Chapters 1 and 2

Biology 2400Dr Krisher or Dr. K(Rhymes with Fisher)email: krisherk@macomb.eduBlog for class info, slide info, exam reviews:macombbio2400.blogspot.com

Attendance and Participation: Mandatory. I will point out in lecture what is important for the exam!
Rules: BE ON TIME. Notify me if you need to leave or will miss class. Do not walk out of lecture: disruptive
Makeup exam-only if arrangements made PRIOR to exam and only if reason is valid and at my discretion.
Lecture: Pay attention, must take notes and keep up. No sleeping, talking, text-messaging, playing on computer. Class discussions.
Lab: Participation is important; Quiz points and take home questions

Chapter 1PART I Introduction to Microbiology 

Science of Microbiology
Microorganisms are central to the functioning of the biosphere

The science of microbiology is the foundation of all the biological sciences

Microorganisms as Cells
The cell is a dynamic entity that forms the fundamental unit of life

The cell can exist alone: macroorganism vs. microorganism

Carry out process of growth, energy generation, and reproductions independently of other cells.

All life began as a microorganism

Basic biological science versus applied biological science

Basic Biological science: processes of microbial life

Applied Biological science: practical uses of microbes

Microbial Cell
Think of Microbe as Compartment
The cell has a barrier, the cytoplasmic membrane, that separates the inside of the cell from the environment.
The nucleus or nucleoid
The cytoplasm
Possibly a cell wall outside the cytoplasmic membrane

Cellular Characteristics
Six features associated with organisms:
metabolism
reproduction
differentiation
communication
movement
evolution

Cellular Functions
Metabolism: use of nutrients to make energy to operate cell functions

Reproduction: Growth and division into two or more daughter cells

Differentiation: process forming new substances or structure

Role of Enzymes
Microbes are machines that carry out chemical transformation.

Enzymes are the catalysts of this chemical machine, greatly accelerating the rate of chemical reactions.

Cells as Coding Devices
Cells are also coding devices that store and process information that is eventually passed on to offspring during reproduction through DNA (deoxyribonucleic acid).

The link between cells as machines and cells as coding devices is growth.

Habitat and Ecosystem
Habitat is the location where a microbial population lives.

Microbial populations can interact and cooperate with each other and environment

Ecosystem: organisms together with the physical and chemical constituents of their environment

Importance of Microbes
Estimates of the total number of microbes on Earth is ~ 5  1030 cells.

The total carbon present in microbes equals that of all plants on Earth
(plant carbon > animal carbon).

Most microbes reside in oceanic and terrestrial subsurfaces.

Most of biomass on Earth is microbial.


Microorganisms change the chemicaland physical properties of their habitats
Removal of nutrients from environment
Excretion of waste products.
Microorganisms are both beneficial and harmful to humans. Pathogens versus Saprophytes

Agricultural Microbiology
Microorganisms are important in the agricultural industry.

Legumes, which live in close association with bacteria that form structures called nodules on their roots,convert atmospheric nitrogen into fixed nitrogen that the plants use for growth.

Bacteria reduce need for plant fertilizer.


Fathers of Microbiology
Robert Hooke was the first to describe microorganisms

Antoni van Leeuwenhoek was the first to describe/see bacteria

Ferdinand Cohn founded the field of bacteriology and discovered bacterial endospores

Louis Pasteur
Spontaneous generation: hypothesis that living organisms can originate from nonliving matter.
Pasteur disproved this idea by comparing:
the growth of microorganisms in one flask containing sterile broth that was exposed to the air
the growth of microorganisms in flask containing sterile broth that was not exposed to the air.

Pasteur’s Experiments

Robert Koch
Koch’s Postulates
The suspected pathogenic organism should be present in all cases of the disease and absent from healthy animals.
The suspected organism should be grown in pure culture—that is, a culture containing a single kind of microorganism.
Cells from a pure culture of the suspected organism should cause disease in a healthy animal.
The organism should be reisolated and shown to be the same as the original

General Microbiology
Culture Media Enrichment Cultures

Beijerinck: Winogradsky: use of inorganic compounds for production of energy by microbes

Early Prevention of Disease
Semmelweis and Handwashing
Lister’s Antiseptic Technique
Nightingale and Nursing
Snow and Epidemiology – infection control and epidemiology
Jenner’s Vaccine – field of immunology
Ehrlich’s “Magic Bullets” – field of chemotherapy


Applied Microbiology
Some subdisciplines of applied microbiology:
medical microbiology,
immunology,
agricultural microbiology,
industrial microbiology,
aquatic microbiology,
marine microbiology, and
microbial ecology

Basic Microbiology
Some subdisciplines of basic microbiology:
microbial systematics,
microbial physiology,
cytology,
microbial biochemistry,
bacterial genetics,
molecular biology.


Chapter 2An Overview of Microbial Life
Cell Structure and Evolutionary History
Elements of Cell and Viral Structure,
Arrangement of DNA in Microbial Cells
The Tree of Life

PART II Microbial Diversity
Physiological Diversity of Microorganisms,
Prokaryotic DiversityEukaryotic Microorganisms

PART I Cell Structure and Evolutionary History  Elements of Cell and Viral Structure
Structural Types of Cells
Two structural types of cells are recognized:

The prokaryote and the eukaryote.

Prokaryotic cells have a simpler internal structure than eukaryotic cells, lacking membrane-enclosed organelles

Basic Structures
All microbial cells share certain basic structures in common, such as
cytoplasm
cytoplasmic membrane
ribosomes
a cell wall (usually)


Viruses are not Prokaryotes

Viruses are not cells but depend on cells for their replication

Ribosomes
Functions:
The cell's protein-synthesizing factories—
are particulate structures composed of RNA (ribonucleic acid)
various proteins suspended in the cytoplasm.

Ribosomes and Proteins
Ribosomes interact with cytoplasmic proteins and messenger and transfer RNAs in the key process of protein synthesis (translation)

Arrangement of DNA in Microbial Cells
Genome: The genes that govern the properties of cells, and a cell's complement of genes.

Chromosomes.
DNA is arranged in cells to form chromosomes
Prokaryotes: usually a single circular chromosome
Eukaryotes: several linear chromosomes exist.

Plasmids

Plasmids are circular extrachromosomal genetic elements (DNA)
nonessential for growth
found in prokaryotes.

Nucleus

The nucleus is a membrane-enclosed structure that contains the chromosomes in eukaryotic cells.
The nucleoid, in contrast, is the aggregated mass of DNA that constitutes the chromosome of cells of Bacteria and Archaea

The Tree of Life

Comparative ribosomal RNA sequencing has defined the three domains of life:
Bacteria, Archaea, and Eukarya.

Eukarya from Bacteria

Molecular sequencing has also shown that the major organelles of Eukarya have evolutionary roots in the Bacteria and has yielded new tools for microbial ecology and clinical microbiology.

Evolution

Evolution is the change in a line of descent over time leading to new species or varieties.

The evolutionary relationships between life forms are the subject of the science of phylogeny.

Plus the genome in the chromosomes in the nucleus:
Mitochondria and chloroplasts of eukaryotes contain their own genomes
(DNA arranged in circular fashion, as in Bacteria) and ribosomes.

Ribosomal RNA Sequencing

Using ribosomal RNA sequencing technology, these organelles have been shown to be highly derived ancestors of specific lineages of Bacteria

Mitochondria and chloroplasts were thus once free-living cells that established stable residency in cells of Eukarya eons ago.

The process by which this stable arrangement developed is known as endosymbiosis.
PART II Microbial Diversity, Physiological Diversity of Microorganisms
All cells need carbon and energy sources

Chemoorganotrophs obtain their energy from the oxidation of organic compounds.
Chemolithotrophs obtain their energy from the oxidation of inorganic compounds.
Phototrophs contain pigments that allow them to use light as an energy source.
Autotrophs use carbon dioxide as their carbon source, whereas heterotrophs use organic carbon
Extremophiles thrive under environmental conditions in which higher organisms cannot survive.

Prokaryotic Diversity
Several lineages are present in the domains Bacteria and Archaea, and an enormous diversity of cell morphologies and physiologies are represented there.
Retrieval and analysis of ribosomal RNA genes from cells in natural samples have shown that many phylogenetically distinct but as yet uncultured prokaryotes exist in nature.

Eukaryotic Microorganisms
Algae,
Protozoa,
Fungi, slime molds
Plant and animal cells

Collectively, microbial eukaryotes are known as the Protista. Some protists, such as the algae, are phototrophic.
Cells of algae and fungi have cell walls, whereas the protozoa do not.
Some algae and fungi have developed mutualistic associations called lichens.