Medical brain notes 43

  Basics of Biotechnology ADVENT OF THE BIOTECHNOLOGY REVOLUTION Biotechnology involves the use of living organisms in industrial processes—particularly in agriculture, food processing, and medicine. Biotechnology has been around since the dawn of time, ever since humans began manipulating the natural environment to improve their food supply, housing, and health. Biotechnology is not limited to humankind. Beavers cut up trees to build homes. Elephants deliberately drink fermented fruit to get an alcohol buzz. People have been making wine, beer, cheese, and bread for centuries. All these processes rely on microorganisms to modify the original ingredients (Fig. 1.1). Over the ages, farmers have chosen higher yielding crops by trial and error, so that many modern crop plants have much larger fruit or seeds than their ancestors (Fig. 1.2). The reason we think of biotechnology as modern is because of recent advances in molecular biology and genetic engineering. Huge strides have been ma...

  Gregor Johann Mendel (1822–1884): Founder of Modern Genetics As a young man, Mendel spent his time doing genetics research and teaching math, physics, and Greek to high school children in Brno (now in the Czech Republic). Mendel studied the inheritance of vari-ous traits of the common garden pea, Pisum sativum, because he was able to raise two generations a year. He studied many differ-ent physical traits of the pea, such as flower color, flower position, seed color and shape, and pod color and shape. Mendel grew differ-ent plants next to each other, looking for traits that mixed together. Luckily, the traits he studied were each due to a single gene that was either dominant or recessive, although he did not know this at the time. Consequently, he never saw them “mix.” For example, when he grew yellow peas next to green peas, the offspring looked exactly like their parents. This showed that traits do not blend in the offspring, which was a common theory at the time.   Next M...

  CHEMICAL STRUCTURE OF NUCLEIC ACIDS The upcoming discussions introduce the organisms used extensively in molecular biology and genetics research. Each of these has genes made of DNA that can be manipulated and studied. Thus a discussion of the basic structure of DNA is essential. The genetic information carried by DNA, together with the mechanisms by which it is expressed, unifies every creature on earth and is what determines our identity. Nucleic acids include two related molecules, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA and RNA are polymers of subunits called  nucleotides , and the order of these nucleotides determines the information content. Nucleotides have three components: a  phosphate group , a five-carbon sugar, and a nitrogen-containing  base  (Fig. 1.3). The   five-carbon sugar or  pentose  is different for DNA and RNA. DNA has  deoxyribose , whereas RNA uses  ribose . These two sugars differ by one hyd...

  PACKAGING OF NUCLEIC ACIDS Bacteria have just a few thousand genes, each approximately 1000 nucleotides long. These are carried on a chromosome that is a single giant circular molecule of DNA. A single DNA double helix with this many genes is about 1000 times too long to fit inside a bacterial cell without being condensed somehow in order to take up less space.   In bacteria, the double helix undergoes  supercoiling  to condense it. Supercoiling is induced by the enzyme  DNA gyrase , which twists the DNA in a left-handed direction so that about 200 nucleotides are found in one supercoil. The twisting causes the DNA to condense. Extra supercoils are removed by  topoisomerase I . The supercoiled DNA forms loops that connect to a protein scaffold (see Fig. 1.4). In humans and plants, vastly more DNA must be packaged, so just adding supercoils is not sufficient. Eukaryotic DNA is wound around proteins called  histones  first. Histones have a positiv...

  BACTERIA AS THE WORKHORSES OF BIOTECHNOLOGY DNA is the common thread of life. DNA is found in every living organism on earth (and even in some entities that are not considered living—see later discussion). Only a tiny selection of these organisms has been studied in the molecular biology laboratory. These few generally have special traits or features that make them easy to grow, study, and manipulate genetically. By now, each model organism has had its entire genome sequenced. The model organisms are used both as a guide to understand other related organisms not investigated in detail and for various more practical biotechnological purposes. Bacteria live everywhere on the planet and are an amazing part of the ecosystem. There are an estimated 5  ×  10 30  bacteria on the earth, with about 90% of these living in the soil and the ocean subsurface. If this estimate is accurate, then about 50% of all living matter is microbial. Bacteria have been found in every enviro...

  ESCHERICHIA COLI  IS THE MODEL BACTERIUM Although extreme bacteria are interesting and useful, more typical bacteria are the routine workhorses for research in molecular biology and biotechnology. The most widely used is  Escherichia coli , a rod-shaped bacterium about 1 by 2.5 microns in size.  E. coli  normally inhabits   the colon of mammals including humans (Fig. 1.6).  E. coli  is a gram-negative bacterium that has an outer membrane, a thin cell wall, and a cytoplasmic membrane surrounding the cellular components. Like all prokaryotes,  E. coli  does not have a nucleus or nuclear membrane, and its chromosome is free in the cytoplasm. The outer surface of  E. coli  carries about 10 flagella that and these can be grown in plastic dishes or flasks using culture media containing growth factors and nutrients. Cell lines must be maintained at 37°C and require an atmosphere rich in carbon dioxide.  Adherent cell lines ...

  ARABIDOPSIS THALIANA , A MODEL FLOWERING PLANT The model organism most widely used in plant genetics and molecular biology is the weed  Arabidopsis thaliana , wild mustard weed or mouse ear cress (Fig. 1.22). Plant research has typically lagged behind research on humans, but there is extensive interest. Growing different crops to feed the world population is incredibly important, and much money is invested in research on the crops most used for food, such as rice, soybean, wheat, and corn. These plants have huge genomes, and most are polyploid—even hexaploid (such as wheat). Therefore, a model organism is essential to learn the basic biology of plants.  Arabidopsis has much the same responses to stress and disease as crop plants. Moreover, many genes involved in reproduction and development are homologous to those in plants with more complex genomes. Arabidopsis  has many convenient features. First, it is easily grown and maintained in a   laboratory setting. ...

  VIRUSES USED IN GENETICS RESEARCH Viruses are entities that border on living. But unlike genuine living organisms, viruses cannot survive outside a host organism. Viruses are pathogens that invade host cells and subvert them to manufacture more viruses. Viruses are simple in principle and yet very powerful. They consist of a protein shell called a  capsid  surrounding a genome made of RNA or DNA. The particle is called a  virion  and, unlike a living cell, has no way to make its own energy or duplicate its own genome. The virus relies on the host to do this work. Viruses come in many different types and can inhabit every living thing from bacteria to humans to plants. Viral diseases in humans are extremely common, and most cause only minor symptoms. For example, when rhinovirus invades, the victim ends up with a runny nose and other cold symptoms and usually feels miserable for a few days. However, viruses do cause a significant number of serious diseases, suc...

  SUBVIRAL INFECTIOUS AGENTS AND OTHER GENE CREATURES We have used the term  gene creatures  to refer to various genetic entities that are sometimes called subviral infectious agents. These creatures exist, but are not considered living  because none of them can produce their own energy, duplicate their own genomes, or live independent of a host. The main advantage a virus has over a gene creature is the ability to survive as an inactive particle outside the host cell. Gene creatures are not normally found outside the host cell.   Satellite viruses  are defective viruses. They can either replicate their genome or package their   genome into a capsid, but they are unable to do both by themselves. Satellite viruses rely on a helper virus to supply the missing components or genes. For example, hepatitis delta virus (HDV) is a small single-stranded RNA satellite virus that infects the liver. Its helper is hepatitis B virus. Bacteriophage P4 is a satellite ...