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Like that of nucleic acids, the molecular structure of proteins has several levels of the organization. The primary structure of a protein is its sequence of amino acids. Through interactions between neighboring amino acids, a polypeptide chain folds and twists into a secondary structure. Two common secondary structures found in proteins are the beta (β) pleated sheet and the alpha (α) helix. Secondary structures interact and fold further to form a tertiary structure, which is the overall, three-dimensional shape of the protein. The secondary and tertiary structures of a protein are largely determined by the primary structure—the amino acid sequence—of the protein. Finally, some proteins consist of two or more polypeptide chains that associate to produce a quaternary structure. Many proteins have an additional level of organization defined by domains. A domain is a group of amino acids that forms a discrete functional unit within the protein. For example, there are several different types of protein domains that function in DNA binding.

Proteins are central to all living processes. Many proteins are enzymes, the biological catalysts that drive the chemical reactions of the cell; others are structural components, providing scaffolding and support for membranes, filaments, bone, and hair. Some proteins help transport substances; others have a regulatory, communication, or defense function. All proteins are polymers composed of amino acids linked end to end. Twenty common amino acids are found in proteins. All of the common amino acids are similar in structure: each consists of a central carbon atom bonded to an amino group, a hydrogen atom, a carboxyl group, and an R (radical) group that differs for each amino acid.

Introns are common in eukaryotic genes but are rare in bacterial genes. For a number of years after their discovery, introns were thought to be entirely absent from prokaryotic genomes, but they have now been observed in archaea, bacteriophages, and even some bacteria. Introns are present in mitochondrial and chloroplast genes as well as the nuclear genes of eukaryotes. Among eukaryotic genomes, the sizes and numbers of introns appear to be directly related to organismal complexity: yeast genes contain only a few short introns, Drosophila introns are longer and more numerous, and most vertebrate genes are interrupted by long introns. All classes of eukaryotic genes—those that encode rRNA, tRNA, and proteins—may contain introns. The numbers and sizes of introns vary widely: some eukaryotic genes have no introns, whereas others may have more than 60; intron length varies from fewer than 200 nucleotides to more than 50,000. Introns tend to be longer than exons, and most eukaryotic genes contain more noncoding nucleotides than coding nucleotides. Finally, most introns do not encode proteins: an intron of one gene is not usually an exon for a different gene.

Early work on gene structure was carried out largely through the examination of mutations in bacteria and viruses. This research led Francis Crick to propose in 1958 that genes and proteins are colinear, that there is a direct correspondence between the nucleotide sequence of DNA and the amino acid sequence of a protein. The concept of colinearity suggests that the number of nucleotides in a gene should be proportional to the number of amino acids in the protein encoded by that gene. In a general sense, this concept is true for genes found in bacterial cells and in many viruses, although these genes are slightly longer than would be expected if colinearity were strictly applied because the mRNAs encoded by the genes contain sequences at their ends that do not specify amino acids. At first, eukaryotic genes and proteins were also assumed to be colinear, but there were hints that eukaryotic gene structure is fundamentally different. Eukaryotic cells were found to contain far more DNA than is required to encode proteins. Furthermore, many large RNA molecules observed in the nucleus were absent from the cytoplasm, suggesting that nuclear RNAs undergo some type of change before they are exported to the cytoplasm.

The ribosome is one of the most abundant molecular complexes in the cell: a single bacterial cell may contain as many as 20,000 ribosomes, and eukaryotic cells possess even more. Ribosomes typically contain about 80% of the total cellular RNA. They are complex structures, each consisting of more than 50 different proteins and RNA molecules. A functional ribosome consists of two subunits, a large ribosomal subunit, and a small ribosomal subunit, each of which consists of one or more RNA molecules and a number of proteins. The sizes of the ribosomes and their RNA components are given in Svedberg (S) units (a measure of how rapidly an object sediments in a centrifugal field). (It is important to note that S units are not additive: combining a 10S structure and a 20S structure does not necessarily produce a 30S structure because the sedimentation rate is affected by the three-dimensional structure of an object as well as by its mass). The three-dimensional structure of the bacterial ribosome has been elucidated in great detail through X-ray crystallography.

The first clue that eukaryotic DNA contains several types of sequences not present in prokaryotic DNA came from studies in which double-stranded DNA was separated and then allowed to reassociate. When double-stranded DNA in solution is heated, the hydrogen bonds that hold the two nucleotide strands together are weakened, and with enough heat, the two strands separate completely, a process called denaturation or melting. The temperature at which DNA denatures, called the melting temperature (Tm), depends on the base sequence of the particular sample of DNA: G–C base pairs have three hydrogen bonds, whereas A–T base pairs have only two, so the separation of G–C pairs requires more heat (energy) than does the separation of A–T pairs. The denaturation of DNA by heating is reversible: if single-stranded DNA is slowly cooled, single strands will collide and hydrogen bonds will form again between complementary base pairs, producing double-stranded DNA. This reaction is called renaturation or reannealing.

Eukaryotic organisms vary dramatically in the amount of DNA per cell, a quantity termed an organism’s C-value. Each cell of a fruit fly, for example, contains 35 times the amount of DNA found in a cell of the bacterium E. coli. In general, eukaryotic cells contain more DNA than prokaryotic cells do, but variation among eukaryotes in their C-values is huge. Human cells contain more than 10 times the amount of DNA found in Drosophila cells, whereas some salamander cells contain 20 times as much DNA as human cells. Clearly, these differences in C-value cannot be explained simply by differences in organismal complexity. So what is all the extra DNA in eukaryotic cells doing? This question has been termed the C-value paradox. We do not yet have a complete answer to the C-value paradox, but analysis of eukaryotic DNA sequences has revealed a complexity that is absent from prokaryotic DNA.

An initial step in identifying DNA as the source of genetic information came with the discovery of a phenomenon called transformation. This phenomenon was first observed in 1928 by Fred Griffith, an English physician whose special interest was the bacterium that causes pneumonia: Streptococcus pneumoniae. Griffith had succeeded in isolating several different strains of S. pneumoniae (type I, II, III, and so forth). In the virulent (disease-causing) forms of a strain, each bacterium is surrounded by a polysaccharide coat, which makes the bacterial colony appear smooth (S) when grown on an agar plate. Griffith found that these virulent forms occasionally mutated to nonvirulent forms, which lack a polysaccharide coat and produce a rough-appearing colony (R).

All cellular RNAs are synthesized from DNA templates through the process of transcription. Transcription is in many ways similar to the process of replication, but a fundamental difference relates to the length of the template used. In replication, all the nucleotides in the DNA molecule are copied, but in transcription, only parts of the DNA molecule are transcribed into RNA. Because not all gene products are needed at the same time or in the same cell, the constant transcription of all of a cell’s genes would be highly inefficient. Furthermore, much of the DNA does not encode any functional product, and transcription of such sequences would be pointless. Transcription is, in fact, a highly selective process: individual genes are transcribed only as their products are needed. However, this selectivity imposes a fundamental problem on the cell: how to recognize individual genes and transcribe them at the proper time and place.

Rifamycins are a group of antibiotics that kill bacterial cells by inhibiting RNA polymerase. These antibiotics are widely used to treat tuberculosis, a disease that kills almost 2 million people worldwide each year. The structures of bacterial and eukaryotic RNA polymerases are sufficiently different that rifamycins can inhibit bacterial RNA polymerases without interfering with eukaryotic RNA polymerases. Recent research has demonstrated that several rifamycins work by binding to the part of the bacterial RNA polymerase that clamps onto DNA and jamming it, thus preventing the RNA polymerase from interacting with the promoter on the DNA.