MODULE BM.2014.Studentfile

BIOLOGY OF MICROBES

MODULE: MICROBIOLOGY

Contributor Modul :Prof. Dr. dr. Sanarto Santoso, DTM&H., Sp.MK (K)

dr. Roekistiningsih, MS, Sp.MK(K)dr. Dewi Santosaningsih, M.Kes

Dr. dr. Dwi Yuni Nur Hidayati, M.Kes

Tutor :Prof. Dr. dr. Sanarto Santoso, DTM&H., Sp.MK(K)Prof. Dr. dr. Noorhamdani AS, DMM., Sp.MK(K)

Prof. Dr. dr. Sumarno, DMM., Sp.MK(K)dr.Roekistiningsih, MS, Sp.MK(K)Dr. dra. Sri Winarsih, Apt., M.Si

Dr. dr. Dwi Yuni Nur Hidayati, M.Kes

FOR STUDENT

LABORATORY OF MICROBIOLOGYMEDICAL FACULTY

BRAWIJAYA UNIVERSITY2014

BIOLOGY OF MICROBES

MODULE 1 MICROBIOLOGY

Sub-module :Basic Bacteriology

FOR STUDENT



Student’s Work Book : Biology of Microbes (2014) Page 1

Sub-module: Introduction, classification, morphology and ultrastructure

Part A: The microbial world Part B: Classification of microorganismsPart C: Microbial morphology and ultrastructure

Direction:The module-task should be written, done by the student individually prior before the small group discussion. To work with the module, the student may refer to the references as mentioned in the last part of this book.


Part A The Microbial World

OverviewFor many people, the words germ, microbe, and microorganism bring to mind a

group of tiny creatures that do no quite fit any of the categories in that old question, “Is it animal, vegetable, or mineral?” Microorganisms are minute living things that individually are too small to be seen with the naked eye. The group includes bacteria, fungi, protozoa, and microscopic algae. It also includes viruses, those noncellular entities sometimes regarded as being at the border of life and nonlife.

We tend to associate these small organisms only with uncomfortable infections. However the majority of microorganisms make crucial contributions to the welfare of the world’s inhabitants by helping to maintain the balance of living organisms and chemicals in our environment.

Today we understand that microorganisms are found almost everywhere. Yet not long ago, before the invention of the microscope, microbes were unknown to scientists. Thousands of people died in devastating epidemics, the causes of which were not understood. Food spoilage often could not be controlled, and entire families died because vaccinations and antibiotics were not available to fight infections.

We can get an idea of how our current concepts of microbiology developed by looking at a few of the historic milestones in microbiology that have changed our lives. Now that we have generally examined how microbes relate to our everyday lives, we will take a look at how the field of microbiology developed from its beginning hundreds of years ago to its current high-technology state.

Learning objectives1. List several ways in which microbes affect our lives.2. Explain the importance of observations made by Hooke and van

Leeuwenhoek.3. Compare the theories of spontaneous generation and biogenesis.4. Identify the contributions to microbiology made by Pasteur.5. Identify the importance of Koch’s Postulates.

Module task1.Briefly state the role played by microorganisms in each of the following :

a. Normal microbiotab. Human insulin productionc. Vaccine production

Jelaskan peran mikroorganisme dalam hal di bawah ini :a. Flora normalb. Produksi insulin manusiac. Produksi vaksin

2.Explain the importance of observations made by Robert Hooke. Jelaskan arti penting penemuan Robert Hooke.


3.Explain the importance of observations made by van Leeuwenhoek. Jelaskan arti penting penemuan van Leeuwenhoek.

4.How did the idea of spontaneous generation come about?Bagaimana asal mula munculnya ide teori spontaneous generation?

5.How did the theory of biogenesis lead the way for the germ theory of disease?Bagaimana teori biogenesis memulai munculnya the germ theory of disease?

6.Explain the contributions to microbiology made by Louis Pasteur. Jelaskan kontribusi Louis Pasteur untuk mikrobiologi.

7.Briefly state about Koch’s postulates. What is the importance of Koch’s postulates?Jelaskan mengenai postulat Koch. Apa arti penting dari postulat Koch?


Part BClassification of Microorganisms

OverviewThe science of classification, especially the classification of living forms, is

called taxonomy, from the Greek words for law and order. The objective of taxonomy is to classify living organisms-that is, to establish the relationship between one group of organisms and another and to differentiate between them. A taxonomic system enables us to classify organisms that have not yet been studied in detail; that is, a previously unknown organism can be identified and then grouped or classified with other organisms that have similar characteristics.

Taxonomy also provides a common reference for identifying organisms already classified. For example, when a bacterium suspected of causing a specific disease is isolated from a patient, characteristics of that isolate are matched to lists of characteristics of previously classified bacteria to identify the isolate. After the bacterium has been identified, drugs can be selected that affect that bacterium.

Finally, taxonomy is a basic and necessary tool for scientists, as it provides a universal language of communication. Modern taxonomy is an exciting and dynamic field; new techniques in molecular biology and genetics are providing new insights into classification and evolution.

Learning objectives1. Define taxonomy2. List the characteristics of the Kingdom Procaryotes that differentiate it from

other kingdoms.3. List the major characteristics used to differentiate among kingdoms in the

five-kingdom system

Module task :1.List and define the five kingdoms used in the five-kingdom system of classification. Sebut dan jelaskan lima kingdom yang digunakan dalam klasifikasi dengan sistem

lima kingdom.2.List the ten bases for the classification of microorganisms. Separate your list into

those test used primarily for taxonomic classification and those used primarily for identification of microorganisms already classified.

Sebutkan 10 dasar klasifikasi mikroorganisma sesuai table di bawah ini.Taxonomic classification Identification of microorganisms

3.List three differences between procaryotic and eucaryotic cells. Sebutkan 3 perbedaan sel prokaryota dengan eukaryota.


Part CMicrobial Morphology and Ultrastructure

OverviewDespite their complexity and variety, all living cells can be divided into two

groups, procaryotes and eucaryotes, based on their ultrastructure as seen with the electron microscope. Plants and animals are entirely composed of eucaryotic cells. In the microbial world, bacteria and cyanobacteria are procaryotes. Other cellular microbes – fungi (yeast and molds), protozoa, and algae-eucaryotes.

Learning objectives1. Identify the three basic shapes of bacteria.2. Describe the structure and function of the glycocalyx, flagella, axial filaments,

fimbriae, and pili.3. Compare and contrast the cell walls of gram-positive bacteria and gram-

negative bacteria.4. Describe the functions of endospores, sporulation, and endospore

germination.

Module task1. Draw the structure of bacterial cell. Gambar struktur sel bakteri.

2. Match the structures to their functions. Cocokkan struktur di bawah ini dengan fungsinya.

1. ________ Cell wall (a) Attachment to surfaces2. ________ Endospore (b) Cell wall formation3. ________ Fimbriae (c) Motility4. ________ Flagella (d) Protection from osmotyc lysis5. ________ Glycocalix (e) Protection from phagocytes6. ________ Pili (f) Resting7. ________ Plasma membrane (g) Proten synthesis8. ________ Ribosomes (h) Selective permeability

(i) Transfer of genetic material

3. Diagram each of the following flagellar arrangements : Gambar bentuk flagella di bawah ini :

a. Lopotrichousb. Monotrichousc. Peritrichousd. Amphitrichouse. Internal flagella (axial filament)

4. Draw the following bacterial shapes : Gambar bentuk bakteri di bawah ini :

a. Spiral


b. Bacillusc. Coccus

5.Endospore formation is called ____(a)_________. It is initiated by

_______(b)__________. Formation of a new cell from an endospore is called __________(c)______________. This process is initiated by ______(d)___________.

Pembentukan endopora disebut ___(a)___________. Diawali oleh proses _______(b)____________. Pembentukan sel baru dari suatu endospora disebut ___________(c)________________. Proses ini diawali oleh ___________(d)________.

6. Diagram cross sections of gram positive and gram negative bacterium cell walls. Gambar potongan melintang dinding sel bakteri gram positif dan gram negatif.


Gram Positive Bacteria

Gram Negative Bacteria

BIOLOGY OF MICROBES


Sub-module :Bacterial Growth & Metabolism

FOR STUDENT




Sub-module: Bacterial Growth and Metabolism

IntroductionMicrobial growth is really referring to the number of cells, not the size of the

cells. Microbes that are growing are increasing in number, accumulating into colonies. The requirements for microbial growth can be divided into two main categories physical and chemical. Physical aspects include temperature, pH, and osmotic pressure. Chemical requirements include sources of Carbon, nitrogen, sulfur, phosphorus, trace elements, oxygen, and organic growth factor.

Bacteria normally reproduce by binary fission. When a few bacteria are inoculated and population is counted at intervals,it is possible to plot a bacterial growth curve that shows the growth of cells over time.

Metabolism is to refer to the sum of all chemical reactions within living organism. Metabolism can be divided into two classes of chemical reaction those are release energy and require energy. The enzyme regulated chemical reaction in living cells.

Learning objectives1. List the requirements for microbial growth into physical aspect and chemical

requirements, the growth of bacterial culture, measurement of microbial growth.

2. List all chemical reactions within living organism, enzyme by living cells, energy production ,carbohydrat metabolism, lipid and protein metabolism

Module tasks

1. Fill in the table below with the carbon source and energy source of each type of organism

Organism Carbon source Energy sourcePhotoautotrophPhotoheterotrophChemoautotrophChemoheterotroph

2. Draw typical bacterial growth curve. Label and define each of the phases. 3. Explain five bacterial categories based on organisms oxygen requirement 4. Most bacteria grow best at pH ……..5. Methods of measuring microbial bacterial growth and categorize each as

either a direct or an indirect methode6. Mention factors influencing activity enzymatic7. Explain microorganisms use two general processes cellular respiration and

fermentation to produce energy from glucose


ReferencesTortora, GJ., Funke BR., Case CL, 1998, Microbiology an introduction 6th ed, Benjamin/Cummings Publishing, USA

Brooks, GF., Butel, JS., Morse, SA., 2001, Jawetz, Melnick, & Adelber’s Medical Microbiology 21st ed, Appleton & Lange, USA


BIOLOGY OF MICROBES


Sub-module :Bacterial Genetics & Genetic Engineering

FOR STUDENT




Microbial Genetics

Overview

Virtually all the microbial traits are controlled or influenced by heredity. The inherited traits of microbes include thair shape and structural features, their metabolism, their ability to interact with other organisms – perhaps causing disease. Individual organisms transmit these chaeacteristics to their offspring through genes, the units of hereditary material that contain the information that determines these characteristics.

Genetics is the study of what genes are, how they carry information, how their information is expressed, and how they replicated and passed to subsequent generations or other organisms.

An understanding of genetics is key to grasping a number of concepts in microbiology. For example, many antibiotics act by inhibiting steps in protein synthesis. Knowing how biological information flows from genes to proteins can help us understand how some antibiotics work, thereby enabling to develop new weapons against disease.

Researchers are trying to solve the difficult medical problem of microbes’ developing antibiotic resistance. A microorganism can become resistant to antibiotics in any of several ways, all of which depend on genetic information. Resistant microbes have somehow obtained gene or set of genes that will prevent the action of antibiotic.

Emerging diseases provide another example of the importance of understanding genetics. New diseases are the result of genetic changes in some existing organism. Currently, biologists are using genetics to discover relatedness among organisms and how life evolved on Earth.

Learning Objectives

01. Describe how DNA serves as genetic information02. Describe the process of DNA replication and protein synthesis03. Explain the regulation of gene expression in bacteria by induction, and

repression.04. Clasify and describe mutations by type05. Differentiate between horizontal and vertical gene transfer06. Describe the function of plasmids and transposons

Modul Tasks

01. Briefly describe the components of DNA, and explain its functional relationship to RNA and protein

02. Describe the process of DNA replication


03. Describe the process of transcription

04. Describe the process of translation, be sure to include the following terms : ribosome, rRNA, tRNA, anticodon, and codon

05. Describe the operon model of gene expression

06. Clasify and describe types of mutation

07. Outline how you would find a morphologic mutant and a biochemical mutant

08. Outline drug dependence caused by mutation

09. Describe types of genetic transfer

10. Define plasmids and transposons, and their role in antibiotic resistamce

References

Brooks G.F., Butel J.S., Morse S.A., 2004. Jawetz, Melnick, & Adelberg’s Medical Microbiology, 23rd ed. The McGraw-Hill Companies, Inc. p 96 - 118

Tortora G.J., Funke B.R., Case C.L., 2004. Microbiology an Introduction, 8 th ed, Pearson Benjamin Cummings. p 210 – 247.


BIOLOGY OF MICROBES


Sub-module :The Control of Microbial Growth

FOR STUDENT




The Control of Microbial Growth

IntroductionThe scientific control of microbial growth began only about 100 years ago. Recall from Pasteur’s work on microorganisms led people to believe that microbes were a possible cause of disease. In the mid-1800, Semmelweis and Lister used this thinking to develop some of the first microbial control practices for medical procedures. These practices included hand washing with microbe-killing chloride of lime and use of the techniques of aseptic surgery to prevent microbial contamination of surgical wounds.Over the last century, scientists have continued to develop a variety of physical methods and chemical agents to control microbial growth.

Learning objective Define the terms related to microbial control: sterilization, disinfection,

antisepsis, degerming, sanitization, and asepsis Describe the effect of microbial control agents on cellular structure Compare the effectiveness of moist heat and dry heat Describe filtration, how low temperature, filtration, dessication, osmotic

pressure suppress microbial growth Explain how radiation kills microbial cells Identify the methods of action and preferred uses of chemical disinfectants Identify the appropriate uses of surface-active agents Identify the method of sterilizing labware and linens and surgery sets

Module task 1. Name the cause of cell death resulting from damage to each other of the

following:a. Cell wall c. proteinsb. Plasma membrane d. nucleic acids

2. If pasteurization does not achieve sterilization, why is milk and food treated by pasteurization?

3. The antimicrobial effect of γ-radiation is due to …………… The antimicrobial effect of ultraviolet radiation is due to …………………4. How do salt and sugar preserved food?5. List 5 (five) factors to consider before selecting a disinfectants/antiseptics!6. Why is it necessary to use strong disinfectants in areas exposed to

tuberculous patients?7. Why are alcohols more effective in 70% solution than absolute alcohol?


BIOLOGY OF MICROBES


Sub-module :Antimicrobial Agents

FOR STUDENT




Antimicrobial agents

IntroductionWhen the body’s normal defense cannot prevent or overcome a disease, it is often treated with chemical drugs (chemotherapy). Like disinfectants, antimicrobial drugs/agents act by interfering with the growth of microbes. But unlike disinfectants, they must often act within the host. Therefore, their effects on the cells and tissues of the host are important. The ideal antimicrobial drugs kill the harmful microbes without damaging the host; this is the principle of selective toxicity.Antibiotics were one of the most important discoveries in the modern medicine. Abdominal wounds or ruptured appendix represented nearly certain death from infection. The use of antimicrobial agents such penicillin and sulfonamide in the treatment of some infections resulted in rapid cures.Today, we are seeing these advances are threatened by the development of resistance of microbes to these drugs.

Learning objectives Identify the contribution of Ehrlich and Fleming to chemotherapy Define these terms: spectrum of activity, broad spectrum versus narrow

spectrum Identify five modes of action of antimicrobial drugs Compare synergism and antagonism in the drugs combination List the commonly used antibacterial drugs Explain the modes of action of antifungal agents Explain the modes of action of antiviral drugs Describe tests for microbial susceptibility to antimicrobial agents Describe the mechanisms of drug resistance

Module task1. What characteristics would an ideal chemotherapeutic agent have?2. Both human cells and pathogens synthesize proteins in the ribosomal sites.

How can antimicrobial agents that target this process be safe to use in humans?

3. Why are antiviral drugs difficult to develop?4. Compare and contrast the actions of polyenes, azoles, allylamines, and

polymyxin!5. What is the difference in drug action of synergists compared with that of

antagonists? Give examples of each!6. What is the definition of cross resistance?7. Mention the mechanism of action of the followings:

a. Penicillin c. Sulfonamideb. Fluoroquinolone d. Macrolide


BIOLOGY OF MICROBES


Sub-module :General Properties of Viruses

FOR STUDENT




General Properties of Viruses

IntroductionViruses differ from all other infectious agents in their structure and biology, particularly in theis reproduction. Although they carry conventional genetic information in their DNA or RNA, they lack the synthetic machinery necessary for yhis information to be processed into new viruses. A virus by itself is metabolicallly inert – it can replicate only after infect a host cell. Viruses can infect every form of life; they cause some of the commonest and many serious diseases of humans, such as smallpox, AIDS, SARS, influenza, chickenpox, dengue fever, morbilli, etc. Some insert their genetic material into the human genome and can cause cancer.However, not all viruses are harmful to humans. Some such as bacteriophages, attack bacteria and have clinical use. This modul is an introduction to viruses and prions: how they infect cells, how they multiply, and how they differ from cellular pathogens.

Learning Objective Differentiate a virus from a bacterium Describe the chemical and physical structure of enveloped and non-

enveloped virus Define viral species, genus, family and give an example Describe how viruses are cultured List techniques used to identify viruses Desribe the life cycle of bacteriophages Compare the multiplication of DNA viruses and RNA viruses Define oncogene and transformed cell Define latent and persistent viral infection Differentiate viruses, viroid, and prion Describe principles and pathogenesis of viral diseases


Outline General characterististics of viruses

Host range Viral size

Viral structure Nucleic acid Capsid and envelope General morphology

Taxonomy of viruses The isolation, cultivation, and identification of viruses

Growing bacteriophage and animal viruses in the laboratory Viral identification

Viral multiplication Multiplication of bacteriophage and animal viruses

Viruses and cancer The transformaion of normal cells into tumor cells DNA oncogenic viruses RNA oncogenic viruses

Latent and persistent viral infection Prion, viroid, and pathogenic viruses Principals and pathogenesis of viral diseases

Task1. List four properties that define a virus! What is virion?2. Why do we classify vruses as obligatory intracellular parasites?3. How are bacteriophages detected and enumerated by plaque method?4. Describe the principal events of attachment, penetration, uncoating, biosynthesis,

and release of an enveloped DNA-containing virus.5. Why are continuous cell lines of more practical use than primary cell cell lines for

culturing viruses? What is unique about continuous cell lines?6. In some viruses, capsomeres function as enzyme as well as structural supports.

Of what advantage is this to the virus?

References1. Brooks GF, JS Butel, SA Morse: Jawetz, Melnick, & Adelberg’s Medical

Microbiology, 23rd edition; chapter 29 & 30, 20042. Tortora GJ, BR Funke, CL Case: Microbiology An Introduction, 7th edition,

chapter 13. 20013. Mims C, HM Dockrell, RV Goering, I Roitt, D Wakelin, M Zuckerman: Medical

Microbiology, 3rd edition, chapter 3, 2004


BIOLOGY OF MICROBES


Sub-module :General Properties of Fungi




General properties of fungi

IntroductionFungi are Eukaryotes, but are quite different from plants an animals; they

began life as a microscopic spore. Characteristically, they are multicellular organisms with a thick chitin-containing cell wall. They may grow as thread-like filaments (hyphae), but many other growth forms occur.

Fungi are ubiquitous as free-living organisms and are of enormous importance commercially in baking, fermenting and in pharmaceuticals. Some form normal flora of our bodies, and others are common causes of local infection in skin, nail and hair. Pathogenic species invade tissues and digest material externally by releasing enzymes, and also take up nutrients directly from host tissues.

Learning objectives Mention at least three characteristics that distinguish fungi from other groups of

Eukaryotes List five ways in which fungi are beneficial Distinguish among septate hyphae, nonseptate hyphae, and mycelia Describe asexual and sexual reproduction in fungi List three basic types af asexual spores found in molds Compare the division of fungi with respect to the formation of sexual spores

Outline/Overview Fungi are chemoheterotrophic eukaryotes with cell walls usually composed of

chitin. Most fungi are beneficial, but some cause mycoses (fungal infections) The nonreproductive body of a folamentous fungus (mold) or yeast (unicellular

fungus) is a thallus. The thallus of mold are omposed of tubular filaments called hyphae. Hyphae are described as either septate or aseptate/nonseptate depending on on the presence of croswalls. A mycelium is a tangle mass of hyphae.

A dimorphic fungus has either type of thallus, depending on environmental conditions.

Most fungi are saprophytic – they acquire nutrients by absorption from dead organisms; other get nutrients from living organisms

Fungi reproduce asexually either by budding or asexual spores, which are categorized according to their mode of development. Most fungi also reproduce sexually via sexual spores.

Most fungi are in the division Zygomycetes produce rough walled zygosporangia. Mycosporidia are intracellular parasites formerly classified as Protozoa, but now classed with zygomycetes based on genetic analysis.

Fungi in the division Ascomycetes, a group of economically important fungi, produce ascospores within sacs called asci.

Fungi in the division Basmidiomycetes, including mushorooms, produce basidiospores at the end of basidia.

Deuteromycetes is an informal grouping of fungi having no known sexual stage.


Task1. What is the basic of classification of fungi?2. Explain dimorphism! Give 2 (two) examples of fungi which have this property!3. What factors contribute to the pathogenicity of fungal infection?4. What dye that we use for staining fungi?5. Explain briefly how to make simple etiologic diagnosis for superficial mycosis!

References:1. Brooks GF, JS Butel, SA Morse: Jawetz, Melnick, & Adelberg’s Medical

Microbiology, 23rd edition; chapter 45, 20042. Tortora GJ, BR Funke, CL Case: Microbiology An Introduction, 6th edition,

chapter 12, 20013. Mims C, HM Dockrell, RV Goering, I Roitt, D Wakelin, M Zuckerman: Medical

Microbiology, 3rd edition, chapter 4, 2004


BIOLOGY OF MICROBES


Sub-module :The Host - Parasite Relationship

FOR STUDENT




The Host - Parasite Relationship

Overview

After understanding the structure and functions of microbes and some idea of the variety of microorganisms that exists, we can consider how the human body and microorganisms interact in term of health and science. A balance exists between host defense mechanisms and the pathogenic mechanisms of microbes. When our defenses resist these pathogenic capabilities, we maintain our health; whereas the pathogen’s capabilities overcome our defenses, disease result.

Pathogenicity is the ability to cause disease, and virulence is the degree or extent of pathogenicity. To cause disease, most pathogens must gain access to the host, adhere to host tissues, penetrate or evade host defense, and damage the host tissues. Some microbes do not cause disease by directly damaging host tissues, but the disease is due to the accumulation of microbial waste products.

If only a few microbes enter the host body, they will probably be overcome by the host’s defense. However, if large numbers of microbes enter our body, the stage may set for diseases, the virulence of microbes is often expressed as the Infectious Dose 50 (ID50).

Humans are generally free of microbes in utero. At birth, normal and characteristic microbial populations begin to establish themselves. After birth, E. coli and other bacteria acquired from foods begin to inhabit the colon. Many other usually harmless microbes establish themselves inside other parts of normal adult body, and its surface. These are called as normal microbiota or normal flora.

Normal cells, tissues, organ, and system of the host body have got some defense mechanism against the microbial invasions. Broadly we classify them into two groups:

Nonspecific defense mechanisms Specific defense mechanisms

Learning objectives

Compare commensalism, mutualism, and parasitism Define normal microbiota Define the pattern of disease Explain the methods of transmission Explain several reasons for emerging and reemerging infectious diseases Define herd immunity Identify several predisposing factors for disease Identify the principal portals of entry and portal of exit Explain how fimbriae, capsules and cell wall components contribute to

pathogenicity Explain how bacterial pathogens damage host cells Contrast the nature and effect of exotoxins and endotoxins


Module Tasks

1. Compare pathogenicity and virulence!2. Describe how hemolysins, leukocidins, coagulases, kinases, hyaluronidases,

siderophores might contribute to pathogenicity.3. Which of the following genera is the most infectious? Explain your answer.

Genus ID50Salmonella 105 cellsLegionella 1 cell

Treponema 50 cellsShigella 200 cells

4. Describe factors contributing to the pathogenicity of virus and fungi. 5. How could social and behavioral change contribute to the alteration of host-

parasite relationship, and what are the effects to humans? 6. What is the aim of host body defense?7. Name the method of transmission of these followings:

Hepatitis B Tuberculosis Tetanus Measles Hepatitis A


MODULE BM.2014.Studentfile

Documents

Transcript of MODULE BM.2014.Studentfile