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Questions Weightage – Microbiology

(GATE 2002-2007)

Classification of 5
Microorganisms
Introduction to 2
Microbiology
Medical Microbiology 7
Microbial Control 10
Microbial Ecology 3
Microbial growth and 22
culture
Microbial Metabolism 4
Microbial Recombination 7
and
Microscopy 1
Regulation of Gene 1
Expression
Structure of Prokaryotic 9
cells
Others 1
Microbiology Total 72

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Index

Introduction to Microbiology 7
Spontaneous generation of Microorganisms 11
Role of Microorganisms in the transformation of Organic matter 13
Microorganisms and Disease 14
Koch’s Postulates 16
Structure Of Prokaryotic Cells 21
General Structure of Prokaryotic cell or Bacteria 21
Glycocalyx/Capsule/Slime 22
Cell Wall 24
Significance of Cell Wall 25
Biosynthesis Of Peptidoglycan 27
Transpeptidation 28
Cell Membrane and Biosynthesis 30
Membrane transport of mechanisms 32
Facilitated Diffusion of Ions 32
Ligand-gated Ion Channels 32
External Ligands 33
Internal Ligands 33
Mechanically-gated Ion Channels 33
Voltage-gated Ion Channels 34
The Patch Clamp Technique 35
Facilitated Diffusion of Molecules 35
Active Transport 36
Direct Active Transport 36
Indirect Active Transport 39
Mesosomes 41
Cytoplasm 41
Endospores 41
Significance of endospores 42
Gas Vesicles 42
Nucleoid (Genetic Material) 43
Plasmid 44
Ribosomes 45
Flagella 46
Pili and Fimbriae 48
Bacterial Locomotion 50
Chemotaxis (Positive and Negative) 51
Inclusion Bodies 51
CLASSIFICATION OF MICROORGANISMS 53
CLASSIFICATION OF BACTERIA 53
CLASSIFICATION OF ARCHAEA 60
CLASSIFICATION OF EUKARYOTIC MICROORGANISMS 60
General Features 61
Protists (Protozoans) 64
General Features 65
MICROBIAL ECOLOGY 67
b. Role of Microorganisms in biogeochemical cycling 71
i. Carbon Cycle 72
ii. Sulphur cycle 74

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iii. Nitrogen cycle 75

c. Soil microbes associated with the vascular plants 76
d. Bioremediation 77
MICROBIAL INTERACTIONS 81
VIRUSES CLASSIFICATION 86
General Properties of Viruses 88
General Structural Characteristics of Viruses 88
Bacteriophage (Bacterial Virus) 89
Phage Genome 91
Animal Viruses 91
Plant Viruses 93
Microbial Growth and Culture 95
Isolation of Microorganisms 95
PURE CULTURE TECHNIQUES 95
ENRICHMENT CULTURE TECHNIQUES 96
MICROBIAL MEDIA AND PRINCIPLES OF MICROBIAL NUTRITION 97
GROWTH CURVE OF MICROORGANISMS 98
Mathematics of Growth (Growth Kinetics) 101
Measuring Microbial Growth 106
Measurement of growth yield 111
GROWTH OF BACTERIAL POPULATION 112
DIAUXIC GROWTH 112
SYNCHRONOUS GROWTH 113
CONTINUOUS CULTURE 114
Effect of environmental factors on growth 115
BACTERIAL BIOFILM FORMATION 118
BIOFOULING 118
Requirement Of Energy 120
Principle Of Energy Generation 120
Carbohydrate Metabolism 121
Glycolysis (Embden-meyerhof pathway) 122
Entner-doudoroff pathway 124
Citric acid Cycle (Krebs’s Cycle/Tri Carboxylic Acid Cycle (TCA)) 126
pentose phosphate pathway (hexose monophosphate pathway or hmp shunt) 127
Glyoxylate Cycle 128
Photosynthesis 130
Properties of Microbial Photosynthetic Systems: 137
Calvin Cycle 138
Lipid Metabolism 139
Fatty acid Synthesis 140
Amino Metabolism 141
Amino acid synthesis 141
Regulation of amino acid synthesis 142
Electron transport chain and Oxidative phosphorylation 143
Electron carriers 144
Redox reactions 145
Bioenergetics 146
Regulation of major metabolic pathways 147
Fermentation 148
Aerobic and anaerobic respiration 148
Chemolithotrophy 150

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NITROGEN FIXATION 150

Light Microscope 156
Magnification 157
Factors Affecting Magnification 158
Resolution And Numerical Aperture 158
Bright Field Microscopy 160
Staining 162
Dark Field Microscopy 166
Phase Contrast Microscopy 168
Fluorescent Microscopy 171
Electron Microscopy 173
Transmission Electron Microscopy 175
Scanning Electron Microscopy 177
Control Of Microbial Growth 180
Sterilization 180
Disinfection 180
Antisepsis 180
Sepsis 181
Asepsis 181
Sterilisation Methods 181
Physical Methods Of Microbial Control 181
Heat 181
Thermal death time (tdt) 181
Decimal Reduction Time (Drt Or D Value) 182
Moist Heat 182
Dry Heat Sterilization 184
Pasteurization 185
Radiation 186
Ionizing Radiation – gamma rays x – rays 186
ASSESSMENT OF EFFICACY 188
1.3.2 Nosocomial infections 196
1.3.3 Opportunistic infections 197
1.3.4 Emerging infectious diseases 197
1.5 Host-Pathogen Interactions 200
1.6 Host defense mechanism against microbial infections 202
1.6.1 Antigens 202
1.6.2. Antibodies 203
1.6.2 Nonspecific Immunity 204
1.6.3 Humoral Immunity 207
1.6.4 Cell-mediated Immunity 208
1.7 Passive immunization 209
General Characteristics Of Antimicrobial Drugs 211
Determining levels Of Antimicrobial Activity 211
Mode of Action of Antibiotics 214
Classification of Antibiotics based on mechanism of action 214
Cell Wall Synthesis Inhibitors 214
Protein Synthesis Inhibitors 217
Nucleic Acid Synthesis Inhibitors 222
ANTIBIOTIC RESISTANCE 223
Antifungal Drugs 224
Antiviral Drugs 226

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Microbial Recombination and Genetic Variation 228

Bacterial genome 228
Basic concepts of microbial genomics 228
Plasmids 229
Transposons 230
Methods of bacterial recombination 232
Transformation 232
Conjugation 232
Transduction 233
Virus life cycle and recombination 234
Phage lambda and its life cycle 234
RNA phages 236
Recombination and Reassortment 236
Mutagenesis 239
Types of mutation 239
Selection of mutants 241
Ames test for mutagenesis 242
Mutations in viruses 242
Chapter 10: Regulation of gene expression 243
Induction 249
Repression 250
MICROBIAL DISEASES 252
HOST PATHOGEN INTERACTIONS 254
Filtration 256
Process 256
Dessication 257
Osmotic Pressure 257
Studying unculturable organisms 257
Using Metagenomics 258
Molecular approaches to microbial taxonomy and phylogeny 259
Microbial Ecology 261

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Introduction to Microbiology
DISCOVERY OF MICROORGANISMS
● Although Robert Hooke (1635-1703) published the first drawings of microorganisms in
his book Micrographia, it is believed that the earliest observation of microbes was made
by an Italian named Francesco Stelluti (1577-1652) using a microscope provided to him
by Galileo
● Micrographia not only had detailed drawings of many microscopic things but also had
information for building microscopes
● This piqued interest in many scientists of that generation who started building their own
improved versions of the microscopes
● One among them was Antony van Leeuwenhoek (1632-1723) of Delft, the Netherlands
who was a cloth merchant
● He designed microscopes that could provide magnifications up to 50 to 300 times
● Micrographia is important not only for its exquisite drawings but also for the information
it provided on building microscopes.
● The microscopes designed by him were so powerful that they ultimately helped him
observe and generate descriptions of both bacteria and Protists

LANDMARK DISCOVERIES RELEVANT TO THE FIELD OF

MICROBIOLOGY
● A lookback at the history of microbiology reveals many important discoveries over years
● A few of the most import discoveries are listed below

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2001 Human Genome Sequencing

2004 Reconstruction of whole genomes of unculturable microorganisms

2005 First comprehensive metaproteomics study of a microbial community

2007 The first phase of the human microbiome started

2008 Short reads technology

2010 Bovine rumen microbiome

2011 Earth Microbiome project foundation

2012 First phase of Human Microbiome project started

2013 First Human Microbiome transplantation

2017 Multi-Omic analysis as forensic tool

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SPONTANEOUS GENERATION OF MICROORGANISMS

● In the beginning when people lacked enough information about the origin of living organisms,
they believed that living organisms were developed from nonliving matter
● This belief or hypothesis that living organisms were derived from nonliving materials is called
the spontaneous generation of microorganisms
● The spontaneous generation theory was disproved by an Italian physician named Francesco Redi
(1626-1697), who carried out a series of experiments on decaying meat
● Before disproving the spontaneous theory, people believed that maggots (larva of flies that
develop from eggs laid by flies) were generated spontaneously on the decaying meat
● To disprove this, he took the meat in three containers, he sealed one container with cork, the
other with gauge that will not allow flies and the third one was left uncovered
● He showed that in the meat sealed with cork no maggots were formed there by disproving the
spontaneous generation of microorganisms

● Similar experiments by others helped discredit the theory for larger organisms
● Louis Pasteur (1822-1895) once and for all settled the matter of spontaneous generation using
his Swan-neck flasks experiment

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ROLE OF MICROORGANISMS IN THE TRANSFORMATION OF ORGANIC MATTER

● Microorganisms play an important role not only in the transformation of organic compounds but
also in the transformation of radionuclides and toxic metals present in the waste.
● The organic material such as leaves, roots, dead organisms, etc. shed into the layers of soil are
broken down to a reusable organic matter by microorganisms present in the soil
● These microorganisms include both bacteria and fungi that have the ability to produce various
kinds of enzymes necessary for degrading these organic materials
● the nature of the organic matter that is generated depends on various factors like age, mode of
transformation, and existing environment
● when organic matter is finally broken down a stable substance that resists further
decomposition called the humus is produced
● This process is called humification
● Soil organisms, including micro-organisms, use soil organic matter as food.
● In the process of breaking down any organic matter, any excess nutrients (N, P and S) are
released into the soil in forms that plants can use.
● This release process is called mineralization.
● So, the transformation of organic matter by microorganisms results in humification and
mineralization which can then be used by plants and other organisms to continue the cycle of
life

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MICROORGANISMS AND DISEASE

● Fracastoro and a few others for the first time suggested that invisible organisms are responsible
for the diseases
● This belief by many scientists of that generation eventually lead to the development of germ
theory of disease
● Agostino Bassi (1773-1856) in 1835 showed that a silkworm disease was caused due to fungal
infection.
● M. J. Berkeley (1803-1889) proved that the great potato blight of Ireland was caused by a water
mold
● Heinrich de Bary a German surgeon and botanist in 1853 (1831-1888) showed that smut and
rust fungi caused cereal crop diseases.
● Joseph lister provided indirect evidence to support germ theory. He developed a system of
antiseptic surgery i.e. he prevented sepsis which results from growth of microorganisms in the
wounds by ensuring that the instruments were heat sterilized (heat kills microorganisms) and
employed phenol on surgical dressings and sometimes sprayed over the surgical area
● This not only led to many successful surgeries in the years to follow but also led to providing an
indirect proof that destroying microorganisms by heating and phenol treatment prevented
infections and subsequent sepsis caused by microorganisms

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KOCH’S POSTULATES
● It was Robert Koch who first demonstrated that bacteria are responsible for the disease
● His experiments with Bacillus anthracis that causes anthrax ultimately proved that
microorganisms are responsible for the diseases
● Based on his experiments he proposed some postulates which are commonly referred to as
Koch's postulates
● These postulates help in establishing a relation between the disease and the causative organism
of that disease.
● An organism is said to be responsible for a particular disease only when the postulates are fully
met
● The four Koch’s postulates are shown in the image below

Important notes: The most important aspect in this chapter is the Koch’s postulates. The rest of the
information is important for understanding the history and development of the subject better but
not so much in the exam point of view

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