triplets encoding the same amino acid. Leucine, for example, is encoded by six triplets. Most "synonyms" differ only in their third nucleotide. The triplets encoding the 20 Amino Acids and the three "stop signals" are shown here.

Each tRNA molecule consists of approximately 80 nucleotides joined into a single long chain that forms loops (Fig. 8-8). The Specificity of an individual tRNA is determined in part by The structure of its anticodon, a three-base sequence through which it recognizes a specific triplet codon on the mRNA.

Fig. 8-8. A. Two-dimensional structure of a tRNA molecule, which consists of approximately 80 nucleotides linked in a single chain. The chain always terminates with the sequence CCA. The amino acid attaches to the specific tRNA precisely at this site. Certain nucleotides are found in all tRNAs (highlighted in gray). Others vary from molecule to molecule. The letters D, , and T designate unusual modified nucleotides characteristic of the tRNA molecule. These unusual nucleotides prevent the formation of certain Hydrogen Bonds and facilitate the establishment of others, thereby determining the characteristic folded STRUCTURE OF THE molecule. Each region of the tRNA molecule apparently has its own unique function. The amino acid attaches to the acceptor stem. The left loop, known as the loop, has a structure identical in all tRNA molecules; it presumably "governs" the binding of tRNA to Ribosomes. Conversely, the right loop, the DHU loop, varies among different tRNA molecules; it is likely involved in selecting the amino acid attached to the acceptor end by an enzyme. Certain nucleotides are bonded to each other by hydrogen bonds (shown by colored lines). The unpaired nucleotides of the third loop (colored region) are called the anticodon. They serve to recognize the mRNA codon. B. The molecule folds to create a three-dimensional structure. This is a photograph of a model.

The base sequences of many types of tRNA have been established. Although these sequences differ, all tRNAs share a similar number of bases and a uniform shape.

The specificity of a tRNA is also determined by its ability to bind to a specific amino acid—the one corresponding to its anticodon. This ability depends on

the action of activating enzymes that recognize specific amino acids and tRNAs. Activating enzymes are key elements in the translation of genetic information; they link each amino acid to its corresponding tRNA.

Ribosomal RNA (rRNA) is found in ribosomes along with specific proteins. A ribosome consists of two subunits, each constructed of specific RNAs and proteins. For example, in Escherichia coli, the small ribosomal subunit contains one type of rRNA, while the large subunit contains two types. mRNA and tRNA come together at the ribosome. Ribosomes presumably position mRNA, tRNA, amino acids, and nascent proteins relative to one another during protein synthesis. Ribosomal proteins are also active; one of them, for instance, Functions as the enzyme that catalyzes peptide bond formation.

In Eukaryotic cells, rRNA is synthesized on the DNA of the nucleolus. Although the ribosomes of these cells are slightly larger than those of E. coli, they possess a similar structure and perform the same functions as bacterial ribosomes.

RNA Transcription from DNA

RNA is transcribed, or copied, from DNA according to THE PRINCIPLE OF complementarity, analogous to The process of DNA replication (Figs. 8-9 and 8-10). Eukaryotic cells contain enzymes called RNA polymerases for the transcription of tRNA, rRNA, and mRNA. Pre-mRNA molecules synthesized on a DNA template in eukaryotic nuclei are 10 to 20 times larger than bacterial mRNA. If eukaryotic RNA is labeled so that radioactive uracil is incorporated into the newly formed molecule for a brief period, the long precursor RNA molecules in The Nucleus exhibit radioactivity. However, only about 10% of this radioactivity is found outside the nucleus, confirming that the bulk of the precursor synthesized in The eukaryotic nucleus plays no role in protein synthesis. The non-coding regions of eukaryotic genes—introns—are transcribed into segments of RNA that never leave the nucleus. The eukaryotic gene sequences that encode the amino acid sequence of a protein are called exons.

Fig. 8-9. A bacterial gene in action. Micrograph (left) showing several mRNA strands being synthesized simultaneously. (In the diagram on the right, the strands are highlighted in color.) The longest strand began synthesis first. As each strand detaches from the active chromosomal fragment (the DNA molecule), ribosomes attach to the mRNA strand and translate it to produce protein. Protein molecules are not visible in the micrograph.

Fig. 8-10. Schematic representation of transcription and translation processes. A. During transcription, a DNA strand serves as a template for the synthesis of a complementary mRNA molecule. B. During translation, Three types of RNA interact with a specific set of enzymes and proteins to form a new polypeptide chain. Ribosomal RNA (rRNA) is a component of the ribosome, which carries out protein synthesis. Bacterial ribosomes contain large (50S) and small (30S) subunits. tRNA ensures the incorporation of the correct amino acids into the growing polypeptide chain. Messenger RNA (mRNA) conveys the information contained in the gene to the ribosome. The information is encoded as a sequence of nucleotide triplets, each encoding a specific amino acid. Each codon is recognized by the complementary anticodon of a tRNA molecule that has previously bound to its corresponding amino acid. In the diagram, Most amino acids are represented by numbered circles; the amino acid Glycine (GLY) has just been "delivered" to the ribosome by its corresponding transfer RNA. Glycine will then be joined by a peptide bond to leucine (LEU), extending the growing chain by one amino acid. Subsequently, the ribosome will shift by the length of an mRNA codon, thereby positioning itself to bind the tRNA carrying Serine (SER).

Following synthesis in the nucleus, long eukaryotic mRNA precursor molecules undergo "Processing". Large fragments of the mRNA precursor, transcribed from introns, are excised from the middle of the molecule by specialized enzymes. The remaining fragments, transcribed from exons, are joined together (splicing) to form the mature eukaryotic mRNA, which is transported from the nucleus into the Cytoplasm. Mature eukaryotic mRNA is virtually identical in size to bacterial mRNA.

Apparently, not only mRNA, but also rRNA and tRNA, are initially transcribed from eukaryotic Chromosomes as large precursor molecules that subsequently undergo highly specific processing. This suggests that eukaryotic genes contain important sequences that are not "related" to the functional mRNA and the resulting synthesized protein, but instead play a different role in gene transcription.

Consequently, the eukaryotic mRNA used for Protein synthesis is actually assembled from fragments of an mRNA precursor transcribed directly from chromosomal DNA. Thus, in both bacteria and eukaryotes, genetic information is transferred from the gene to the mRNA molecule and then to the polypeptide chain (the "central dogma"¹ of genetics). However, in eukaryotes, processing introduces an additional step: gene —> primary transcript —> mRNA —> polypeptide chain.

¹ Nowadays, the once-popular Concept of the "central dogma" can be considered outdated, as it emphasized the unidirectional flow of information from DNA to RNA, whereas in 1970 The phenomenon of reverse transcription was discovered—the synthesis of DNA from RNA using an enzyme present in certain Viruses. Thus, information transfer can proceed both from DNA to RNA and from RNA to DNA. — Transl. note.

mRNA Translation (Protein Synthesis)

During mRNA translation, the codon sequence is read in the 5' — 3' direction, similarly to DNA replication (Fig. 8-10). The initial segment of the mRNA molecule is involved in ribosome binding. In bacteria, the small ribosomal subunit carries a special tRNA (which binds N-formylmethionine) and moves along the mRNA molecule until it "encounters" the AUG codon corresponding to N-formylmethionine; after that, the small ribosomal subunit binds the N-formylmethionine molecule at a specific site on the ribosome, forming the initiation complex. Eukaryotes, in contrast, do not have the protein synthesis-initiating AUG codon; instead, they "use" a chemically modified form of guanine, specifically 7-methylguanosine.

In both bacteria and eukaryotes, the growing end of the protein chain is attached by a tRNA molecule to the ribosome-mRNA complex (Fig. 8-10). The next amino acid, linked to a specific tRNA molecule, enters the complex and attaches via its anticodon to the codon (the next three mRNA bases). The amino group of the incoming amino acid releases a proton to the ribosome and forms a peptide bond with the growing protein chain. As a result, the entire chain is now bound to the newly arrived tRNA-amino acid complex, while the tRNA from which the amino acid has just been removed dissociates. The ribosome continues to move along the mRNA (by one codon at a time) together with the polypeptide chain. At each step, another amino acid is added, and the entire process repeats.

Synthesis of polypeptide chains terminates when the ribosome "encounters" one of the three termination codons: UAA, UAG, or UGA. These so-called nonsense codons do not encode amino acids; their presence leads to the Cleavage of the bond between the final amino acid of the protein and the corresponding tRNA. Protein synthesis then ceases.