1. MICROBIOLOGY AYDIN ÇÖL Viruses and Bacteria

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3. 5 min What we have learnt? QUESTIONS? (ABOUT 10) 4/43/42/4 1/4

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5. Microbiology is the study of microorganisms, a large and diverse group of organisms that exist as single cells or cell clusters. Microbial cells are thus distinct from the cells of animals and plants, which are unable to live alone in nature but can exist only as parts of multicellular organisms.

6. A single microbial cell is generally able to carry out its life processes of growth, energy generation, and reproduction independently of other cells, either of the same kind or of different kinds. Microbiology is a basic biological science. An understanding of the biology of higher organisms, including even humans, depends on a thorough knowledge of microbiology.

7. Microbiology is concerned with: living cells and how they work microorganisms, an important class of cells capable of free-living existence microbial diversity what microbes do, in the world at large, in human society, in our own bodies, as well as in the bodies of animals and plants.

8. A BRIEF HISTORY OF MICROBIOLOGY Development of microscopy: 1590: Hans and Zacharias Janssen (Dutch lens grinders) mounted two lenses in a tube to produce the first compound microscope. 1660: Robert Hooke (1635-1703) published Micrographia, containing drawings and detailed observations of biological materials made with the best compound microscope and illumination system of the time.

9. 1836: Theodor Schwann (1810-1882) helped develop the cell theory of living organisms, namely that all living organisms are composed of one or more cells and that the cell is the basic functional unit of living organisms. Development of microscopy: 1676: Anton van Leeuwenhoek (1632-1723) was the first person to observe microorganisms.

10. Proof that microbes cause disease 1857: Louis Pasteur proposed the “germ theory” of disease. 1861: Louis Pasteur’s (1822-1895) famous experiments with swan-necked flasks finally proved that microorganisms do not arise by spontaneous generation. This eventually led to: Development of sterilization Development of aseptic technique

11. 1876: Robert Koch (1843-1910). German bacteriologist was the first to cultivate anthrax bacteria outside the body using blood serum at body temperature. Building on Pasteur's “germ theory”, he subsequently published “Koch’s postulates” (1884), the critical test for the involvement of a microorganism

12. in a disease: 1. The agent must be present in every case of the disease. 2. The agent must be isolated and cultured in vitro. 3. The disease must be reproduced when a pure culture of the agent is inoculated into a susceptible host. 4. The agent must be recoverable from the experimentally-infected host.

13. The involvement of a microorganism in a disease eventually led to development of: pure culture techniques Stains, Agar, Culture media, Petri dishes 1931: Ernst Ruska constructed the first electron microscope.

14. WHY IS MICROBIOLOGY IMPORTANT? 1. Disease: Since the discovery of infectious microbes, most infectious diseases are controlled by; sanitation, preventive medicine, and chemotherapy. 2. Agriculture: Microbes are vital in processing materials in soil, e.g. nitrogen, sulfur, etc. 3. Food and drink: Microbial fermentation is responsible for all alcoholic beverages, breads, pickles, cheeses, etc. Control of food and drink spoilage is a major concern of the food industry.

15. 4. Chemical products: Microbes have an incredible variety of metabolic tricks, and can be used to produce acetone and other commercial solvents, pharmaceuticals, antibiotics, preservatives, etc. 5. Basic research: Microbes grow fast and produce enormous numbers of offspring. It is easy to find events that occur only 1 in a billion times if in has100 billion bacteria in a test tube. Crucial to modern biology. 6. Biotechnology: E.g. genetic engineering, ability to move genes freely from one organism to another, select genes of interest and amplify their expression. Bacteria are natural hosts for such activities.

16. There are 4 basic groups of microbes: a. Viruses b. Monera c. Protista d. Fungi Section 1 Viruses Section 2 Bacteria Table of Contents

17. Is a Virus Alive? All living things are made of cells, are able to grow and reproduce, and are guided by information stored in their DNA. Viruses are segments of nucleic acids contained in a protein coat. Viruses are not cells. Viruses are pathogens—agents that cause disease. Viruses do not grow, do not have homeostasis, and do not metabolize.

18. Virus

19. Pathogen

20. Is a Virus Alive?, continued Discovery of Viruses Near the end of the nineteenth century, scientists were trying to find the cause of tobacco mosaic disease, which stunts the growth of tobacco plants. In 1935, biologist Wendell Stanley of the Rockefeller Institute purified tobacco mosaic virus (TMV) and determined that the purified virus is a crystal. Stanley concluded that TMV is a chemical rather than an organism.

21. Viral Structure The virus protein coat, or capsid, may contain either RNA or DNA, but not both. Many viruses have a membrane, or envelope, surrounding the capsid. The envelope helps the virus enter cells. It consists of proteins, lipids, and glycoproteins, which are proteins with attached carbohydrate molecules that are derived from the host cell.

22. Parts of a Virus

23. Viral Structure, continued Some viruses are long rods that form filaments. Spherical viruses are typically studded with receptors. A helical virus is rodlike in appearance, with capsid proteins winding around the core in a spiral. Viruses that infect bacteria, called bacteriophages, have a complicated structure. A T4 bacteriophage, for example, has a polyhedron capsid attached to a helical tail.

24. Structures of TMV and Influenza Virus

25. Structures of Adenovirus and Bacteriophage

26. Bacteriophage

27. Viral Reproduction Viruses must rely on living cells (host cells) for replication. Before a virus can replicate, it must first infect a living cell. An animal virus enters its host cell by endocytosis. A bacterial virus, or bacteriophage, punches a hole in the bacterial cell wall and injects its DNA into the cell.

28. Viral Reproduction, continued Lytic Cycle In bacterial viruses, the cycle of viral infection, replication, and cell destruction is called the lytic cycle. After the viral genes have entered the cell, they use the host cell to replicate viral genes and to make viral proteins, such as capsids. The proteins are then assembled with the replicated viral genes to form complete viruses. The host cell is broken open and releases newly made viruses.

29. Lytic Cycle

30. Viral Reproduction, continued Lysogenic Cycle During an infection, some viruses stay inside the cells but instead of producing virus particles, the viral gene is inserted into the host chromosome and is called a provirus. Whenever the cell divides, the provirus also divides, resulting in two infected host cells. In this cycle, called the lysogenic cycle, the viral genome replicates without destroying the host cell.

31. Prophages and Proviruses

32. Lysogenic Cycle

33. Viral Replication in Bacteria

34. Relationships between the Lytic and Lysogenic Cycles

35. Viral Reproduction, continued Host Cell Specificity Viruses are often restricted to certain kinds of cells. Viruses may have originated when fragments of host genes escaped or were expelled from cells. The hypothesis that viruses originated from a variety of host cells may explain why there are so many different kinds of viruses. Biologists think there are at least as many kinds of viruses as there are kinds of organisms.

36. Viral Reproduction, continued Structure of HIV—an Enveloped Virus The human immunodeficiency virus (HIV) causes acquired immune deficiency syndrome (AIDS). Within HIV’s envelope lies the capsid, which in turn encloses the virus’s genetic material. In the case of HIV, the genetic material is composed of two molecules of single-stranded RNA.

37. How HIV Infects Cells Attachment Studding the surface of each HIV are spikes composed of a glycoprotein. This particular glycoprotein precisely fits a human cell surface receptor called CD4. Thus the HIV glycoprotein can bind to any cell that possesses CD4 receptors.

38. How HIV Infects Cells, continued Entry into Macrophages HIV cannot enter a cell merely by docking onto a CD4 receptor. Rather, the glycoprotein must also activate a second co-receptor, called CCR5. It is this event at CCR5 that starts endocytosis. Because human macrophages possess both CD4 and CCR5 receptors, HIV can enter macrophages.

39. How HIV Infects Cells, continued Replication Once inside a cell, the HIV particle sheds its capsid. The particle then releases an enzyme called reverse transcriptase. Reverse transcriptase copies the naked viral RNA into a complementary DNA version. Translation of the viral DNA by the host cell’s machinery directs the production of many copies of the virus.

40. Infection of Macrophage by HIV

41. How HIV Infects Cells, continued AIDS For years after the initial infection, HIV continues to replicate (and mutate). Eventually and by chance, HIV’s surface glycoproteins change to the point that they now recognize a new cell surface receptor. This receptor is found on the subset of lymphocytes called T cells. Unlike its activity in macrophages, HIV reproduces in T cells and then destroys them. It is this destruction of the body’s T cells that blocks the body’s immune response and signals the onset of AIDS.

42. AIDS (Acquired Immune Deficiency Syndrome)

43. Viral Diseases Perhaps the most lethal virus in human history is the influenza virus. Certain viruses can also cause some types of cancer. Viruses associated with human cancers include hepatitis B (liver cancer), Epstein-Barr virus (Burkitt’s lymphoma), and human papilloma virus (cervical cancer).

44. Important Viral Diseases

45. Viral Diseases, continued Emerging Viruses Viruses that evolve in geographically isolated areas and are pathogenic to humans are called emerging viruses. These new pathogens are dangerous to public health. People become infected when they have contact with the normal hosts of these viruses. Examples of emerging viruses include West Nile virus and hantavirus.

46. Viral Diseases, continued Prions and Viroids Prions are composed of proteins but have no nucleic acid. A disease-causing prion is folded into a shape that does not allow the prion to function. Contact with a misfolded prion will cause a normal prion to misfold, too. In this way the misfolding spreads. A viroid is a single strand of RNA that has no capsid. Viroids are important infectious disease agents in plants.

47. Objectives List seven differences between bacteria and eukaryotic cells. Describe three different ways bacteria can obtain energy. Describe the external and internal structure of Escherichia coli. Distinguish two ways that bacteria cause disease. Identify three ways that bacteria benefit humans.

48. Bacteria

49. Characteristics of Bacteria

50. Bacterial Structure Bacteria differ from eukaryotes in at least seven ways. Bacteria are prokaryotes. Unlike eukaryotes, prokaryotes lack a cell nucleus. Most bacterial cells are about 1 µm in diameter; most eukaryotic cells are more than 10 times that size.

51. Bacterial Structure, continued All bacteria are single cells. Bacterial chromosomes consist of a single circular piece of DNA. Eukaryotic chromosomes are linear pieces of DNA that are associated with proteins. Bacteria reproduce by binary fission, a process in which one cell pinches into two cells.

52. Bacterial Structure, continued Bacterial flagella are simple structures composed of a single fiber of protein that spins like a corkscrew to move the cell. Some bacteria also have shorter, thicker outgrowths called pili. Bacteria have many metabolic abilities that eukaryotes lack. For example, bacteria perform several different kinds of anaerobic and aerobic processes, while eukaryotes are mostly aerobic organisms.

53. Structure of Cilia and Flagella

54. Pilus

55. Structural Characteristics of a Bacterial Cell

56. Parts of a Prokaryotic Cell

57. Comparing Organisms That Are Unicellular and Multicellular

58. Bacterial Cell Shapes A bacterial cell is usually one of three basic shapes: bacillus, a rod-shaped cell; coccus, a round-shaped cell; or spirillum, a spiral cell. Members of the kingdom Eubacteria have a cell wall made of peptidoglycan, a network of polysaccharide molecules linked together with chains of amino acids. Outside the cell wall and membrane, many bacteria have a gel-like layer called a capsule.

59. Three Bacterial Cell Shapes

60. Bacterial Capsule

61. Bacterial Cell Shapes, continued Eubacteria can have two types of cell walls, distinguished by a dye staining technique called the Gram stain. Gram staining is important in medicine because the two groups of eubacteria differ in their susceptibility to different antibiotics. Antibiotics are chemicals that interfere with life processes in bacteria.

62. Gram Staining

63. Gram Stain

64. Bacterial Cell Shapes, continued Some bacteria form thick-walled endospores around their chromosomes and a small bit of cytoplasm when they are exposed to harsh conditions. Pili enable bacteria to adhere to the surface of sources of nutrition, such as your skin. Some kinds of pili enable bacteria to exchange genetic material through a process called conjugation. Conjugation is a process in which two organisms exchange genetic material.

65. Conjugation

66. Escherichia coli

67. Obtaining Energy Photosynthesis Photosynthetic bacteria can be classified into four major groups based on the photosynthetic pigments they contain: purple nonsulfur bacteria, green sulfur bacteria, purple sulfur bacteria, and cyanobacteria. Green sulfur bacteria and purple sulfur bacteria grow in anaerobic environments. Cyanobacteria are thought to have made the Earth’s oxygen atmosphere.

68. Obtaining Energy, continued Chemoautotrophs Bacteria called chemoautotrophs obtain energy by removing electrons from inorganic molecules such as ammonia and hydrogen sulfide or from organic molecules such as methane. In the presence of one of these hydrogen-rich chemicals, chemoautotrophic bacteria can manufacture all their own amino acids and proteins.

69. Chemoautotroph

70. Obtaining Energy, continued Heterotrophs Most bacteria are heterotrophs. Many are aerobic, that is, they live in the presence of oxygen. Some other bacteria can live without oxygen. Together with fungi, heterotrophic bacteria are the principal decomposers of the living world; they break down the bodies of dead organisms and make the nutrients available to other organisms.

71. Pathogenic Bacteria Bacteria Can Metabolize Their Host Heterotrophic bacteria obtain nutrients by secreting enzymes that break down complex organic structures in their environment and then absorbing them. If that environment is your throat or lungs, this can cause serious problems. Several common bacterial diseases include dental cavities, strep throat, tuberculosis, and acne.

72. Important Bacterial Diseases

73. Pathogenic Bacteria, continued Bacterial Toxins The second way bacteria cause disease is by secreting chemical compounds into their environment. These chemicals, called toxins, are poisonous to eukaryotic cells. When bacteria grow in food and produce toxins, the toxins can cause illness in humans who eat those contaminated foods. Most bacteria can be killed by boiling water or various chemicals.

74. Pathogenic Bacteria, continued Biowarfare Biowarfare is the deliberate exposure of people to biological toxins or pathogens such as bacteria or viruses. Biologists are working on new approaches to recognize the onset of an attack with a bioweapon, to treat infected people, and to slow the spread of any outbreak of disease.

75. Antibiotics In 1928, the British bacteriologist Alexander Fleming discovered the antibiotic penicillin. Today different antibiotics are used to interfere with different cellular processes. Because these processes do not occur in viruses, antibiotics are not effective against them.

76. Antibiotics, continued Antibiotic-Resistant Bacteria Some bacteria have become resistant to antibiotics. Susceptible bacteria are eliminated from the population, and resistant bacteria survive and reproduce, thus passing on their resistance traits. Usually, if the full course of the antibiotic is administered, all the targeted bacteria are killed and there is no chance for a resistant strain to develop. If antibiotic treatment ends prematurely, some of the more-resistant bacteria may survive and reproduce.

77. Importance of Bacteria Food and Chemical Production Many of the foods that we eat, such as pickles, cheese, sauerkraut, olives, vinegar, and sourdough bread, are processed by specific kinds of bacteria. Humans are able to use different bacteria to produce different kinds of chemicals for industrial uses. Genetic engineering companies use genetically engineered bacteria to produce their many products, such as drugs for medicine and complex chemicals for research.

78. Bacteria and Food

79. Importance of Bacteria, continued Mining and Environmental Uses of Bacteria Mining companies can use bacteria to concentrate desired elements from low-grade ore. Bacteria metabolize different organic chemicals and are therefore used to help clean up environmental disasters such as petroleum and chemical spills. Powders containing petroleum-metabolizing bacteria are used to help clean oil spills. Mining and Environmental Uses of Bacteria Mining companies can use bacteria to concentrate desired elements from low-grade ore. Bacteria metabolize different organic chemicals and are therefore used to help clean up environmental disasters such as petroleum and chemical spills. Powders containing petroleum-metabolizing bacteria are used to help clean oil spills.

80. QUESTIONS?

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