BIOLOGY
YEAR 1
QUARTER 2
2018/2019
Microbiology
SUMMARY OF THE COURSE MICROBIOLOGY
NWI-BB033
ELISE REUVEKAMP
,Content
Chapter 1: The microbial world ............................................................................................................... 2
Chapter 3: Microbial metabolism............................................................................................................ 6
Chapter 2: Microbial cell structure and function .................................................................................... 7
Chapter 5: microbial growth and its control ......................................................................................... 14
Chapter 7: Molecular biology of microbial growth ............................................................................... 21
Chapter 8: Viruses and their replication / Chapter 10: viral genomics, diversity and ecology ............. 24
Chapter 24: Microbial symbioses with humans .................................................................................... 29
Chapter 25: microbial infection and pathogenesis ............................................................................... 31
,Chapter 1: The microbial world
1.1 What are microorganisms
A microorganism is a small organism consisting of one cell or a cluster of cells. They can be very
diverse in form and function, they inhabit every environment supporting life. Microorganisms affect
human life (health, infectious diseases, food and water, fuel)
- After antibiotics you will be very vulnerable, because the pathogens will be killed but your
microbiome will die as well.
- In the three of life overall, only the plants fungi and animals are macroorganisms
To study microorganisms the microscope, cultures, medium and growth are the needed tools. To
derive a single colony you make a streak plate, of which the last streak will probably contain single
colonies, which are derived from one cell, this one cell has given rise to a lot of cells that form one
colony which is genetically identical. If this single colony were to be transferred to a new plate, it will
contain a pure culture.
1.2 The cell: a living compartment that interacts with the environment and other cells
Elements of a microbial structure:
- Cytoplasmic membrane, which form the barrier inside versus outside
- Cytoplasm: aqueous solution with macromolecules, small organics, ions, ribosomes
- Ribosomes: protein-synthesizing structures
- Cell wall: present in all prokaryotes, which confers structural strength
The difference between prokaryote and eukaryotic cells is that a prokaryote cell has no membrane-
enclosed organelles and no nucleus. On the other hand eukaryotic cells contain organelles and DNA
enclosed in a membrane-bound nucleus. So eukaryotic cells have compartmentalisation
The DNA of eukaryotes and prokaryotes differ from each other, as eukaryotic DNA is involves linear
chromosomes within a nucleus and prokaryotic DNA is generally a single circular chromosome that
aggregates to form the nucleoid region, also it may have plasmids that confer special properties and
it is very compact.
Metabolism is the chemical transformation of nutrients, it is the sum of all chemical reactions in the
cell. Together with growth and evolution, metabolism forms the properties that all cells have. Some
other properties of some cells are differentiation, communication, genetic exchange and motility.
Metabolism can be the metabolism of genetic functions and catalytic functions that together link to
growth and cell division
Chemotroph: chemicals as energy source
- Chemoorganotroph = oxidation of organic compounds
- Chemolithotroph = oxidation in inorganic compounds
Phototroph: light as energy source
1.3 Life on Earth
, Ecosystem refers to all living organisms plus physical and chemical constituents of their environment.
Microbial ecology: the study of microbes in their natural environment
1.4 Impact on Human Society
Microorganisms can be both beneficial and harmful to humans, because microorganisms are agents
of disease, but the microbiome of a human is also needed and beneficial, also in food and agriculture
microbes are used, they can also be valuable for human products, energy generation and
environmental clean-up.
Many agriculture depend on microbial activities for example:
- Nitrogen-fixing bacteria: Beneficial for plants (ammonium) and bacteria (to survive)
- Cellulose-degrading microbes in rumen (cows)
- Human nutrition: gut microbiome digests complex carbohydrates in humans, synthesize
vitamins and other nutrients
Microorganisms and food:
- Negative impacts: can cause food spoilage and foodborne diseases
- Positive impacts: improving food safety, preservation, dairy products and other foods
Microorganisms and industry:
Biofilm = growth on submerged surfaces
Industrial microbiology: massive growth of naturally occurring microbes to make low-cost products
Biotechnology: genetically engineered microbes making high-value products in small amounts
Biofuels: production of methane and ethanol
Bioremediation = cleaning up pollutants
- Microorganisms are also used for wastewater treatment
1.4 Light microscopy
Light microscopy uses visible light to illuminate cells, it has to ability to magnify to object. The
resolution of an optical microscope is defined as the shortest distance between two points on a
specimen that can still be distinguished by the observer or camera system as separate entities.
- Objective lens: magnifies 10-100x
- Ocular lens: magnifies 10x
Staining improves the contrast to the microscope slide. Dyes are organic compounds that bind to
specific cellular materials.
- Basic dyes are positively charged and bind strongly to negatively charged cell components
Differential stains give different kinds of cells different colours, for example a gram negative stain.
Differences in cell wall structure bacterial groups can be divided into two major groups: gram
positive bacteria (appear purple) and gram negative bacteria (appear pink)
Types of microscopy:
YEAR 1
QUARTER 2
2018/2019
Microbiology
SUMMARY OF THE COURSE MICROBIOLOGY
NWI-BB033
ELISE REUVEKAMP
,Content
Chapter 1: The microbial world ............................................................................................................... 2
Chapter 3: Microbial metabolism............................................................................................................ 6
Chapter 2: Microbial cell structure and function .................................................................................... 7
Chapter 5: microbial growth and its control ......................................................................................... 14
Chapter 7: Molecular biology of microbial growth ............................................................................... 21
Chapter 8: Viruses and their replication / Chapter 10: viral genomics, diversity and ecology ............. 24
Chapter 24: Microbial symbioses with humans .................................................................................... 29
Chapter 25: microbial infection and pathogenesis ............................................................................... 31
,Chapter 1: The microbial world
1.1 What are microorganisms
A microorganism is a small organism consisting of one cell or a cluster of cells. They can be very
diverse in form and function, they inhabit every environment supporting life. Microorganisms affect
human life (health, infectious diseases, food and water, fuel)
- After antibiotics you will be very vulnerable, because the pathogens will be killed but your
microbiome will die as well.
- In the three of life overall, only the plants fungi and animals are macroorganisms
To study microorganisms the microscope, cultures, medium and growth are the needed tools. To
derive a single colony you make a streak plate, of which the last streak will probably contain single
colonies, which are derived from one cell, this one cell has given rise to a lot of cells that form one
colony which is genetically identical. If this single colony were to be transferred to a new plate, it will
contain a pure culture.
1.2 The cell: a living compartment that interacts with the environment and other cells
Elements of a microbial structure:
- Cytoplasmic membrane, which form the barrier inside versus outside
- Cytoplasm: aqueous solution with macromolecules, small organics, ions, ribosomes
- Ribosomes: protein-synthesizing structures
- Cell wall: present in all prokaryotes, which confers structural strength
The difference between prokaryote and eukaryotic cells is that a prokaryote cell has no membrane-
enclosed organelles and no nucleus. On the other hand eukaryotic cells contain organelles and DNA
enclosed in a membrane-bound nucleus. So eukaryotic cells have compartmentalisation
The DNA of eukaryotes and prokaryotes differ from each other, as eukaryotic DNA is involves linear
chromosomes within a nucleus and prokaryotic DNA is generally a single circular chromosome that
aggregates to form the nucleoid region, also it may have plasmids that confer special properties and
it is very compact.
Metabolism is the chemical transformation of nutrients, it is the sum of all chemical reactions in the
cell. Together with growth and evolution, metabolism forms the properties that all cells have. Some
other properties of some cells are differentiation, communication, genetic exchange and motility.
Metabolism can be the metabolism of genetic functions and catalytic functions that together link to
growth and cell division
Chemotroph: chemicals as energy source
- Chemoorganotroph = oxidation of organic compounds
- Chemolithotroph = oxidation in inorganic compounds
Phototroph: light as energy source
1.3 Life on Earth
, Ecosystem refers to all living organisms plus physical and chemical constituents of their environment.
Microbial ecology: the study of microbes in their natural environment
1.4 Impact on Human Society
Microorganisms can be both beneficial and harmful to humans, because microorganisms are agents
of disease, but the microbiome of a human is also needed and beneficial, also in food and agriculture
microbes are used, they can also be valuable for human products, energy generation and
environmental clean-up.
Many agriculture depend on microbial activities for example:
- Nitrogen-fixing bacteria: Beneficial for plants (ammonium) and bacteria (to survive)
- Cellulose-degrading microbes in rumen (cows)
- Human nutrition: gut microbiome digests complex carbohydrates in humans, synthesize
vitamins and other nutrients
Microorganisms and food:
- Negative impacts: can cause food spoilage and foodborne diseases
- Positive impacts: improving food safety, preservation, dairy products and other foods
Microorganisms and industry:
Biofilm = growth on submerged surfaces
Industrial microbiology: massive growth of naturally occurring microbes to make low-cost products
Biotechnology: genetically engineered microbes making high-value products in small amounts
Biofuels: production of methane and ethanol
Bioremediation = cleaning up pollutants
- Microorganisms are also used for wastewater treatment
1.4 Light microscopy
Light microscopy uses visible light to illuminate cells, it has to ability to magnify to object. The
resolution of an optical microscope is defined as the shortest distance between two points on a
specimen that can still be distinguished by the observer or camera system as separate entities.
- Objective lens: magnifies 10-100x
- Ocular lens: magnifies 10x
Staining improves the contrast to the microscope slide. Dyes are organic compounds that bind to
specific cellular materials.
- Basic dyes are positively charged and bind strongly to negatively charged cell components
Differential stains give different kinds of cells different colours, for example a gram negative stain.
Differences in cell wall structure bacterial groups can be divided into two major groups: gram
positive bacteria (appear purple) and gram negative bacteria (appear pink)
Types of microscopy:
