BBS2710
Microbial
Physiology
Module Notes
Prepared: Semester I, 1999
Modified: Semester I, 2002
Table of Contents
Proposed Course Time Table ………………………………………………………….. A
Assignment Topic ………………………………………………………………………… B
Module 1: Introduction to Microbial Physiology 10
1.1 Introduction to Microbial Physiology 11
What is Microbial Physiology? 11
The Importance of Microorganisms 11
Description of Microorganisms 11
The Importance of Microorganisms in Physiology 12
Description of the Escherichia coli model. 13
The Composition of Escherichia coli. 12
Cell Structure and Function 13
Discussion of the Bacterial Cell Structure. 14
1.2 Macromolecular Synthesis 16
DNA and Replication 16
Nucleoid 18
Topoisomerases 18
DNA Replication. 19
Initiation and Regulation 19
Elongation 20
Termination and Partitioning 20
RNA and Transcription 21
RNA Polymerase 21
Initiation 22
Promoter Function 23
Elongation 23
Termination 24
RNA Turnover 25
RNA Processing 25
Protein Synthesis: Translation 27
1.3 Structural Assembly 34
Structures of Proteins 34
How are proteins secreted? 35
Degradation of Proteins 35
Lipids 36
Synthesis of the Gram Positive Cell Wall: Peptidoglycan Synthesis 37
Teichoic acids. 38
The Gram Negative Cell Wall 38
Lipopolysaccharides 38
Lipoproteins 39
Other proteins 39
Flagella Assembly. 39
Pili and Fimbriae 39
The Glycocalyx. 40
The Motility of Flagellated Bacteria. 40
Questions 42
Module 2: Bacterial Growth, Environmental Effect and Strategies 44
Factors affecting bacterial growth: 45
How do bacterial cells grow? 45
Growth Rate (k) 45
Measurement of growth in the Lab. 46
Population Growth Phases. 46
Temperature as a Influential factor 47
Effect of Temperature on Cell Physiology. 47
Why does the cell pause mid-cycle? 48
Upper Temperature Limits 48
Lower Temperature Limits 48
Lethal Effects of Temperature 49
Bacteria that make Ice 49
Osmotic Pressure Effects 49
Hydrostatic Pressure 50
pH 50
Low Nutrient Levels. 51
Oxygen Dependence 51
Low Water Availability 52
Light Availability. 52
Questions 53
Module 3: Genetic Adaptation 55
3.1 General features of the bacterial genome 56
Complement of Genes 56
Genetic organisation in bacteria 56
Arrangement of genes on the bacterial chromosome 56
3.2 Plasmids 58
Conjugative Plasmids 58
Functions encoded by plasmids 58
3.3 Mutations and Repair 59
The effects of mutations on phenotype 59
Types of mutations 60
Macrolesions 60
Deletions 60
Duplications 60
Inversions 61
Insertions 61
Microlesions 61
Insertion and deletion of a single base pair: Frameshift mutations 61
A. Wild-type 62
B. Single nucleotide-pair insertion 62
Transitions and transversions 64
Nonsense, missense and silent mutations 64
Repair Mechanisms 65
Inducing Mutations 65
Photoreactivation 66
Mismatch Repair 66
Excision Repair 67
SOS Repair 70
3.4 Transposable Elements 70
Insertion sequences (IS) 70
Composite transposons (Tn) 71
Roles of transposable elements 72
3.5 Exchange of genetic material between organisms 73
Recombination 73
Generalised transduction 76
Specialised transduction 77
Questions 80
Module 4: Physiological Adaptation 82
4.1 Coordination of Metabolic Reactions 83
4.2 Regulation of Enzyme Activity 87
4.3 Regulation of Gene Expression 89
4.4 Specific Examples 92
Histidine Biosynthesis 92
Biosynthesis of the Aspartate family of Amino Acids 93
The lac Operon 96
The trp Operon 98
Questions 102
Module 5: Energy and Metabolism 104
5.1 Energy Production: An Overview 105
Oxidation and Reduction reactions 106
Generation of ATP 106
Substrate-level Phosphorylation 107
Oxidative Phosphorylation 107
Photophosphorylation 107
5.2 Glycolysis and Aerobic Respiration 108
Respiration 109
Gylcolysis 109
Aerobic Respiration 111
The TCA Cycle 111
Electron Transport Chain 114
Generation of ATP by Chemiosmosis 115
5.3 Alternative Approaches to Respiration 119
Pentose-phosphate pathway 119
Entner-Doudoroff Pathway 119
Anaerobic Respiration 119
5.4 Fermentation 120
Lactic Acid fermentation 121
Alcohol Fermentation 122
5.5 Photosynthesis 123
The Light Reaction 123
The Dark Reaction 124
5.6 Summary of Energy Producing Mechanims 126
Photoautotrophs 127
Photoheterotrophs 127
Chemoautotrophs 127
Chemoheterotrophs 127
Questions 128
TABLE OF FIGURES
Figure 1:1 Electron micrograph of an E. coli cell 13
Figure 1:2 The eukaryotic cell 13
Figure 1:3 The bacterial cell 13
Figure 1:4 The DNA double helix 16
Figure 1:5 Base pairing and anti-parallel nature of the DNA double helix 17
Figure 1:6 A-DNA and B-DNA 18
Figure 1:7 Activities of DNA topoisomerase II 19
Figure 1:8 Deoxyribonucleotides and ribonucleotides 21
Figure 1:9 Stages of transcription 22
Figure 1:10 Structure of a typical E. coli promoter 23
Figure 1:11 Features of the E. coli RNA polymerase transcription site 24
Figure 1:12 Dyad symmetry and the formation of transcription terminators 24
Figure 1:13 The Universal Code 27
Figure 1:14 The initiation of translation in E. coli 30
Figure 1:15 Polypeptide chain elongation in E. coli 32
Figure 1:16 Polypeptide chain termination in E. coli 33
Figure 3:1 The universal genetic code 63
Figure 3:2 Transitions and Transversions 64
Figure 3:3 Structural elements of IS50 70
Figure 3:4 Target site duplication following transposition 71
Figure 3:5 Composite transposons 71
Figure 3:6 Homolgous recombination 73
Figure 3:7 DNA exchange following crossing-over events 74
Figure 3:8 Transformation 75
Figure 3:9 Insertion of transformed DNA 75
Figure 3:10 Generalised Transduction 76
Figure 3:11 Specialised Transduction 77
Figure 3:12 Bacterial Mating 78
Figure 3:13 Conjugation 79
Figure 4:1 Relationship between genotype and phenotype 83
Figure 4:2 Overview of pathways responsible for the synthesis of most molecules 84
Figure 4:3 Enzyme catalysis 87
Figure 4:4 Feedback inhibition 88
Figure 4:5 Competitive inhibition 89
Figure 4:6 Central Dogma of Molecular Biology 90
Figure 4:7 Structural features of an operon 91
Figure 4:8 Pathway for histidine biosynthesis 92
Figure 4:9 Diaminopimelic Pathway in E. coli 93
Figure 4:10 Synthesis of Aspartic acid family amino acids in Corynebacterium 94
Figure 4:11 The lac operon 96
Figure 4:12 Induction of the lac operon 97
Figure 4:13 The Trp operon 98
Figure 4:14 Trp operon: Repression 99
Figure 4:15 Elements of the Trp attenuator 100
Figure 4:16 Secondary structure formed in the Trp attenuator 100
Figure 4:17 Secondary structures formed in the presence of tryptophan 101
Figure 4:18 The attenuator in the absence of tryptophan 101
Figure 5:1 Simple overview of microbial metabolism 105
Figure 5:2 Generation of cellular energy 105
Figure 5:3 REDOX reactions 106
Figure 5:4 Overview of respiration and fermentation 108
Figure 5:5 Glycolysis 110
Figure 5:6 The TCA cycle 112
Figure 5:7 Electron transport chain 114
Figure 5:8 Chemiosmotic generation of ATP 115
Figure 5:9 Electron transport chain 116
Figure 5:10 Summary of respiration 118
Figure 5:11 Overview of fermentation 120
Figure 5:12 Lactic acid fermentation 121
Figure 5:13 Alcohol fermentation 122
Figure 5:14 Oxygenic photosynthesis 124
Figure 5:15 Anoxygenic photosynthesis 124
Figure 5:16 The dark reaction 125
Figure 5:17 Summary of energy producing pathways 126
Figure 5:18 Summary of microbial metabolisms 127
2710BBS PROPOSED COURSE TIMETABLE
Week / Date / Module / Topic / Who1 / Fri 01 March / 1 / Introduction to Molecular Physiology / Bharat
2 / Fri 08 March / 1 / Macromolecular Synthesis / Ben
3 / Fri 15 March / 1 / Structural Assembly / Ben
4 / Mon 18 March / Revision / Ben
4 / Fri 22 March / 1 / Module 1 Quiz / Ben
5 / Fri 29 March / Public holiday – Good Friday
Mid semester break
6 / Fri 12 April / 4 / Physiological Adaptation 1 / Ben
7 / Fri 19 April / 4 / Physiological Adaptation 2 / Ben
8 / Fri 26 April / 5 / Energy and Metabolism / Ben
9 / Fri 3 May / 4-5 / Revision / Ben
10 / Fri 10 May / 2 / Bacterial Growth / Bharat
11 / Fri 17 May / 3 / Genetic Adaptation 1 / Bharat
12 / Mon 20 May / Modules 4 & 5 Quiz 2 / Bharat
12 / Fri 24 May / 3 / Genetic Adaptation 2 (Assignment due) / Bharat
13 / Fri 31 May / 2-3 / Revision / Bharat
14 / Fri 7 June / - / General Revision / Bharat
BBS 2710 Microbial Physiology Assignment
Assignment: Written 1000 words, excluding list of references
Marks: 10%
Due Date: 24th May (week 12) at 8.00 am prior to the start of Microbial Physiology Lectures
Topic: Microbes from Extreme Environments.
Summary: The past 20 years research on a diverse array of extreme environment ecosystems has lead to an explosion in our knowledge and we are now able to define the limits to the boundaries of life on our planet. Extreme environments include environments which posses extremities in heat (deep sea hydrothermal vents, terrestrial volcanic systems), ions (hypersaline lakes, soda lakes), pH (acidic or alkaline) and pressure (subsurface environments such as the deep sea ocean floor, oil fields). Oxygen free (anoxic, anaerobic) environments are also regarded as extreme environments. Cells that live in extreme environments are collectively called “extremophiles”. Extremophiles have adapted not only to cope with harshness but also thrive in these environments using different protective / adaptive mechanisms which include modifications to their cell structures and macromolecules.
As part of the assignment you are required to search the literature and provide a list of specific environments that are regarded as extreme environments. Choose one of the environments you have listed and provide information on its: (a) location and distribution (b) physicochemical properties (c) group of microbes that exist and (d) cellular mechanisms that allow them to cope with and thrive in the environment that you have chosen for the assignment. Remember to correctly cite the references in your assignment.
References: These are provided to get you started but you may need to refer to more.
Journal References (Available at GU Nathan / Logan Libraries)
FEMS Microbiology Letters
FEMS Microbiology Reviews
International Journal of Systematic Bacteriology
Reviews in Microbiology
Systematic and Applied Microbiology
Journal of Bacteriology
Applied and Environmental Microbiology
Extremophiles
Book References:
Madigan, Matrinko and Parker. Brock Biology of Microorganisms. Prentice Hall, 9th edition, 2000
Atlas. Principles of Microbiology. WCB Publishers, 2nd edition
Web addresses:
http://www.ncbi.nlm.nih.gov/Entrez/ (Search with keywords in PubMed)
http://trishul.sci.gu.edu.au/sites.html#MBL (lists useful sites in Microbiology)
Module 1
Introduction
to
Microbial
Physiology
Module 1 Introduction to Microbial Physiology Page 16
Module 1: Introduction to Microbial Physiology
Topics
1. Introduction to Microbial Physiology as a subject
2. Macromolecular Synthesis
3. Structural Assembly
F Aims and Objectives
* Introduce microbial physiology as a subject
* Describe the importance of microorganisms and their diversity in nature
* Describe Escherichia coli and the general molecular and structural composition of cells
* Describe the difference between Gram-positive and Gram-negative cells
þ You should be able to…
* discuss what microbial physiology involves
* discuss why E. coli is such a useful organism to use as a model for microbial physiology
* draw a typical prokaryotic cell, noting structures and functions
* describe the difference between Gram-positive and Gram-negative cells
* describe the difference between eukaryotic and prokaryotic cell types
* recall that all life is divided into three domains and a large diversity is present in the Bacterial and Archaeal domains
$ Learning exercise
Ø revise the function of organelles in eukaryotic cells
1.1 Introduction to Microbial Physiology
What is Microbial Physiology?
Physiology is the understanding of the processes of life as mediated by its structures, operating together to accomplish the common tasks of life. Microbial Physiology is an understanding of cell structure, growth factors, metabolism and genetic composition of microorganisms. It introduces the inter-relatedness of Microbiology, Biochemistry, and Genetics while understanding the functioning of the bacterial cell. Microbial Physiology looks at the simpler single-cell organisms as a paradigm for trying to understand much more complex organisms. In doing this, we can understand how the cell functions in the environment, how it can alter to suit changes in the environment, and how it can produce a new cell from very simple substrates available in the environment.
The Importance of Microorganisms
Microorganisms play a very important part in very nearly every environmental niche found on our planet. From under the ice at the north and south poles at -10ºC in seawater, to deep beneath the Earth's surface. They are found in both in solid rock and in volcanically heated pools that can reach temperatures over 100ºC. Bacteria can survive and reproduce in deep seas where barometric pressures can easily squash a human. Bacteria have evolved to form such a diverse group of organisms that we humans have not yet catalogued a tenth of 1% of their variety.
Not only are bacteria found in very unusual natural environments, but also bacteria with special or unusual characteristics are put to everyday use. Antibiotics from bacteria are just one important discovery. They are put to use to reduce the hazards of wastewaters created from industries. They degrade hardy and dangerous compounds (bioremediation) and ferment substrates to produce important metabolites. They are essential to element cycling on our earth, carbon and nitrogen especially. They are important in the nutrition of all organisms. The ruminant animals would not survive if it were not for the bacteria present in their guts.
The most important characteristic of microorganisms is that they have evolved as part of a microbial community. One species of bacteria may start a process, or do a particular step, but a complete community is required for nearly all life on earth. Each species is singularly different, and even within species there is variability. This is the crux of Microbial Physiology. To try to understand a part, so we can come closer to understanding the whole, both in relation to microbial communities, and complex, multicellular organisms.
Description of Microorganisms
All life is divided into three domains. The domain Eukarya contains all multicellular, and some single-celled organisms. They are generally identified by the presence of a membrane-bound nucleus within the cell. The domains Bacteria and Archaea contain the single-celled organisms with no membrane-bound nucleus. They are generally much smaller and have a much simpler structure and genome than the domain Eukarya. The term "bacteria" (NB: lower case "b" in "bacteria") refer to the prokaryotes (domains Bacteria and Archaea) while "Bacteria" will only refer to the domain Bacteria.