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Understanding Genetics - Dna Codes For Proteins

amino mrna acids figure

From the perspective of genetics, the DNA molecule has two major attributes. The first is that it is able to replicate—to make an exact copy of itself that can be passed to another cell, thereby conveying its precise genetic characteristics. Figure 2.1 is a diagram that shows how DNA replication produces two completely new and identical daughter strands of DNA. The second critical attribute is that it stores detailed instructions to manufacture specific proteins—molecules that are essential to every aspect of life. DNA is a blueprint or template for making proteins, and much of the behavior and physiology (life processes and functions) of a living organism depends on the repertoire of proteins its DNA molecules know how to manufacture.

The function of DNA depends on its structure. The double strand of DNA is composed of individual building blocks called nucleotides that are paired and connected by chemical bonds. A nucleotide contains one of four nitrogenous bases: the purines (nitrogenous bases with two rings) adenine (A) and guanine (G), or the pyrimidines (nitrogenous bases with one ring; pyrimidines are smaller than purines) cytosine (C) and thymine (T). The two strands of DNA lie side by side to create a predictable sequence of nitrogenous base pairs. (See Figure 2.2.) A stable DNA structure is formed when the two strands are a constant distance apart, which can occur only when a purine (A or G) on one strand is paired with a pyrimidine (T or C) on the other strand. A can only pair with T, and G can only pair with C.

Proteins are molecules that perform all the chemical reactions necessary for life and provide structure and shape to cells. The properties of each protein depend primarily on its shape, which is determined by the sequence of its building blocks, known as amino acids. Proteins may be tough like collagen, the most abundant protein in the human body, or they may be stretchy like elastin, a protein that mixes with collagen to make softer, more flexible tissues such as skin. Figure 2.3 shows the shapes of four types of protein structures.

DNA replication.
DNA Replication Argosy Publishing, Thomson Gale.

Proteins can act as structural components, building the tissues of the body. For example, some of the proteins in an egg include a bond that acts like an axle, allowing other parts of the molecule to spin around like wheels. But when the egg is heated, these bonds break or "denature," locking the "wheels" of the molecule in place. This is why an egg gets hard when you cook it.

Enzymes such as lactase, which helps in the digestion of lactose (milk sugar), and hormones such as insulin (a hormone that regulates carbohydrate metabolism by controlling blood sugar levels) are proteins that act to facilitate and direct chemical reactions. Defense proteins, which are able to combat invasion by bacteria or viruses, are embedded in the walls of cells and act as channels, determining which substances to let into the cell and which to block. Some bacteria know how to make proteins that protect them from antibiotics (substances such as penicillin and streptomycin that inhibit the growth of or destroy microorganisms), while the human immune system can make proteins that target bacteria or other germs FIGURE 2.2
Deoxyribonucleic acid (DNA)
SOURCE: "Deoxyribonucleic Acid (DNA)" in Talking Glossary of Genetic Terms, U.S. Department of Health and Human Services, National Institutes of Health, National Human Genome Research Institute, February 3, 2005)
for destruction. Many essential biological processes depend on the highly specific functions of proteins.

Proteins and Amino Acids

All proteins are composed of building blocks called amino acids. (See Figure 2.4.) There are twenty different kinds of amino acids, and each has a slightly different chemical composition. The structure and function of each protein depends on its amino acid sequence—in a protein containing a hundred amino acids, a change in a single one may dramatically affect the function of the protein. Amino acids are small molecular groups that act like FIGURE 2.3
SOURCE: "Protein," in Talking Glossary of Genetic Terms, U.S. Department of Health and Human Services, National Institutes of Health, National Human Genome Research Institute, February 3, 2005)
jigsaw puzzle pieces, linking together in a chain to make up the protein. Each amino acid links to its neighbor with a special kind of covalent bond (covalent bonds hold atoms together) called a peptide bond. Many amino acids link together, side by side, to make a protein. Figure 2.5 is a diagram of a protein structure. Proteins range in length from fifty to five hundred amino acids, linked head to tail.

In addition to its ability to form a peptide bond to its neighbor, amino acids also contain molecular appendages called side groups. Depending on the particular atomic arrangement of the side group, neighboring amino acids experience different pushes and pulls as they attract or repel one another. The combination of the side-by-side peptide bond linking the amino acids into a chain, along with the extra influences of the side groups, "twists" a protein into a specific shape. This shape is called the protein's conformation, which determines how the protein interacts with other molecules.

Amino acid
SOURCE: "Amino Acid," in Talking Glossary of Genetic Terms, U.S. Department of Health and Human Services, National Institutes of Health, National Human Genome Research Institute, February 3, 2005)

Schematic diagram of protein primary structure
SOURCE: "Schematic diagram of protein primary structure. Amino acids are linked head to tail, so that at one end there is a free amino group, and at the other a free carboxyl group. Proteins are typically 50–500 amino acids in length," in Genetics, vol. 3, K–P, Macmillan Reference USA, Gale Group, 2002

Genes and Proteins

Along the length of a DNA molecule there are regions that hold the instructions to manufacture specific proteins—a specific sequence of amino acids linked side by side. These regions are called protein-encoding genes and are an essential element of our modern understanding of genetics. Like a jukebox that holds a hundred songs but only plays the one you select at any given time, a DNA molecule can contain anywhere from a dozen to several thousand of these protein-encoding genes. However, as with the jukebox, at any given time only some of these genes will be "expressed"; that is, switched on to actively produce the protein they know how to make.

The protein-synthesizing instructions present in DNA are interpreted and acted on by ribonucleic acid (RNA). RNA, as its name suggests, is similar to DNA, except that the sugar in RNA is ribose (instead of deoxyribose), the base uracil (U) replaces thymine (T), and RNA molecules are usually single-stranded and shorter than DNA molecules. (See Figure 2.6.) RNA is used to transcribe and translate the genetic code contained in DNA. Transcription is the process by which a molecule of messenger RNA (mRNA) is made, and translation is the synthesis of a protein using mRNA code. Figure 2.7 shows transcription of mRNA and how mRNA is involved in protein synthesis (translation).

Genetic Synthesis of Proteins

How does a gene make a protein? The process of protein synthesis is quite complex. This overview describes the basic sequence of protein synthesis, which includes the following steps:

  1. A gene is triggered for expression—to synthesize a protein.
  2. Half of the gene is copied into a single strand of mRNA in a process called transcription.
  3. The mRNA anchors to a ribosome, an organelle (or membrane-bound cell compartment) where protein synthesis occurs.
  4. Each sequence of three bases on the mRNA, called a codon, uses the right type of transfer RNA (tRNA) to pick up a corresponding amino acid from the cell. (See Figure 2.8.)
  5. A string of amino acids is assembled on the ribosome, side by side, in the same order as the codons of the mRNA, which, in turn, correspond to the sequence of bases from the original DNA molecule in a process called translation.
  6. When the codons have all been read and the entire sequence of amino acids has been assembled, the protein is released to twist into its final form.

First, the DNA molecule receives a trigger telling it to express a particular gene. Many influences may trigger gene expression including chemical signals from hormones and energetic signals from light or other electromagnetic energy. For example, the spiral backbone of the DNA molecule can actually carry pulsed electrical signals that participate in activating gene expression.

Once a gene has been triggered for expression, a special enzyme system causes the DNA's double spiral to spring apart between the beginning and end of the gene sequence. The process is similar to a zipper with teeth that remain connected above and below a certain area, but pop open to create a gap along part of the zipper's length. At this point, the DNA base pairs that make up the gene sequence are separated. DNA replication is based on the understanding that any exposed nucleotide thymine (T) will pick up an adenine (A) and vice versa, while an exposed cytosine (C) will connect to an available guanine (G) and vice versa. Here the same process takes place except that instead of unzipping and copying the entire length of the FIGURE 2.6
Ribonucleic acid (RNA)
SOURCE: "Ribonucleic Acid (RNA)," in Talking Glossary of Genetic Terms, U.S. Department of Health and Human Services, National Institutes of Health, National Human Genome Research Institute, February 3, 2005)
DNA molecule, only the region between the beginning and end of the gene is copied. And instead of making a new double spiral, only one side of the gene is replicated, creating a special, single strand of bases called mRNA.

Once the mRNA has made a copy of one side of the gene, it separates from the DNA molecule. The DNA returns to its original state and the mRNA molecule breaks away, eventually connecting to an organelle in the cell called a ribosome. (Figure 2.9 is a drawing of a ribosome.) Here it anchors to another type of RNA called ribosomal RNA (rRNA). This is where the actual protein synthesis takes place. Using a special genetic coding system, each sequence of three bases on the mRNA copied from the gene is used to "catch" a corresponding amino acid floating inside the cell. These sequences of three bases are the codons, and they link to tRNA. A different form of tRNA is used to catch each different type of amino acid. The tRNA then catches the appropriate amino acid.

One after another, the mRNA's codons cause the corresponding tRNAs to be captured and linked, side by FIGURE 2.7
SOURCE: "mRNA," in Talking Glossary of Genetic Terms, U.S. Department of Health and Human Services, National Institutes of Health, National Human Genome Research Institute, February 3, 2005)
side, using the peptide bonds to connect them. When the last codon has been read and the entire peptide sequence is complete, the newly formed protein molecule is released from the ribosome. When this happens, all the side groups are able to interact, twisting the protein into its final shape. In this way, a protein-encoding gene is able to manufacture a protein from a series of DNA bases.

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