BIO 207: EXAM 1
Introduction to Microbiology
• Microbiology: the study of microorganisms, single-celled microscopic organisms,
which are microscopic but not cellular.
o They are independent entities that carry out their life processes
independently of other cells
o They are the smallest forms of life
o Unlike other cells, microbial cells can be grown to extremely high densities
in small-scale lab cultures, making them readily amenable to rapid
biochemical and genetic study
• The science of microbiology: understanding the living world of microscopic
organisms and applying our understanding of microbial life processes for the
benefit of humankind and planet earth.
• Cell: fundamental unit of life
• Isolated from other entities by a membrane—it is a compartment that maintains
the correct proportions of internal constituents, prevents leakage, while the wall
lends structural strength to the cell.
• Properties of cellular life (all cells):
o Metabolism: take up nutrients from the environment and transform them
into new cell materials and waste products. Energy is conserved in a form
that can be drawn upon by the cell to support the synthesis of key
Final result of metabolism: form 2 cells
o Growth: increase in cell number from cell division
o Evolution: process of descent with modification, based on reproductive
fitness. Typically a slow process but can be fast in microbial cells.
• Common properties of cellular life:
o Motility, typically by self-propulsion
o Differentiation: can produce modified cells specialized for growth,
dispersal, or survival
o Communication: respond to chemical signals in their environment
including those produced by other cells
• Cells can be biochemical catalysts or can be genetic entities
o Biochemical catalysts: carries out chemical reactions that constitute
Enzymes: cell’s catalytic machinery, supplies energy and
precursors for the biosynthesis of all cell components
o Genetic entities: genetic coding devices that can replicate DNA and
process it to form RNA and protein
o Catalytic and genetic functions are highly coordinated Microorganisms and their environments
• Population: group of cells derived from a single parental cell by successive cell
• Habitat: immediate environment in which a microbial population lives
• Microbial communities: populations of cells interact with other populations
• Ecosystem: all living organisms, together with the physical and chemical
components of their environment
Evolution and the extent of microbial life
• Cellular life present on earth about 3.8 bya
• Cyanobacteria (oxygenic phototrophs): began the slow oxygenation of earth
about 3 bya. Triggered by increases in oxygen levels in the atmosphere,
multicellular life forms eventually evolved and continued to increase in complexity
• Led to the evolution of 3 major lineages of microbial cells
o Eukarya: ancestors of plants and animals
• Microbial cells constitute the major fraction of biomass on earth and are key
reservoirs of essential nutrients for life
o Most of them reside underground, in the oceanic and terrestrial
Impact of microorganisms on humans
• Leading cause of death used to be infectious diseases… but today, they are
much less deadly
o Pathogens: microorganisms that cause infectious diseases
• Control of infectious disease: improved sanitary and public health practices, use
of antimicrobial agents such as antibiotics
• Agriculture: a number of major crop plants are legumes, which live in close
association with bacteria that form structures called nodules. The bacteria in
nodules convert atmospheric nitrogen into ammonia that the plants use for
growth. Microorganisms also inhabit ruminant animals, which help these animals
thrive on cellulose-rich food.
• However, microorganisms can also cause foodborne illnesses such as E.coli or
• Some microorganisms produce biofuels.
• Microbial bioremediation: used to clean up human pollution, and to produce
commercially valuable products by industrial microbiology and biotechnology.
o Works in 2 ways: introducing specific microorganisms to a polluted
environment, or by adding nutrients that stimulate pre-existing
microorganisms the degrade the pollutants
Pathways of discovery in microbiology
Robert Hooke Discovery of microorganisms Van Leeuwenhoek Discovery of bacteria
Louis Pasteur Mechanism of fermentation, defeat of
spontaneous generation, principles of
Ferdinand Cohn Discovery of endospores, Beggiatoa and
Robert Koch Koch’s postulates, pure culture
microbiology, discovery of agents in
tuberculosis and cholera
Pasteur and the defeat of spontaneous generation
• Spontaneous generation: organisms that arise spontaneously from nonliving
o Put a nonsterile liquid into a flask, and drew the neck of the flask out in
flame, and sterilized the liquid by extensive heating
o Liquid cooled slowly and dust and microorganisms were trapped in the
bend of the flask. After a long time, the liquid remained sterile indefinitely
o Then the flask was tipped so microorganisms could contact the sterile
liquid, and after a short period of time, the liquid putrefied
o Disproved spontaneous generation
Koch, infectious disease, and pure culture microbiology
• Koch’s postulates: criteria for definitively linking a specific microorganism to a
o The disease-causing organisms must always be present in animals
suffering from the disease but not in healthy animals
o The organism must be cultivated in a pure culture away from the animal
o The isolated organisms must cause the disease when inoculated into
healthy susceptible animals
o The organism must be isolated from the newly infected animals and
cultured again in the laboratory, after which it should be seen to be the
same as the original organism
• Pure culture: when a microorganisms is isolated and grown away from other
microorganisms in laboratory culture
o Agar: remains solid at room temp, can be made into liquid to pour into
sterile vessels, not degraded by most bacteria, typically yields a
• Microorganisms are essential for the well-being of the planet and its plants and
• Metabolism, growth, and evolution are necessary properties of living systems.
Cells must coordinate energy production and consumption with the flow of
genetic information during cellular events leading up to cell division.
• Microorganisms exist in nature in populations that interact with other populations
in microbial communities the activities of microorganisms in microbial communities can greatly affect and rapidly change the chemical and physical
properties of their habitats.
• Beijerinck and Winogradsky studied bacteria that inhabit soil and water. Out of
their work came the enrichment culture technique and the concepts of
chemolithotrophy and nitrogen fixation.
CHAPTER 2 &
Elements of microbial structure
• All cells have:
o Cytoplasmic membrane: separates the cytoplasm from the outside
o Cell wall: lends structural strength to a cell. It is relatively permeable and
located outside the membrane.
• Prokaryotes: bacteria and archaea
o Smaller internal structure, in which organelles are absent
o Can couple transcription directly to translation because DNA is in
cytoplasm and not enclosed within a nucleus
o Typical cell size is 1-5um long
o Haploid: contain a single copy of each gene
o House DNA in a nucleus (membrane-enclosed)
o Larger and more complex
o Key processes of DNA replication, transcription, and translation are
partitioned. Replication and synthesis inside nucleus, translation in
o Presence of membrane-enclosed organelles, such as mitochondria,
chloroplasts, ribosomes, etc.
o Diploid: contain two copies of each gene
• Viruses: they are not cells
o Much smaller, not a dynamic, open system but is static and stable, unable
to change or replace its parts by itself
o Only when it infects a cell does it acquire the ability to reproduce
o No metabolic capabilities of their own, lack ribosomes and contain only a
single form of nucleic acid
Arrangement of DNA in microbial cells
• Nucleus: DNA inside is organized to form chromosomes (Eukaryotes)
• Nucleoid: aggregation of chromosomes within a cell. (Prokaryotes)
• Plasmid: small circles of DNA distinct from chromosome. Typically contain genes
that confer a special property on a cell, rather than essential genes.
The evolutionary tree of life
• Evolution occurs in any self-replicating system • Phylogeny: evolutionary relationships between organisms. Phylogenetic
relatinships between cells can be deduced by comparing the genetic information
that exists in their nucleic acids or proteins
• Carl Woese: pioneered the use of comparative rRNA sequence analysis as a
measure of microbial phylogeny
The 3 domains of life
more closely related to eukarya than bacteria
• Eukarya: ancestors of multicellular organisms.
o Mitochondria and chloroplasts have been shown to be highly derived
ancestors of specific lineages of bacteria.
o Endosymbiosis: the theory of how this stable arrangement of cells led to
the modern eukaryotic cell with organelles
• Chemoorganotrophs: organisms that conserve energy from organic chemicals.
• Energy is conserved from the oxidation of the compound and is stored in the cell
• Aerobes: can obtain energy from an organic compound
only in the presence of oxygen
• Anaerobes: can obtain energy only in the
absence of oxygen
• Chemolithotrophs: organisms that obtain energy
from the oxidation of inorganic
compounds. Occurs only in prokaryotes.
• Phototrophs: do not require
chemicals as a source of energy.
Oxygenic and anoxygenic.
• Heterotrophs: require organic
compounds as their carbon source
• Autotrophs: use
carbon dioxide as their
carbon source =
autotrophs • Extremophiles: organisms inhabiting extreme environments. Don’t just tolerate
the environment, but require it in order to grow.
The evolutionary process
• Adaptive mutations in DNA sequence variation: improve the fitness of an
• Horizontal gene transfer: can bring in genes from near or distantly related
lineages as cells exchange genes by any of several mechanisms
Genes employed in phylogenetic analysis
• 16S ribosomal RNA (rRNA): universally distributed, functionally constant,
sufficiently conserved (slow-changing), and are of adequate length to provide a
deep view of evolutionary relationships.
• RDP: contains a collection of such sequences nd provides computational
programs for analytical purposes
• Molecular clocks: sequences that change at a constant rate, of shared
evolutionary ancestry, that encode functionally equivalent molecules. Allows the
time in the past when the 2 sequences diverged from a common ancestral
sequence to be estimated
Analytical analysis of evolution
• PCR: binds to gene of interest, allowing DNA polymerase to bind to and copy the
o Primer design: matter of deciding which sequence to use to amplify a
specific gene and then actually constructing the sequence
• Sequence alignment: aligns sequences and identify genes homologous to a
specific sequence from among the many thousands already sequenced
• Phylogenetic trees: consists of nodes and braches
o Tips of branches represent species that exist now
o Nodes: points in evolution where an ancestor diverged into 2 new
o Branches: define both the order of descent and the ancestry of the nodes,
and the length represents the number of changes that have occurred
along that branch
• Universal phylogenetic tree: genealogy of all life on earth
• Bacteria: proteobacteria—collectively shows all known forms of microbial
• Archaea: two major phyla—Crenarchaeota and Euryachaeota
• In rocks 3.5 billion years old or younger, microbial formations called stromatolites
are abundant and show extensive microbial diversification
• Early bacteria and archaea diverged from a common ancestor as long as 4 bya.
Microbial metabolism diversified on early earth with the evolution of
methanogenesis and anoxygenic photosynthesis. Oxygenic photosynthesis eventually led to an oxic earth, banded iron formations, and great bursts in
metabolic and cellular evolution.
• Eukaryotic cell developed from endosymbiotic events. Most likely scenario: H2
producing species of bacteria was incorporated as an endosymbiont into a H2
consuming species of archaea. The modern eukaryotic cell is a chimera with
genes and characteristics from both bacteria and arachaea.
• Genes govern the properties of cells, and cell’s complement of genes is called its
genome. DNA is arranged in cells as chromosomes. In eukaryotes—linear, in
• Morphology: cell shape
• Though cell morphology is easily recognized, it is in general a poor predictor of
other properties of a cell
• Selective forces likely to be in play in setting the morphology of a given species:
optimization for nutrient uptake, swimming motility in viscous environments or
near surfaces, etc. However, it is genetically directed and has evolved to
Cell size and
• Very large cells
not common in
• • A
dvantages to being small: higher surface-to-volume
ratio, supports a faster rate of nutrient exchange, grow faster,
and with a given amount of resources, will support a larger population of small
cells than of large cells.
• Mutation rates roughly the same in all cells. In prokaryotes, there is the capacity
for more rapid growth and evolution because they are small and are genetically
haploid (allowing mutations to be expressed immediately). • However, cannot be too small because you need to consider the volume needed
to house the essential components of a free-living cell.
The cytoplasmic membrane
• A thin barrier that surrounds the cell and separates the cytoplasm from the cell’s
environment. If membrane is broken, the cytoplasm will leak and the cell will die.
• Composition of membranes: phospholipid bilayer with hydrophobic tails and
hydrophilic heads, and proteins embedded on it.
o Membrane proteins: major proteins have hydrophobic surfaces. Outer
surface interacts with the environment and inner side interacts with
proteins involved in energy-yielding reactions. These proteins are called
integral membrane proteins.
o Arranged in clusters which allows proteins that need to interact to be
adjacent to one another.
o In bacteria and eukarya, ester linkages bond the fatty lipids the glycerol.
• Cytoplasmic membranes of some bacteria are strengthened by hopanoids.
• Archaeal membranes: lack true fatty acid side chains and instead, the side
chains are composed of repeating units of the hydrophobic 5-carbon
o Lipids contain ether bonds
o Forms a lipid monolayer: extremely resistant to heat denaturation and are
therefore widely distributed in hyperthermophiles.
Functions of the cytoplasmic membrane
• Permeability barrier: small hydrophobic molecules pass the membrane by
diffusion, and polar and charged molecules do not diffuse but are transported
o However, water passes freely because it is small and there are transport
proteins, called aquaporins, that accelerates the movement of water
across the membrane
• Transport proteins: accumulate solutes against the concentration gradient.
o Shows a saturation effect: if concentration of substrate is high enough to
saturate the transporter, the rate of uptake becomes maximal.
o High specificity: react only with a single molecule
o Highly regulated
• The site of generation and use of the proton motive force
• Inclusions function as energy reserves and as reservoirs of structural building
• Carbon storage polymers
o PHB: synthesized when there is an excess of carbon and are broken
down for biosynthetic or energy purposes
o Glycogen: storehouse of both carbon and energy. Consumed when
carbon is limited
• Polyphosphate and sulfur
o Can be degraded and used as sources of phosphate for nucleic acid and
phospholipid biocyntheses o Phosphate is often a limiting nutrient in natural environments
o Many gram-negative prokaryotes can oxidize reduced sulfur compounds…
elemental sulfur accumulates and remains in the cell as long as the
source of reduced sulfur is still present.
• Magnetic storage inclusions: magnetosomes
o Allows bacteria to orient themselves specifically within a magnetic field
o Imparts a magnetic dipole on a cell… but major function is unknown.
o Surrounded by a thin membrane containing phospholipids, proteins, and
• A gas-filled structure made of protein. Confers buoyancy on a cell when present
in the cytoplasm in large numbers. They decrease cell density
• Spindle-shaped structures and are hollow, yet rigid. Can be seen under
microscopes… gas vacuoles.
• Composed of 2 different proteins: GvpA—forms the vesicle shell and is very rigid,
and GvpC—functions to strengthen the shell by cross-linking copies of GvpA
• Chemotaxis: movement toward or away from a chemical
o Most research has been done with E. coli.
o In the absence of a gradient, cells move in a random fashion.
Run—cell swimming forward in a smooth fashion. Flagellar motor
Tumble—cell stops and jiggles about. Flagellum rotates clockwise.
o If there is a gradient, the organism will move up the concentration gradient
towards the attractant… a directed movement.
o Sense by chemoreceptors, which bind the chemicals and begin the
process of sensory transduction to the flagellum.
o Measuring chemotaxis: insert capillary into a bacterial suspension, which
forms a chemical gradient. The control capillary has a salt solution (neither
attractant nor a repellant), and the cell concentration inside capillary is
same as outside. In a capillary with an attractant, accumulation of bacteria
in the capillary and vice versa.
• Phototaxis: movement of a cell toward light
o Advantage: allows organism to orient itself most efficiently to receive light
o Bacteriochlorophylls and carotenoids
o 2 different light-mediated taxes are observed in phototrophic bacteria:
Scotophobotaxis: occurs when a phototrophic bacterium happens
to swim outside the illuminated fi