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Copyright © 2011 Pearson Education Inc.
Microbial growth and nutrition
Growth requirements
Organisms use a variety of nutrients for their energy needs and
to build organic molecules and cellular structures
Most common nutrients – those containing necessary elements
such as carbon, oxygen, nitrogen, and hydrogen
Microbes obtain nutrients from variety of sources
Carbon is backbone of all organic components present in cell
(we are carbon based life forms)
Hydrogen and oxygen are also found in many organic molecules
Electrons play a role in energy production (e.g. electron
transport chain) and reduction of molecules during biosynthesis
(e.g. CO2 to form organic molecules)

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Microbial growth
In microbes, growth is an increase in size and in a population
Result of microbial growth is the formation of discrete colony.
A colony is an aggregation of cells arising from single parent
cell
Reproduction results in growth in population
Micronutrients (trace elements)
In addition to macroelements (macronutrients), cells also need
micronutrients (trace elements) for metabolism and growth.
Manganese (Mn), Zinc (Zn), Cobalt (Co), Molybdenum (Mo),
Nickel (Ni), and Copper (Cu).
Required in trace amounts

Often supplied in water or in media components
Ubiquitous in nature
Serve as part of enzymes and cofactors
Some organisms have particular requirements besides the macro
and micronutrients.
Growth Requirements
Chemical and energy requirements
Carbon and energy requirements
Two groups of organisms based on source of carbon:
Autotrophs: Those using an inorganic carbon source (carbon
dioxide) are autotrophs
Heterotrophs: Those catabolizing reduced organic molecules
(proteins, carbohydrates, amino acids, and fatty acids) are
heterotrophs
Two groups of organisms based on source of energy
Chemotrophs: Those that acquire energy from redox reactions
involving inorganic and organic chemicals are chemotrophs
Phototrophs: Those that use light as their energy source are
phototrophs
Two groups of organisms based on based on electron source
Lithotrophs use reduced inorganic substances
Organotrophs obtain electrons from organic compounds
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Groups of organisms based on carbon and energy source
Four basic groups of organisms: Based on their carbon and
energy sources, most organisms are categorized into one of four
basic groups: photoautotrophs, chemoautotrophs,
photoheterotrophs and chemoheterotrophs (See table below)
Major groups of organisms based on carbon and energy source
Growth Requirements
Oxygen requirements
Oxygen is essential for obligate aerobes (final electron acceptor
in ETC)
Oxygen is deadly for obligate anaerobes. How can this be true?
Neither gaseous O2 nor oxygen covalently bound in compounds
is poisonous
The forms of oxygen that are toxic are those that are highly
reactive (reactive oxygen species or ROS)
ROS are excellent oxidizing agents
Resulting chain of oxidations cause irreparable damage to cells
by oxidizing compounds such as proteins and lipids

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Oxygen requirements
Classification of organisms based on oxygen requirements
Aerobes – undergo aerobic respiration
Anaerobes – do not use aerobic metabolism
Facultative anaerobes – can maintain life via fermentation or
anaerobic respiration or by aerobic respiration (e.g. E. coli)
Aerotolerant anaerobes – do not use aerobic metabolism but
have some enzymes that detoxify oxygen’s poisonous forms
(e.g. Lactobacilli)
Microaerophiles – aerobes (e.g. Helicobacter pylori) that
require oxygen levels from 2-10% and have a limited ability to
detoxify hydrogen peroxide and superoxide radicals
Oxygen requirements
Identifying the oxygen requirements of organisms
Strict aerobes – require oxygenStrict anaerobes – require no

oxygenMicroaerophiles
requires 2–10% O2Facultative anaerobes
do not require O2 but grow better in its presence Aerotolerant
anaerobes – tolerate presence of oxygen;
grow with or without O2
Growth Requirements
Four toxic forms of oxygen
Singlet oxygen (1O2) – molecular oxygen with electrons
boosted to higher energy state, e.g. during aerobic metabolism
A very reactive oxidizing agent used by phagocytic cells to kill
invading pathogens
Produced during photosynthesis, so phototropic organisms have
carotenoids that prevent toxicity by removing the excess energy
of singlet oxygen
Superoxide radicals (O2-) – some form during incomplete
reduction of oxygen during electron transport in aerobes
(aerobic respiration) and during metabolism by anaerobes
(anaerobic respiration) in the presence of oxygen
So reactive that aerobes produce superoxide dismutases (SODs)
to detoxify superoxide radicals (O2-)
Anaerobes lack superoxide dismutase and die as a result of
oxidizing reactions of superoxide radicals formed in the
presence of oxygen

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Growth Requirements
Four toxic forms of oxygen (continued)
Peroxide anion (O22–): hydrogen peroxide formed during
reactions catalyzed by superoxide dismutase and other
metabolic reactions contains another highly reactive oxidant,
peroxide anion (O22–); makes hydrogen peroxide an effective
antimicrobial agent
Catalase converts hydrogen peroxide to water and molecular
oxygen and peroxidase in the presence of a reducing agent
(NADH+) breaks down hydrogen peroxide to water without
forming oxygen
2H2O2 ↔ 2H2O + O2
H2O2 + 2NADH ↔ 2H2O + 2NAD+
Aerobes contain either catalase or peroxidase to detoxify
peroxide anion
Obligate anaerobes either lack both enzymes or have only a
small amount of each
Growth Requirements

Four toxic forms of oxygen (continued)
Hydroxyl radical (OH·)
Hydroxyl radical – results from ionizing radiation and from
incomplete reduction of hydrogen peroxide:
H2O2 + e- + H+ → H2O + OH·
The most reactive of the four toxic forms of oxygen
Not a threat to aerobes due to action of catalase and peroxidase
Aerobes also use antioxidants such as vitamins C and E to
protect against toxic oxygen products
Antioxidants provide electrons that reduce toxic forms of
oxygen
Catalase test
Figure 6.2
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Growth Requirements
Nitrogen and other requirements
Nitrogen is an essential element contained in many organic and

inorganic compounds or nutrients. Anabolism often ceases due
to insufficient nitrogen needed for proteins and nucleotides.
Often, nitrogen is growth limiting nutrient
All cells recycle nitrogen from amino acids and nucleotides
The reduction of nitrogen gas to ammonia (nitrogen fixation) by
certain bacteria is essential to life on Earth because nitrogen is
made available in a usable form
Other chemical requirements are:
Phosphorus: required for phospholipid membranes, DNA, RNA,
ATP, and some proteins
Sulfur: a component of sulfur-containing amino acids, disulfide
bonds critical to tertiary structure of proteins, and in vitamins
(thiamin and biotin)
Trace elements: only required in small amounts, but usually
found in sufficient quantities in tap water
Growth factors: necessary organic chemicals (vitamins, certain
amino acids, purines, pyrimidines, cholesterol, NADH, and
heme) that cannot be synthesized by certain organisms)
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Growth Requirements
Amino acids
needed for protein synthesis
Purines and pyrimidines
needed for nucleic acid synthesis
Vitamins

function as enzyme cofactors
Heme
for synthesis of cytochromes
Other chemical requirements
Growth Requirements
Physical requirements
In addition to chemical (nutrients) requirements, organisms
need temperature, pH, osmolality and pressure for growth.
Temperature
Plays important role in microbial life (growth limiting factor)
At higher temperature, proteins denature and lose their function
Effect of temperature on lipid-containing membranes of cells
and organelles
If too low, membranes become rigid and fragile
If too high, membranes become too fluid and cannot contain the
cell or organelle
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Effects of temperature on microbial growth
Figure 6.4
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Effects of temperature on microbial growth
Categories of microbes based on temperature range
Different temperatures have different effects on microbial
growth and survival
Based on preferred temperature ranges (minimum, optimum and
maximum growth temperature) at which organisms are able to
conduct metabolism, microbes are categorized into four groups:
Psychrophiles: grow best at temperatures below about 15ºC
(some cause food spoilage in refrigerators)
Mesophiles: grow best in temperatures ranging from 20ºC to
40ºC (include human and animal pathogens)
Thermophiles: these grow best in temperatures ranging from 40
ºC and 80ºC (thermoduric organisms are mesophiles that briefly
survive high temperature and cause food spoilage, e.g.,
pasteurized and canned food stuff)
Hyperthermophiles: grow in water above 80ºC (e.g. archaea)
and others more than 100C. Thermophiles and
hyperthermophiles do not cause diseases

Categories of microbes based on temperatures for growth
Figure 6.5
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An example of a psychrophile
Figure 6.6
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Growth Requirements
Chemical requirements
Organisms are sensitive to changes in acidity because, H+ and
OH- interfere with H-bonding in proteins and nucleic acids
Most bacteria and protozoa grow best in a narrow range around
neutral pH (6.5-7.5) – these organisms are called neutrophiles
Other bacteria and fungi are acidophiles – grow best in acidic

habitats (acido-tolerant). Helicobacter pylori grows in the
stomach by neutralizing acid by secreting bicarbonate and
urease
Acidic waste products can help preserve foods by preventing
further microbial growth
Alkalinophiles live in alkaline soils and water up to pH 11.5.
Vibrio cholerae grows best at pH 9.0 outside of the body in
water
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Growth Requirements
Physical effects of water
Microbes require water to dissolve enzymes and nutrients
required in metabolism
Water is important reactant in many metabolic reactions
Most cells die in the absence of water
Some have cell walls that retain water (e.g. Mycobacterium
tuberculosis has a waxy substance called mycolic acid)
Endospores and cysts can cease most metabolic activity for
years
Two physical effects of water on microbes:
Osmotic pressure: Pressure exerted on a semipermeable

membrane by a solution containing solutes that cannot freely
cross membrane (dissolved molecules and ions in a solution)
Hydrostatic pressure: Water exerts pressure in proportion to its
depth. For every additional 10m of depth, water pressure
increases 1 atmosphere. Organisms that live under extreme
hydrostatic pressure are called barophiles
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Growth Requirements
Solution
s and physical effects of solutions
Osmotic pressure
The pressure exerted on a semipermeable membrane by a
solution containing solutes that cannot freely cross membrane
(related to concentration of dissolved molecules and ions in a
solution)

Hypotonic solutions: have lower solute concentrations; cells
placed in these solutions will swell and burst
Hypertonic solutions: have greater solute concentrations. Cells
placed in these solutions will undergo plasmolysis (shriveling
of cytoplasm). This effect helps preserve some foods and
restricts organisms to certain environments
Two categories of organisms growing under hypertonic
environments: Obligate halophiles (grow in up to 30% salt) and
facultative halophiles (can tolerate high salt concentrations ,
e.g. S. aureus does not require salt but can tolerates up to 20%
concentration)
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Growth Requirements
Ecological associations and relationships
Associations and biofilms
Organisms live in association with individuals of their own or
with different species
Antagonistic relationships: when one organism harms or kills
another
Synergistic relationships: members cooperate such that each
benefits from the relationship
Symbiotic relationships: organisms live interdependently such
that they rarely live outside the relationship
Biofilms: Complex relationships among numerous individual
microorganisms
Develop an extracellular matrix: matrix adheres cells to one
another; allows attachment to a substrate; sequesters nutrients
and may protect individuals in the biofilm

Biofilms formation on surfaces is often as a result of quorum
sensing
Biofilm-forming organisms have the ability to cause diseases in
humans. Salmonella enterica, Pseudomonas aeroginosa and
Staphylococcus aureus cause dental plaque on teeth
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Plaque on a human toothAssociations and Biofilms
Biofilms
Complex relationships among numerous microorganisms
Form on surfaces, medical devices, mucous membranes of
digestive system
Form as a result of quorum sensing
Many microorganisms more harmful as part of a biofilm
Scientists seeking ways to prevent biofilm formation

Biofilm development
Culturing Microorganisms
Culturing microorganisms
Inoculum: a sample (specimen) introduced into medium (liquid
or solid). There are 3 types of specimens (samples):
Environmental specimens
Stored specimens
Clinical specimens (clinical sampling):
Disease diagnosis and treatment depend upon correct clinical
specimens collection, transportation and isolation and
identification of pathogens

Clinical specimens (e.g. feces, saliva, blood, sputum,
cerebrospinal fluid etc.) must be collected in sterile containers
and be free of contaminants
Collected specimens must be properly labeled and transported
quickly to a lab in transport medium to avoid death of
pathogens
Culture: refers to act of cultivating microorganisms or the
microorganisms that are cultivated
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Culture media: Majority of prokaryotes have never been grown
in culture media. There are six types of general culture media:
Defined (synthetic) media: one in which the exact composition
is known (for fastidious organisms requiring a relatively large
number of growth factors such as blood)
Complex media: contain nutrients released by the partial
digestion of yeast, beef, soy, or proteins (casein from milk).
The exact chemical composition of media is unknown but used
to culture organisms whose exact nutritional needs are
unknown, including fastidious organisms
Selective media: contain substances that either favor the growth
of particular microorganisms or inhibit the growth of unwanted
ones. Eosin, methylene blue, crystal violet dyes and bile salts
inhibit Gram-positive organisms. High concentration of salt
favors the growth of S. aureus and slightly low pH favors the
growth of fungi
Differential media: media formulated to either differentiate

visible changes in medium or differences in the appearance of
colonies. Presence or absence of hemolysis in blood agar by
Streptococci
Anaerobic media: anaerobes require culturing media with
reducing compounds (e. g. sodium thioglycollate) that
chemically combine with free oxygen and remove it with from
medium
Transport media: media to transport clinical specimens to labs
(maintain ratios among different microorganisms in samples,
prevent contamination and keep organisms alive for short period
of time
Examples of culture media
Slant tube containing solid media

Obtaining pure culture
Cultures are composed of cells arising from a single progenitor
The progenitor from which a particular pure culture (axenic) is
derived is called colony forming unit (CFU)
Aseptic technique is used to prevent contamination of sterile
substances or objects
Two common isolation techniques:
Streak Plates
Pour Plates
The streak-plate method of isolation

The pour-plate method of isolation
Characteristics of bacterial colonies
Figure 6.8
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An example of the use of a selective medium
Figure 6.12
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The use of blood agar as a differential medium
Figure 6.13
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The use of carbohydrate tubes as differential media
Figure 6.14
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MacConkey agar as a selective and differential medium
Figure 6.15

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Special culture techniques
Techniques developed for culturing microorganisms
Animal and cell culture: technique used for growing microbes
for which artificial media are inadequate (e.g. Mycobaterium
leprae in armadillos and Treponema pallidum in rabbits)
Low-oxygen culture: carbon dioxide incubators (candle jars)
maintain relatively high concentration of carbon dioxide and
low levels of oxygen. GasPacks (chemical released combine
with free oxygen and create anaerobic atmosphere). Strict
anaerobes are studied in labs using large anaerobic glove boxes.
Ideal for growing aerotolerant anaerobes, microaerophiles and
capnophiles (e.g. Neisseria gonorrhoeae)

Enrichment culture: enhance the growth of less abundant but
potentially important microorganisms
Use of selective media and cold incubation in the refrigerator
(cold enrichment)
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GasPack Candle Jar

Preserving cultures
Refrigeration: preserving and storing microorganisms in the
cold for short period of time
Deep-freezing: freezing cells at temperatures from -50 Celsius
to -95 Celsius and used for long-term (years) storage
Lyophilization (freeze-drying): removal of water from frozen
cultures using intense vacuum
Used for long-term preservation and storage (decades)
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Growth of Microbial Populations
Growth of microbial populations

Most unicellular microorganisms reproduce by binary fission
(divide into two cells and each of these new cells divide in two
to make four and so on)
This type of growth is called logarithmic or exponential growth,
different from arithmetic growth (simple addition)
Phases of microbial growth
A graph that is used to plot the number of organisms in a
growing population over time is known as a growth curve
When bacteria are inoculated into a liquid media, there are four
distinct phases to a population’s growth curve (see figure below
for phases of microbial growth):
Lag phase
Log phase
Stationary phase
Death phase

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Generation (doubling) time
Time required for the population to double in size
Varies depending on species of microorganism and
environmental conditions
Range is from 10 minutes for some bacteria to several days for
some eukaryotic microorganisms
Binary fission

The arithmetic of generation time
Where n = number of generations
A comparison of arithmetic and logarithmic growth
Figure 6.19
Arithmetic growth
Logarithmic growth
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The growth curve
Observed when microorganisms are cultivated in batch culture
Culture incubated in a closed vessel with a single batch of
medium
Usually plotted as logarithm of cell number versus time

Time required for a bacterial cell to grow and divide
Dependent on chemical and physical conditions
Has four distinct phases: Lag, exponential, stationary and death
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Measuring microbial reproduction
Estimating the number of microorganisms in a sample is
important for determining the severity of urinary tract
infections, effectiveness of pasteurization, degree of fecal
contamination of water and effectiveness of disinfectants and
antibiotics

Direct methods for determining the number of microorganisms
in a given amount of sample are:
Serial dilution and viable plate counts
Membrane filtration
Most probable number
Microscopic counts
Electronic counters
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Viable plate count
Ten-fold serial dilution of samples are made in liquid medium
and 0.1ml of each dilution is either directly poured onto a plate

and spread or mixed with melted agar medium and poured into
plates
After incubation, plates with colonies ranging from 30 to 300
are counted and the number of colonies counted (CFU) is
multiplied by the reciprocal of the dilution (dilution factor) to
estimate/determine the number of bacteria per ml of the original
culture
Membrane filtration
More accurate viable count for samples with few number of
microorganisms (e.g. fecal bacteria in a stream or pond)
Samples are filtered and microorganisms trapped on membrane
filter are transferred onto solid medium and incubated
The number of bacteria in the original sample is estimated from
the number of colonies (CFU) determined on the growth
medium multiplied by the volume of sample filtered
Serial dilution and viable plate count

Figure 6.22
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Membrane filtration
Microscopic Counts
Microscopic counts
Suitable for stained prokaryotes and relatively large eukaryotes
Sample placed on cell counter (Petroff-Hauser Counting
Chamber) and the number of bacteria in 25 large squares is
counted and averaged

The number of bacteria per ml of bacterial suspension is
calculated by multiplying the mean number of bacteria per
square by 1.25X106 (25X50X1X103)
Advantageous when there are more than 10X106 cells ml or
when a speedy estimate of population size is required
Method cannot differentiate between dead and live cells and
difficult to count motile cells
Microscopic Counts
Most probable number (MPN)
Most probable number (MPN)
Method used for statistical estimation of the number of
microorganisms that will not grow on solid media (e.g. algae

seldom form distinct colonies), when bacterial counts are
required routinely, and when samples of waste-water, drinking
water and food samples contain too few organisms to use a
viable plate count
Positive tubes that show turbidity, pH change or gas production
in each set of tubes are counted (e.g. 4, 2, 1, figures below) and
compared to the numbers in an MPN table to estimate the
number of organisms per 100 ml of sample
Electronic counters
Coulter counter (useful for counting larger cells of yeasts, algae
and protozoa) and flow cytometry (counts bacteria and other
cells differentially stained with fluorescent dyes or tagged with
fluorescent antibodies)
The most probable number method (MPN)
Figure 6.24

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Measuring microbial growth
Indirect methods
Metabolic Activity: Estimates the number of cells in a culture
(whose metabolic rate is established) by measuring changes in
such things as nutrient utilization, waste production or pH

Dry Weight: microorganisms are filtered from their culture
medium, dried and weighed; method is suitable for broth culture
Turbidity: An indirect method for estimating the growth of
microbial population by measuring changes in turbidity using
spectrophotometer; easy and rapid results but only useful if the
concentration of cells exceeds 1 million per ml; method does
not distinguish between dead and live cells
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Indirectly measuring population size
Figure 6.26
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Measuring microbial growth
Genetic methods
Isolate DNA sequences of un-culturable prokaryotes
Used to estimate the number of these microbes
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Microscopy, Staining, and Classification

General principles of microscopy
Wavelength of radiation
Resolution
Contrast
Magnification
Wavelength of radiation
Distance between two corresponding parts of a wave of
radiation (from crest to crest or trough to trough)
visible light or electromagnetic, including X-rays, microwaves
and radio waves)
The shorter the wave length of radiation, the stronger the
resolving power
The electromagnetic spectrum

Resolution (resolving power)
Ability to distinguish between objects that are close together
Resolution is determined by the wavelength of light used and
numerical aperture of lens. Resolution distance is dependent on
wave length of light, electron beam and/or numerical aperture
of the lens
Modern microscopes use shorter wave length radiation and have
lenses with larger numerical apertures
Limit of resolution for light microscope is about 0.2 µm.
Contrast
Difference in intensity between two objects or between an
object and its background
Important in determining resolution (clarity of an image)
Staining increases contrast
Resolution and contrast determine the magnification of a
microscope
Use of light that is in phase increases contrast

Magnification
An increase in size of an object.
Results when a beam of radiation bends as it passes through a
lens
Curved lenses refract light and magnetic fields (magnetic
lenses) refract electron beams
Lenses refract (bend) radiation because they are optically dense
compared to other media (air or water)
Magnification depends on the thickness of the lens, its
curvature and the speed of light through its medium (substance
such as glass, lens, air or water)
Lenses and the bending of light
When a ray of light passes from one medium to another,
refraction occurs (the light is bent at the interface).

The refractive index (n) is a measure of how greatly a substance
slows the velocity of light. The direction and magnitude of
bending are determined by the refractive indices of the two
media forming the interface.
Refraction
Light beam enters head on
Light beam enters glass at angle to normal
Air
n = 1
Air
n = 1
Air
n = 1
Air
n = 1
Glass
n = ~1.5
Glass

n = ~1.5
Dashed line depicts the normal
Light
Light
Bending of light through a rism
Prism
Air
Air
Glass
Normal
Normal
Light
n = 1
n = 1
n = ~1.5
Slowed down
Sped up
Can also say the air is less optically dense than glass.
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F = focal point
The Convex Lens
f = focal length
Lens
Air
Air
Glass
magnification
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Refractive Properties of Lenses
Flat glass
Convex lens (less round)
Convex lens (more round)
Concave lens

Light refraction and image magnification
Units of Measurement
Range of Light and Electron Microscopes
Light
Electron
Rhodospirillum rubrum
Photoionization microscopy
These are all things you absolutely can not see without
microscopes. Know that viruses are smaller than a um and can
not be seen with light microscope. Know that bacteria are in the
um in sizes and can typically be seen with light microscope.

Thin section TEM at bottom right.
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Types of microscopes
Light microscopes include:Bright-field Dark-fieldPhase-
contrastFluorescenceConfocal
Modern microscopes use visible light to illuminate cells and are
compound, meaning that they have two sets of lenses.
Bright-field microscopes aren’t ideal for viewing unpigmented
and unstained cells due to lack of contrast. What if you need to
see living cells?
These light microscopes are more useful:
Dark-field microscopePhase-contrast microscopeDifferential
interference (DIC) microscope.
© 2014 Pearson Education, Inc.
Types of microscopy
Light MicroscopyBright-field microscopesSimpleContain a
single magnifying lensSimilar to magnifying glassLeeuwenhoek
used simple microscope to observe microorganisms

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Types of microscopyLight MicroscopyBright-field
microscopesCompoundSeries of lenses for magnificationLight
passes through specimen into objective lens Oil immersion lens
increases resolutionHave one or two ocular lensesTotal
magnification = magnification of objective lens X magnification
of ocular lensMost have condenser lens (direct light through
specimen)
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A bright-field, compound light microscope.
Coarse focusing knob

Moves the stage up and
down to focus the image
Illuminator
Light source
Diaphragm
Controls the amount of
light entering the condenser
Condenser
Focuses light
through specimen
Stage
Holds the microscope
slide in position
Objective lenses
Primary lenses that
magnify the specimen
Body
Transmits the image from the
objective lens to the ocular lens
using prisms
Ocular lens
Remagnifies the image formed by
the objective lens

Line of vision
Ocular lens
Path of light
Prism
Body
Objective
lenses
Specimen
Condenser
lenses
Illuminator

Fine focusing knob
Base
Arm
Routinely used in microbiology to examine both stained and
unstained specimens. Specimens are visualized because of
differences in contrast (density) between specimen and
surroundings.
Named for its ability to form a dark image against a brighter
background.
Parfocal – specimen remains in focus as you change objectives.
Multiply objective and ocular magnification to obtain total
magnification.

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The effect of immersion oil on resolution
Glass cover slip
Slide
Specimen
Light source
Without immersion oil
Lenses
Immersion oil
Glass cover slip
Slide
Light source
With immersion oil

Microscope
objective
Refracted light
rays lost to lens
Microscope
objective
More light
enters lens
Immersion oil redirects light rays by minimizing refraction and
prevents reflection, resulting in increased numerical aperture
and resolution.
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Dark-Field MicroscopeProduces detailed images of living,
unstained specimens by changing the way in which they are
illuminated.
Unreflected and unrefracted rays do not enter the objective.

Object appears bright on black background.
Dark-Field Microscopy
Treponema pallidum (syphilis)
Useful for study of internal structure of eukaryotic
microorganisms and for observing motility.
S. Cerevisiae
Microscopy
Light microscopy
Phase microscopes
Used to examine living organisms or specimens that would be
damaged or altered by attaching them to slides or staining them
These microscopes treat one set of light rays differently from
another set
Light rays in phase produce brighter image, while light rays out
of phase produce darker image

Contrast is created because light waves are ½ wavelength out of
phase
Two types
Phase Contrast Microscope: produce shapely defined images in
which fine structures can be seen in living cells; useful for
observing cilia and flagella
Differential Interference Contrast Microscope(Nomarski
microscopes): Create phase interference patterns; gives the
image a three-dimensional or shadowed appearance
Phase-Contrast Microscope
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Four kinds of light microscopy

Fluorescent microscopy
Fluorophores are molecules that absorb energy and emit light,
this is the basis of fluorescence microscopy. When some
molecules absorb radiant energy, they become excited and
release much of their trapped energy as light (emission).
Fluorescence light is emitted very quickly by the excited
molecule as it gives up its trapped energy and returns to a more
stable state.
Explain how antibodies are used in fluorescence microscopy.
Mbl is a cytoskeletal protein of Bacillis subtilis.
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Immunofluorescence

StainingMost microorganisms are difficult to view by bright-
field microscopyColoring specimen with stain increases contrast
and resolutionSpecimens must be prepared for stainingThin
smear (film) of microorganisms on glass slides is made prior to
staining Smear is allowed to air-dry and then heat-fixed to glass
surface
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StainingPrinciples of StainingMicrobiological stains/dyes used
as stains are usually salts composed of cation and anion and
contain one colored substance (chromophore)
Acidic dyes (anionic chromophores) stain alkaline structures
(positively charged molecules). Acidic dyes are also used in
negative staining
Basic dyes (cationic chromophores) stain acidic structures
(negatively charged molecules). They are used more commonly

in microbiology because most microbial cells are negatively
charged.
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Types of stainingSimple stains
Differential stains Gram stainAcid-fast stainEndospore stain
Special stains Negative (capsule) stainFlagellar stain
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Simple StainingCommonly used and easy.
Fixed smear is covered with a single basic dye such as crystal
violet, excess stain is washed off with water, and blotted dry.
Used to determine the size, shape, and arrangement of bacterial
and archaeal cells.

Differential Stains
Distinguish organisms based on their staining properties.
For example, the Gram stain, developed in 1884 by the
Danish physician Christian Gram, is the most widely
employed staining method in bacteriology.
Gram stain divides most bacteria (but not archaea) into two
groups – those that stain gram negative and those that stain
gram positive.
Acid-fast stain

Mixed stain: Gram positive (purple) Acid-fast stain
and Gram negative stain (pink)
The Gram Staining Procedure
Special stains: Preparation and staining of specimens
Most dyes are used to directly stain the cell or object of interest
to make internal and external structures of the cell more visible.
Some dyes (special stains, e.g., India ink) are used in negative
staining, where the background but not the cell is stained. The
unstained cells appear as bright objects against a dark
background.
Negative stain (Capsule stain)

Flagella
Flagellar stain of Proteus vulgaris
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Staining and microscopy
Staining
Staining for Electron MicroscopyChemicals containing heavy
metals used for transmission electron microscopy Stains may
bind molecules in specimens or the backgroundElectrons

replace light as the illuminating beamWavelength of electron
beam is much shorter than light, resulting in much higher
resolutionAllows for study of microbial morphology in great
detail
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Electron Microscopy
The Transmission Electron Microscope (TEM)Electrons scatter
when they pass through thin sections of a specimen
Transmitted electrons are under vacuum which reduces scatter
and are used to produce clear image
Denser regions in specimen, scatter more electrons and appear
darker
Wavelength of an electron in a TEM can be as short as 2.5 pm
as in picometers as in 2.5 x 10-12 m
That’s ~100,000 times shorter wavelength than a light

microscope uses.
*
Transmission electron microscope (TEM)
Specimen is coated with plastic and cut really thin 20-100 nm
thick slices.
*
The Scanning Electron MicroscopeUses electrons reflected from
the surface of a specimen that is coated in metal to create
detailed image
Produces a realistic 3-dimensional image of specimen’s surface
features
Resolution of 7 nm.
Can determine actual in situ location of microorganisms in
ecological niches

*
Scanning Electron Microscope (SEM)
Mycobacterium tuberculosis
Classification and Identification of Microorganisms
Classification and identification of microorganisms
Taxonomy is the science of classifying and naming organisms
Taxonomy consists of:
classification (assigning organisms to taxa based upon
similarities)
Nomenclature (rules of naming organisms) and
Identification (determining which individual organism or

population belongs to a particular taxa)
Enables scientists to organize large amounts of information
about organisms
Make predictions based on knowledge of similar organisms
Linnaeus, Whittaker, and taxonomic categories
Linnaeus
Linnaeus provided system that standardized the naming and
classification of organisms based on characteristics they have in
common
Grouped similar organisms that can successfully interbreed into
categories called species
Used binomial nomenclature in his system
Binomial Nomenclature (assigning two names to every
organism)

Linnaeus proposed only two kingdoms: animalia and plantae
Whitaker proposed taxonomic approach based on five kingdoms:
Animalia, Plantae, Fungi, Protista, and Prokaryotae (widely
accepted)
Taxonomic categories
Linnaeus’s goal was classifying and naming organisms as a
means of cataloging them
Today, more modern goal of understanding relationships among
groups of organisms
Major goal of modern taxonomy is to reflect phylogenetic
hierarchy (derivation from common ancestors)
Greater emphasis on comparisons of organisms’ genetic
material led to proposal to add a new, most inclusive taxon, the
domain

Domains
Taxonomists compare nucleotide sequences of the smaller rRNA
subunits of both prokaryotes and eukaryotes
Carl Woese compared nucleotide sequences of rRNA subunits.
rRNA molecules are present in all cells and changes in their
nucleotide sequence presumably occur rarely
Proposal of three domains as determined by ribosomal
nucleotide sequences: Bacteria, Archaea and Eukarya
Cells in the three domains also differ with respect to many other
characteristics
Levels in Linnaean taxonomic scheme
Whittaker’s five-kingdom taxonomic scheme

Taxonomic and identifying characteristics
Main criteria and laboratory techniques used for classifying and
identifying microorganisms are:
Macroscopic and microscopic examination
Differential staining
Growth (cultural ) characteristics
Serological tests - microbial interaction with antibodies
Phage typing - microbial susceptibility to viruses
Nucleic acid analysis
Biochemical tests and microbial environmental requirements
(temperature and pH).
Two biochemical tests for identifying bacteria
An agglutination test, one type of serological test

Phage typing
Taxonomic Keys
Dichotomous keys
Series of paired statements where only one of two “either/or”
choices applies to any particular organism
Key directs user to another pair of statements, or provides name
of organism
Use of dichotomous taxonomic key
RICHLAND COLLEGE, Department of Biology,School of
Mathematics, Science & Health ProfessionsMicrobiology
syllabus for on-science majors

Instructor Information
Name: Admassu Mitiku
Email: [email protected]
Office Phone: 972-238-6140
Course Information
Course title: Microbiology for Non-Science Majors
Course number: Biol 2420
Section number: 85201
Semester/Year: Summer 2020
Credit hour: 4
Online meeting times

Monday to Friday: Mornings until noon. Meet via college email
Saturday/Sunday: 5:00 8:00pm. Meet via college email
Important dates
Certification Date: 08/06/2020
Drop Date: 07/16/2020
Final exam: Tuesday, August 4, 2020
General course information
Prerequisite:
BIOL 1406 or BIOL 2401 or SCIT 1407. One of the following
must be met: Student cannot take both BIOL 2420 and BIOL
2421 to satisfy the Core science credit.
Course Description:
Study of the morphology, physiology, and taxonomy of
representative groups of pathogenic and nonpathogenic
microorganisms. Emphasis is placed on applications to humans.

Pure cultures of microorganisms grown on selected media are
used in learning laboratory techniques. Includes a brief preview
of food microbes, public health, and immunology. Designed for
non-science majors and allied health students. (3 Lecture, 4
Lab.)
Student learning outcomes:
Upon successful completion of this online course lecture and
lab parts, students will:
1. Describe distinctive characteristics and diverse growth
requirements of prokaryotic organisms compared to eukaryotic
organisms.
2. Provide examples of the impact of microorganisms on
agriculture, environment, ecosystem, energy, and human health,
including biofilms.
3. Distinguish between mechanisms of physical and chemical
agents to control microbial populations.
4. Explain the unique characteristics of bacterial metabolism
and bacterial genetics.

5. Describe evidence for the evolution of cells, organelles, and
major metabolic pathways from early prokaryotes and how
phylogenetic trees reflect evolutionary relationships.
6. Compare characteristics and replication of acellular
infectious agents (viruses and prions) with characteristics and
reproduction of cellular infectious agents (prokaryotes and
eukaryotes).
7. Describe functions of host defenses and the immune system
in combating infectious diseases and explain how
immunizations protect against specific diseases.
8. Explain transmission and virulence mechanisms of cellular
and acellular infectious agents.
Upon successful completion of this course lab part, students
will:
1. Use and comply with laboratory safety rules, procedures, and
universal precautions.
2. Demonstrate proficient use of a compound light microscope.
3. Describe and prepare widely used stains and wet mounts, and
discuss their significance in identification of microorganisms.
4. Perform basic microbiology procedures using aseptic
techniques for transfer, isolation and observation of commonly
encountered, clinically significant bacteria.
5. Use different types of bacterial culture media to grow,

isolate, and identify microorganisms.
6. Perform basic bacterial identification procedures using
biochemical tests.
7. Estimate the number of microorganisms in a sample using
methods such as direct counts, viable plate counts, or
spectrophotometric measurements.
8. Demonstrate basic identification protocols based on
microscopic morphology of some common fungi and parasites.
Texas core course objectives: Students will be able to describe
the morphology, physiology, and taxonomy of representative
groups of pathogenic and non-pathogenic organisms, and apply
techniques used in growing pure cultures as it relates to humans
and public health issues.
Required course materials:
A. Text book: Microbiology with Diseases by Taxonomy,
6thedition by Robert W. Bauman.
B. Mastering Microbiology: Three options to buy required
course materials for Mastering Microbiology online
work/assignments:
1. Print Textbook + etext + mastering code ISBN:
9780135159927
2. Books a la carte + etext + mastering code ISBN:
9780135204337
3. Mastering code alone + eText (no book) ISBN:
9780135174722

Please make sure that thecode you purchase (either from a book
store or online) matchesthe textbook, "Microbiology with
Diseases by Taxonomy 6th edition" and NOT
“Microbiology with Diseases by Body Systems". Please be
advised that access code is mandatory for this course.
A lab manual is available online at this link:
https://web.archive.org/web/20190113211746/http://delrio.dccc
d.edu/jreynolds/microbiology/RLCmicroindex.html Link also
has other resources, such as: hand-outs on safety in
microbiology lab, practice questions for lab quizzes and
practical exams, graphics/images and videos.
You need to check manual from this link. Link also includes
course materials such as, lab practical graphics, practice
questions for labpractical exams that go along with the lab
manual, Lab. safety handouts and video links for lab
procedures. e-Campus - http://ecampus.dcccd.edu – Please visit
this site as often as possible for course materials: Syllabus,
PowerPoint lecture notes, study guides for lab quizzes/lecture
tests, lab assignments, videos/audios, guide lines for Unknown
ID report writing, lab assignments and grades etc. are all posted
on e-Campus.
Institutional Policies
Institutional Policies relating to this course can be accessed

from the following link:
www.richlandcollege.edu/syllabipoliciesOther course policies
Attendance: Attendance is necessary for class/lab participation
and course work. There will be no make-up opportunities if a
student misses lab practical exams or lecture exams. However,
there could be make-up for missed quizzes, tests and
assignments if a student can present concrete evidence
(example: medical reasons, etc.). Student should contact
instructor in advance and at a reasonable time and submit
evidence for absence for quiz/test and assignment re-sets.
Plagiarism/cheating: Plagiarism, defined asdeliberate use of
someone else’s language, ideas, or other original (not common-
knowledge) material without acknowledging its source.
Plagiarism is not allowed in any online assignments or home
works. Cheating in this course,in any mannerand circumstance
is not allowed. Any student violating any of the above rule(s)
will get a ZERO. Grading and grading scales
Students may earn a maximum of 1000 points for the lecture,
lab components and individual/group assignments
combined. Table below lists the details of lecture and lab
components and point distributions. In addition, a maximum of
50 extra credit points are allowed to count on top of the total
grade (1000pts).
Break down of grade components and grading scale for letter
grade are assigned as follows:

Course componentsGrade points
1 Final Exam (Comprehensive)100 3 Lecture tests (100 pts
each)300 Online Mastering quizzes 100
Practical exam # 1 100
Practical exam # 2
50
3 Lab quizzes(50 pts each)150
1 Lab assignment 50
Unknown ID (Enteric bacteria) 100
Unknown ID (Staph/Strep)50
----------------- Total 1000
Grading Scale: Final letter grades are determined following
standard procedure (standard grading scale) as follows: 900 -
1000 = A; 800 - 899 = B; 700 - 799 = C; 600 - 699 = D; less
than 600 = F
Lab schedule for Biol-2420-85201 Summer 2020
Biology 2421 Microbiology for Science Majors Summer 2020
Week and Unit
Reading assigned in Microbiology text
Lab
Graded assignment
Due date
WEEK 1: short week starts 6/4

Ch1- Introduction to history of Microbiology
Ch2- Microbial chemistry
-Aseptic transfer of bacteria
-Pure culture techniques
-Microscopy use and preparation of specimens
WEEK 2:
Starts 6/8
Ch3- Microbial structures and function
Ch4- Microscopy and staining
-Gram Stain
-Endo-spore stain,
-Acid-fast stain (AFS)
-Capsule Stain
-Flagella stain
-Motility and motility tests
WEEK 3:
Starts 6/15
Lecture exam # 1 (chapters; 1-4)
Ch5- Microbial metabolism
Ch6- Microbial nutrition and growth

July 16 – LAST DAY TO WITHDRAW
-Colony Morphology
-Dilutions & Pipetting
-Counting Bacteria
-Environmental Conditions & Growth
-Effects of Temperature
-Protozoa
-Fungi
Lab assignment (Pipetting and /dilutions) – 50 pts
06/18/20
Lec. Test # 1 opens on Monday, June 15 @10:00am and closes
on Monday, June 15 @midnight
WEEK 4:
Starts 6/22
Ch7- Microbial genetics
Ch8- Recombinant DNA technology
Lab quiz # 1
-Antibiotic (Kirby-Bauer) Sensitivity

-Antimicrobial Chemicals
-Ecto-parasites
-Helminths
Lab quiz # 1 opens on Monday June 22 @10:00am and closes on
Monday, June 22 24 @midnight
WEEK 5:
Starts 6/29
Ch9- Control of microbial growth in the environment
Ch10 –Control of microbial growth in the human
Lecture exam # 2 (chapters: 5-8)
Practical exam # 1
Unknown (Enteric bacteria) ID
-Oxygen Requirements
-Biochemical tests: IMViC, TTC, Phenol Red broth, Oxidase,
Catalase, Nitrate, Decarboxylase, Deaminase, Gelatin, Skim
Milk, Lipid, Starch, Urea
.

Practical exam # 1 opens on Monday, June 29 @10:00m and
closes on Monday, June [email protected]
Lec. Test # 2 opens on Monday, July 6 @10:am and closes on
Monday, July 6 @midnight
WEEK 6:
Starts 7/6
Ch13- Viruses and viroids
Ch14- Infection and infectious disease
-API 20E identification
-Complete enteric bacteria unknown ID
WEEK 7:
Starts 7/13
Lecture exam # 3 (chapters: 9, 10, 13 and 14)
Lab quiz # 2-Staphylococci unknown ID
-Serological Testing
-Complete Staph unknown and submit report
Lec. Test # 3 opens on Friday, July 17 @10:00am and closes on
Friday, July 17 @midnight
WEEK 8:
Starts 7/20
Ch17- Vaccines and immunization

-Streptococci unknown ID
-Serological Testing
-Complete Strep unknown and submit report
-Bacteriophages
-Urine culture
Lab quiz # 3
Essay (Extra credit) – 50 pts
Saturday July [email protected]
Lab quiz # 3 opens on Saturday, July 25 @10:00am and closes
on Saturday, July 25 @midnight.
WEEK 9:
Starts 7/27
Practical exam # 2
Practical exam opens on Friday, July 31 @10:00am and closes
on Friday, July 31 @midnight
WEEK 10:
Starts 8/3
Final exam (Comprehensive) – Exam opens on Tuesday, August
4 @10:00am and closes on Tuesday, August 4 @midnight

Disclaimer: The instructor reserves the right to amend syllabus,
course contents, grading procedures, and/or other related items
as conditions dictate. Students will be notified of any changes
that are to be made in advance via email (or ecampus
announcement).
1
1
RICHLAND COLLEGE,
Department of Biology
,
School of Mathematics, Science & Health Professions
Microbiology syllabus for on
-
science majors

Email:
[email protected]
Office Phone:
972
-
238
-
6140
Course Information
Course title: Microbiology for Non
-
Science Majors
Course number: B
iol
2420
Section number: 852
0

1
Semester/Year:
Summer
2020
Credit hour: 4
Online m
eeting times
Monday to Friday:
Mornings until noon. Meet
via
college email
Saturday/Sunday: 5:00 8:00pm. Meet
via
college email
Important dates

Certification Date:
08/06/2020
Drop Date:
07/16/2020
Final exam:
Tuesday
, August
4
, 2020
G
eneral course information
Prerequisite:
BIOL 1406 or BIOL 2401 or SCIT 1407.
One of the following must be met: Student cannot take both
BIOL 2420 and BIOL 2421 to satisfy the Core science credit.

Course Description:
representative groups of pathogenic and
nonpathogenic microorg
anisms. Emphasis is placed on applications to humans. Pure
cultures of
microorganisms grown on selected media are used in learning
laboratory techniques. Includes a brief
preview of food microbes, public health, and immunology.
Designed for non
-
science maj
ors and allied
health students. (3 Lecture, 4 Lab.)
1
RICHLAND COLLEGE, Department of Biology,
School of Mathematics, Science & Health Professions
Microbiology syllabus for on-science majors

Email: [email protected]
Office Phone: 972-238-6140
Course Information
Course title: Microbiology for Non-Science Majors
Course number: Biol 2420
Section number: 85201
Semester/Year: Summer 2020
Credit hour: 4
Online meeting times
Monday to Friday: Mornings until noon. Meet via college email
Saturday/Sunday: 5:00 8:00pm. Meet via college email
Important dates
Certification Date: 08/06/2020
Drop Date: 07/16/2020
Final exam: Tuesday, August 4, 2020
General course information
Prerequisite:

BIOL 1406 or BIOL 2401 or SCIT 1407. One of the following
must be met: Student cannot take both
BIOL 2420 and BIOL 2421 to satisfy the Core science credit.
Course Description:
representative groups of pathogenic and
nonpathogenic microorganisms. Emphasis is placed on
applications to humans. Pure cultures of
microorganisms grown on selected media are used in learning
laboratory techniques. Includes a brief
preview of food microbes, public health, and immunology.
Designed for non-science majors and allied
health students. (3 Lecture, 4 Lab.)
Lecture prepared by Mindy Miller-Kittrell, University of

Tennessee, Knoxville
M I C R O B I O L O G Y
WITH DISEASES BY TAXONOMY, THIRD EDITION
Chapter 5
Microbial Metabolism
*
Basic Chemical Reactions Underlying Metabolism
Metabolism
Collection of controlled biochemical reactions
The ultimate function of metabolism is to reproduce the
organism
Basics of metabolic processes
Every cell acquires nutrients necessary for metabolism

Metabolism requires energy from light or catabolism of
nutrients
Energy is stored in chemical bonds of ATP
Cells catabolize nutrients to form building blocks (precursor
metabolites)
Precursor metabolites, ATP, and enzymes used in anabolic or
biosynthetic reactions
Cells build macromolecules using enzymes and ATP from
building blocks
Cells reproduce once they have achieved a certain size
*

Catabolism and anabolism
A series of reactions in metabolism are called pathways. There
are two major classes of metabolic reactions:
Catabolic pathways
Break larger molecules into smaller products
Exergonic (release energy)
Anabolic pathways
Synthesize large molecules from the smaller products of
catabolism
Endergonic (require more energy than they release)
*

Metabolism composed of catabolic and anabolic reactions
Figure 5.1
*
Metabolism
Oxidation - reduction reactions (Redox reactions)
Transfer of electrons from molecule that donates (electron
donor) electron to molecule that accepts electrons (electron
acceptor)
Metabolic reactions in which electrons are accepted are
reduction reactions and reactions in which electrons are donated
are oxidation reactions
These reactions are always coupled - always occur
simultaneously

Cells use electron carriers to carry electrons (often in H atoms)
from one cell location to another
There are three important electron carriers:
Nicotinamide adenine dinucleotide (NAD+)
Nicotinamide adenine dinucleotide phosphate (NADP+)
Flavine adenine dinucleotide (FAD+) → FADH2
*
Oxidation-reduction (Redox) reactions or redox reactions
Figure 5.2
*
Oxidation-reduction or redox reactions

ATP Production and Energy Storage
Organisms release energy from nutrients
Can be concentrated and stored in high-energy phosphate bonds
of ATP
Phosphorylation – organic/inorganic phosphate is added to
substrate (ADP)
Cells phosphorylate ADP to ATP in three ways:
Substrate-level phosphorylation: transfer of phosphate to ADP
from phosphorylated organic compound
Oxidative phosphorylation: Energy from redox (respiration)
used to attach phosphate to ADP
Photophosphorylation: Light energy used to phosphorylate ADP
Anabolic pathways use some energy of ATP by breaking a
phosphate bond

*
The roles of enzymes in metabolism
There are six categories of enzymes based on mode of action:
Hydrolases: breakdown macromolecules by adding water in
hydrolysis reaction
Isomerases: rearrange atoms within a molecule (neither
catabolic nor anabolic)
Ligases or polymerases: join two molecules together (anabolic)
Lyases: split large molecule (catabolic)

Oxidoreductases: remove electrons from (oxidized) or add
electrons to (reduced) substrates (catabolic and anabolic
pathways)
Transferases: transfer functional groups (amino, phosphate)
between molecules (anabolic)
The roles of enzymes in metabolism (continued)
Enzymes are organic catalysts – increase the likelihood of a
reaction but are not permanently changed
Many protein enzymes are complete in themselves and
composed entirely of protein (chains of amino acids, folded into
tertiary structure).
Some are RNA molecules called ribozymes
Others composed of protein portions called apoenzymes
Apoenzymes are inactive if not bound to non-protein cofactors

(inorganic ions or coenzymes)
Binding of apoenzyme and its cofactor(s) yields holoenzyme
*
Makeup of a protein enzyme
Figure 5.3
*
Makeup of a protein enzyme
Enzyme activity
Catalyzes reactions within cells by lowering activation energy,

energy needed to trigger a chemical reaction
Enzymes have functional sites (active sites) which are
complementary to the shape of their substrates (molecules upon
which enzymes act on)
Enzyme-substrate reaction is specific and is critical to enzyme
activity
Reaction forms a temporary and intermediate compound called
enzyme-substrate complex
During an enzyme-substrate reaction, chemical bonds are either
broken to form new products or linked together to form a single
product from two reactants
Finally, enzyme disassociates from the newly formed molecules
and is ready to associate with another substrate molecule
The effect of enzymes on chemical reactions
Figure 5.4

*
Effect of enzymes on chemical reactions
Enzymes fitted to substrates
Figure 5.5
*
Enzymes fitted to substrates-overview
The process of enzymatic activity
Figure 5.6
*
The process of enzymatic activity

Factors influencing the rate of enzymatic reactions
Many factors influence the rate of enzymatic reactions
Enzyme and substrate concentrations
Temperature
pH
Presence of inhibitors
Inhibitors
Substances that block an enzyme’s active site
Do not denature enzymes
Three types of inhibitors:
*

Factors influencing the rate of enzymatic reactions (continued)
Three types of inhibitors:
Competitive inhibitors: Fit into an enzyme’s active site and
prevent substrate from binding. Binding results in temporary or
permanent loss of enzyme activity
Noncompetitive inhibitors: do not bind to active site but prevent
enzymatic activity by binding to an allosteric site. Binding at an
allosteric site alters the shape of enzyme at the active site so
that substrate cannot bind
Feedback (negative) inhibitors: the end-products of a series of
reactions is an allosteric inhibitor of an enzyme in an earlier
part of the pathway
Factors that affect enzyme activity

Figure 5.7
*
Effects of temperature, pH, and substrate concentration on
enzyme activity
Denaturation of protein enzymes
Figure 5.8
*
Denaturation of protein enzymes
Competitive inhibition of enzyme activity
Figure 5.9
*

Competitive inhibition of enzyme activity
Allosteric control of enzyme activity
Figure 5.10
*
Allosteric control of enzyme activity
Feedback Inhibition
Figure 5.11
*
Feedback inhibition-overview

Carbohydrate Catabolism
Carbohydrate catabolism
Many organisms oxidize carbohydrates as the primary energy
source for anabolic reactions
Glucose used most commonly (also used are: other sugars,
amino acids and fats after first converted to glucose)
Glucose is catabolized by either:
Cellular respiration → Utilizes glycolysis, Krebs cycle, and
electron transport chain; results in complete breakdown of
glucose to carbon dioxide and water; large amounts of ATP
produced
Fermentation → Utilizes glycolysis then converts pyruvic acid
into organic fermentation products (organic waste products).
Lacks Krebs cycle and electron transport chain, thus,
fermentation results in the production of much less ATP
*

Summary of glucose catabolism
Figure 5.12
*
Summary of glucose catabolism
Glycolysis (Embden-Meyerhof pathway)
Occurs in the cytoplasm of most cells
Involves splitting of a six-carbon glucose into two three-carbon
sugar molecules
Direct transfer of phosphate between two substrates (PEP and
ADP) occurs four times – substrate level phosphorylation.
Two ATP molecules invested by substrate level phosphorylation

to lyse glucose and 4 molecules of ATP produced
Net gain of two ATP molecules, two molecules of NADH, and
precursor metabolite pyruvic acid
Glycolysis is divided into three stages involving 10 total steps:
Energy-Investment Stage
Lysis Stage
Energy-Conserving Stage
*
Glycolysis
Figure 5.13
*

Glycolysis-overview
Substrate-level phosphorylation
Figure 5.14
*
Substrate-level phosphorylation
Cellular respiration
Resultant pyruvic acid from glycolysis completely oxidized to
produce ATP by a series of redox reactions. There are three
stages of cellular respiration:
Synthesis of acetyl-CoA
Krebs cycle
Final series of redox reactions which constitute an electron

transport
chain (ETC)
Synthesis of acetyl-CoA
Acetyl coenzyme A (Acetyl CoA) formed from pyruvic acid by
enzymatic removal of CO2 (decarboxylation) and joining
acetate to form coenzyme A
Synthesis results in:
Two molecules of acetyl-CoA
Two molecules of CO2
Two molecules of NADH
*
Formation of acetyl-CoA
Figure 5.15

*
Formation of acetyl-CoA
Cellular Respiration
The Krebs cycle
Great amount of energy remains in bonds of acetyl-CoA
A series of eight enzymatically catalyzed reactions that transfer
much of this energy to coenzymes, NAD+ and FAD+. Two
carbons in acetate are oxidized and the coenzymes are reduced
Occurs in cytoplasm of prokaryotes and in matrix of
mitochondria in eukaryotes. There are eight types of reactions
in Krebs cycle:
Anabolism of citric acid (step 1)
Isomerization reactions (steps 2, 7 and 8)
Hydration reaction (Step 7)

Redox reactions (steps 3,4,6 and 8)
De-carboxylations (steps 3 and 4)
Substrate-level phosphorylation (step 5)
*
The Krebs cycle
Figure 5.16
*
The Krebs cycle
The Krebs Cycle

For every two molecules of acetyl-CoA that pass through the
Krebs Cycle:
Two molecules of ATP (step 5) and four molecules of CO2
(steps 3 and 4) are produced. A molecule of guanosine
triphosphate (GTP), which is similar to ATP serves as an
intermediary
Redox reactions produce six molecules of NADH (steps 3, 4 and
8) and two molecules of FADH2 (step 6)
In the Krebs cycle, little energy is captured directly in high-
energy phosphate bonds, but much energy is transferred via
electrons to NADH and FADH2.
*

Electron transport chain (ETC)
The most significant production of ATP occurs through stepwise
release of energy from a series of redox reactions between
molecules known as an electron transport chain (ETC)
Consists of series of membrane-bound carrier molecules that
pass electrons from one to another and ultimately to a final
electron acceptor
Energy from electrons used to pump protons (H+) across the
membrane, establishing a proton gradient that generates ATP
via chemiosmosis
Located in the inner membranes of mitochondria (cristae) of
eukaryotes and in the cytoplasmic membrane of prokaryotes
NADH and FADH2 donate electrons as hydrogen atoms
(electrons and protons); whereas carrier molecules only pass the
electrons down the chain
*

An electron transport chain
Figure 5.17
*
An electron transport chain
Electron transport chain (ETC)
Four categories of carrier molecules:
Flavoproteins: integral membrane proteins that contain a
coenzyme derived from riboflavin (vitamin B2): FMN is the
initial carrier and FAD is a coenzyme

Ubiquinones: lipid-soluble, non-protein carriers derived from
vitamin K; in mitochondria, ubiquinone is called coenzyme Q
Metal-containing proteins: mixed group of integral proteins
containing iron, sulfur and copper atoms that can alternate
between the reduced and oxidized states
Cytochromes: integral proteins associated with heme, pigmented
molecule found in the hemoglobin of blood
Some organisms can vary their carrier molecules under different
environmental conditions: In aerobic respiration (aerobes),
oxygen serves as final electron acceptor to yield water. In
anaerobic respiration (anaerobes), molecules other than oxygen
serve as the final electron acceptor
*
Possible arrangement of an electron transport chain

Figure 5.18
*
One possible arrangement of an electron transport chain
Chemiosmosis
Use of electrochemical gradients to generate ATP. Chemicals
diffuse from areas of high concentration to areas of low
concentration and toward an electrical charge opposite their
own. The blockage of diffusion creates potential energy
Membranes maintain electrochemical gradient by keeping one or
more chemicals in higher concentration on one side
Cells use energy released in redox reactions of ETC to create
electrochemical gradient known as proton gradient, which has
potential energy known as proton motive force.

H+ ions (protons) propelled by proton motive force, flow down
electrochemical gradient through protein channels called ATP
synthases (ATPase) that phosphorylate ADP to ATP
ETC is called oxidative phosphorylation because proton
gradient created by oxidation of components of ETC
Total of ~34 ATP molecules formed from one molecule of
glucose
*
Alternative pathways to glycolysis

Yield fewer molecules of ATP than glycolysis
Reduce coenzymes and yield different metabolites needed in
anabolic pathways
Two pathways:
Pentose phosphate pathway
Entner-Doudoroff pathway
*
Figure 5.19
*
Pentose phosphate pathway

*
Entner-Douoroff pathway
Fermentation
Sometimes cells cannot completely oxidize glucose by cellular
respiration
Cells require constant source of NAD+ that cannot be obtained
by simply using glycolysis and the Krebs cycle
In respiration, electron transport regenerates NAD+ from
NADH
Fermentation pathways provide cells with alternative source of
NAD+

Partial oxidation of sugar (or other metabolites) to release
energy using an organic molecule as an electron acceptor rather
than ETC (NADH oxidized to NAD+ while organic molecule
reduced)
*
Fermentation:
In the simple fermentation reaction, NADH reduces pyruvic
acid (from glycolysis) to form lactic acid. Another simple
fermentation pathway involves a decarboxylation reaction and
reduction results to form ethanol.

Fermentation products and organisms that produce them
Figure 5.22
*
Representative fermentation products and the organisms that
produce them
Other Catabolic Pathways
Other catabolic pathways
Lipid Catabolism
Protein Catabolism
Lipid and protein molecules contain abundant energy in their
chemical bonds. First converted into precursor metabolites,
which serve as substrates in glycolysis and the Krebs cycle.

Lipid catabolism
Fats (glycerol and fatty acids) important in ATP and metabolite
production
Lipases hydrolyze bonds attaching glycerol to fatty acids
Glycerol converted to DHAP and oxidized to pyruvic acid
Fatty acids degraded by beta-oxidation and converted to acetyl-
CoA
NADH and FADH2 generated during beta-oxidation are utilized
in the Krebs cycle to produce ATP
*

Catabolism of a fat molecule
Protein Catabolism
Protein catabolism
Some microorganisms (bacteria and fungi) catabolize proteins
as main source of energy and metabolites
Other cells catabolize proteins and fat only when carbon sources
are not available
Proteins too large to cross cell membranes; proteases split
proteins into amino acids
Amino acids further broken down by deamination and altered
molecules enter the Krebs cycle
Amino groups either recycled to synthesize other amino acids or
excreted as wastes

Protein catabolism
Figure 5.24
*
Protein catabolism in microbes
PhotosynthesisMany organisms synthesize their own organic
molecules from inorganic carbon dioxide
Most of these organisms capture light energy and use it to
synthesize carbohydrates from CO2 and H2O by a process
called photosynthesis
*

PhotosynthesisChemicals and Structures
Chlorophylls
Important to organisms that capture light energy with pigment
molecules
Composed of hydrocarbon tail attached to light-absorbing active
site centered on magnesium ion
Active sites structurally similar to cytochrome molecules in
ETC
Structural differences cause absorption at different wavelengths
*
Photosystems
Arrangement of molecules of chlorophyll and other pigments to
form light-harvesting matrices

Embedded in cellular membranes called thylakoids
In prokaryotes – invagination of cytoplasmic membrane
In eukaryotes – formed from inner membrane of chloroplasts
Arranged in stacks called grana
Stroma is space between outer membrane of grana and thylakoid
membrane
*
Photosynthesic structures in a prokaryote
Figure 5.25
*
Photosynthetic structures in a prokaryote

Two types of photosystems
Photosystem I (PS I)
Photosystem II (PS II)
Photosystems absorb light energy and use redox reactions to
store energy in the form of ATP and NADPH
Light-dependent reactions depend on light energy
Light-independent reactions synthesize glucose from carbon
dioxide and water
*

PhotosynthesisLight-Dependent Reactions
As electrons move down the chain, their energy is used to pump
protons across the membrane
Photophosphorylation uses proton motive force to generate ATP
Photophosphorylation can be cyclic or noncyclic
*
Reaction center of photosystem
Figure 5.26
*
Reaction center of a photosystem

The light-dependent reactions of photosynthesis
Figure 5.27
*
Photosynthesis: photophosphorylation-overview
Photosynthesis
Light-Independent Reactions
Do not require light directly
Use ATP and NADPH generated by light-dependent reactions
Key reaction is carbon fixation by Calvin-Benson cycle
Three steps

*
Simplified diagram of the Calvin-Benson cycle
Figure 5.28
*
Simplified diagram of the Calvin-Benson cycle
Other Anabolic Pathways
Other anabolic pathways
Anabolic reactions are synthesis reactions requiring energy and
a source of metabolites
Energy derived from ATP from catabolic reactions
Many anabolic pathways are the reverse of catabolic pathways

Reactions that can proceed in either direction are amphibolic
*
Gluconeogenesis
Figure 5.29
*
Role of gluconeogenesis in the biosynthesis of complex
carbohydrates
Biosynthesis of fat
Figure 5.30

*
Biosynthesis of fat
Synthesis of amino acids by amination and transamination
Figure 5.31
*
Synthesis of amino acids via amination and transamination
The biosynthesis of nucleotides
Figure 5.32
*
Biosynthesis of nucleotides

Integration and Regulation of Metabolic Function
Cells synthesize or degrade channel and transport proteins
Cells often synthesize enzymes needed to catabolize a substrate
only when substrate is available
If two energy sources are available, cells catabolize the more
energy efficient of the two first
Cells synthesize metabolites they need, cease synthesis if
metabolite is available
Eukaryotic cells isolate enzymes of different metabolic
pathways within membrane-bounded organelles
Cells use allosteric sites on enzymes to control activity of
enzymes
Feedback inhibition slows/stops anabolic pathways when
product is in abundance

Cells regulate amphibolic pathways by requiring different
coenzymes for each pathway
*
Two types of regulatory mechanisms
Control of gene expression
Cells control amount and timing of protein (enzyme) production
Control of metabolic expression
Cells control activity of proteins (enzymes) once produced
*

Integration of cellular metabolism
Figure 5.33
*
Integration of cellular metabolism
Microbial cell structure and function
Cell Structure and Function
The four processes of life
The four processes of life that describe the characteristics of all
living organisms:

Metabolism
Growth
Responsiveness
Reproduction
Prokaryotic and Eukaryotic Cells: An Overview
ProkaryotesLack membrane-bound nucleus (nuclear material), a
cytoskeleton, membrane-bound organelles, and internal
membranous structures.
Have simple structures compared
to eukaryotes
Composed of bacteria and archaea
Are typically small in size (~1.0 μm in
diameter
*

Typical prokaryotic cell
Different morphologic features of bacterial cellsCells with
unusual shapes Vibrios – Resemble rods but are comma
shaped.Spirilla – rigid, spiral shaped cells. Usually with tufts of
flagella at each end. Actinomycetes – typically form
filamentous structures. They lie between bacteria and
filamentous fungi.Pleomorphic - bacteria with variable in
shape.

External Structures of Bacterial Cells
Glycocalyces
Gelatinous, sticky substance surrounding the outside of the cell
Composed of polysaccharides, polypeptides, or both
Two types of external structures: capsule and slime layer
Capsules
Composed of organized repeating units of organic chemicals
Firmly attached to cell surfaces
Protect cells from drying out
May prevent bacteria from being recognized and destroyed by
host immune and phagocytic cells
Enable bacteria to cause diseases (capsules are virulence
factors)

Slime layer
Loosely attached to cell surface
Protects cells from drying out
Sticky layer allows prokaryotes to attach to surfaces
Water soluble
Slime layers have little or no medical importance/significance
Flagella structure and function
Long, whip-like structures that extend beyond surface of the
cell
Are responsible for movement: 360º rotation of flagellum

propels bacterium through environment (run or tumble)
Rotation can be clockwise or counterclockwise and reversible
Prokaryotes move in response to stimuli:
Positive (stimulus) taxis – organisms move towards food or
light;
Negative (stimulus taxis – organisms move away from danger
Flagella are not present on all bacteria
Flagellar arrangements
Monotrichous: Cells with a single flagellum
Lophotrichous: Cells with a tuft of flagella at one end of the
cell

Amphitichous: Cells with flagella at both ends
Peritrichous: Cells covered with flagella
Fimbriae
Non-motile, rod-like proteinaceous extensions
on cell surfaces
Sticky, proteinaceous, bristle-like projections

Used by bacteria to adhere to one another,
to hosts, and to substances in environment
(e.g., Neisseria gonorrhoeae adhering on mucus
membranes)
May be hundreds per cell
Are shorter than flagella
Serve an important function in biofilms formations (slimy
masses of bacteria adhering to one another and to a substrate by
means of fimbriae and glycocalyces)
Pili
Long, hollow tubules composed of pilin
Longer than fimbriae but shorter than flagella
Bacteria typically only have one or two per cell

Also known as conjugation (sex) pili
Bacteria use pili to move across a substrate or towards another
bacterium
Pili mediate the transfer of DNA from one cell to another: join
two bacterial cells and help transfer DNA (conjugation)
Bacterial cell walls
Give bacterial cells characteristic shapes
Protects cell from osmotic forces
Assists some cells in attaching to other cells or other surfaces
Most bacteria have cell walls composed of peptidoglycan. A
complex polysaccharide material that covers the entire surface
of the cell and is composed of alternating sugars, N-
acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)

Cell walls help in eluding antimicrobial drugs or resisting
antimicrobial drugs (certain antibiotics can target cell walls of
bacteria, e.g., penicillin attacks cell wall)
A few bacteria lack a cell walls entirely (e.g., Mycoplasma
pneumoniae)
Scientists describe two basic types of bacterial cell walls:
Gram-positive and Gram-negative
Possible structure of peptidoglycan
Gram-positive bacterial cell walls
Relatively thick layer of peptidoglycan
Contains unique polysaccharides called teichoic acids

Some covalently linked to lipids, forming lipoteichoic acids that
anchor peptidoglycan to cell membrane
Peptidoglycan retains crystal violet dye and cells appear purple
following Gram Staining Procedure
Acid-fast bacteria contain up to 60% mycolic acid, a waxy lipid
Helps cells survive desiccation and resist stain with regular
water-based dyes
Gram-positive bacterial cell wall structure
Gram-negative bacterial cell wall structure
Gram-negative bacterial cell walls
Have only a thin layer of peptidoglycan

Have a bilayer membrane (composed of phospholipid bilayers,
channel proteins or porins and lipopolysaccharide or
endotoxin) outside of peptidoglycan
Lipid portion (called lipid A) - released from dead and
disintegrating cell walls may trigger endotoxic shock (fever,
vasodilation, hypotension, inflammation and blood clotting in
patients)
May be impediment to the treatment of disease
Following Gram staining procedure, cells appear pink
Gram-negative bacterial cell wall structure
Bacterial Cytoplasmic Membranes
Structure of prokaryotic cytoplasmic membrane

Cytoplasmic membrane (also known as cell membrane or plasma
membrane) is a phospholipid bilayer composed of lipids and
associated proteins
A phospholipid molecule is bipolar (has a hydrophilic and a
hydrophobic ends)
Approximately half the cytoplasmic membrane is composed of
proteins (integral proteins, peripheral proteins and
glycoproteins)
Protein components of cytoplasmic membranes act as
recognition proteins, enzymes, receptors, carriers or channels
Proteins and lipids within membranes flow freely (fluid mosaic
model or membrane fluidity) and allow easy passage of
substance into and out of the cell
Structure of prokaryotic cytoplasmic membrane

Bacterial cytoplasmic membranes
Functions of cytoplasmic membrane
Energy storage
Controls passage of substances into and out of the cell -
selectively permeable (allows some substances to cross it, while
preventing the crossing of others)
Naturally impermeable to most substances, but proteins
(receptors, channels and carriers) allow substances to cross
membrane
Membranes maintain a concentration gradient and electrical
gradient - chemicals with concentration gradients across
membranes have electrical charges and a corresponding
electrical gradient
Chemical and electrical gradients collectively are known as
electrochemical gradient
Energy found in electrochemical gradient can be used to

transport substances across the membrane
Movement of substances across membranes occurs by passive or
active processes of
transport
Electrical potential of a cytoplasmic membrane
Passive processes of transport
Electrochemical gradient provides a source of energy. The cell
does not expend its ATP energy reserve for the following three
passive processes of transport:
Diffusion
Facilitated diffusion
Osmosis

Diffusion
Net movement of a chemical down its concentration gradient-
from an area of high concentration to an area of low
concentration
Requires no energy out put by the cell, a common feature of all
passive processes
Chemicals that are small or lipid soluble (e.g., oxygen, CO2,
alcohol and fatty acids) can diffuse through the lipid portion of
the membrane; larger molecules like proteins and glucose
cannot – selectively permeable
Facilitated diffusion
Integral proteins (channels, carriers etc.) facilitate the diffusion
of large or electrically charged molecules through phospholipids
bilayer of membranes

Cells expend no energy in facilitated diffusion. Electrochemical
gradient provides all the necessary energy
Non-specific channel proteins (common in prokaryotes) allow
the passage of a wide range of chemicals with the right size or
electrical charge
Specific channel proteins (common among eukaryotic cells)
carry only specific substrates. These have specific binding site
that are selective for one substance
Passive processes of movement
Solutes, solvents and solutions
Concentration of solutes and solutions
Three classes of solutions according to their concentrations of
solutes and solvents:

Isotonic solutions: have the same concentration of solutes and
water on either sides of selectively permeable membrane;
neither side of membrane experience a net loss or gain of water
Hypertonic solution: contains higher concentration of solutes
relative to the solvent
Hypotonic solutions: contains lower concentration of solutes in
comparison
Hypotonic and hypertonic refer to the concentration of solute,
even though osmosis refers to the movement of the solvent,
which in cells is water
Osmosis
Osmosis
Diffusion of water across a selectively permeable (not to all
solutes such as proteins, salts, amino acids or glucose)
membrane

Water crosses from the side of the membrane that contains a
higher concentration of water molecules (lower concentration of
solute) to the side that contains a lower concentration of water
molecules(higher concentration of solute)
When water pressure is at equilibrium, activity of osmosis stops
Like other chemicals, water moves down its concentration
gradient from hypotonic solution into a hypertonic solution
The osmotic movement of water out of a cell and shriveling of
its cytoplasm is called plasmolysis
Osmosis
Effects of different solutions on cells

Prokaryotic Cytoplasmic Membranes
Active processes of transport
Require the cell to expend energy (ATP) to move materials
across cytoplasmic membranes against their electrochemical
gradients
Utilizes trans-membrane carrier proteins. When only one
substance is transported at a time, the carrier protein is called a
uniport
Simultaneous transport of two chemicals, but in opposite
directions (one into the cells and the other out of the cell) at the
same time is called antiport
When two substance move together in the same direction across
the membrane by means of a single carrier protein, the process
of transport is termed symport
Active processes of transport in prokaryotes is by means of
carrier proteins and a special process called group translocation
(where substances are chemically modified during transport)

Mechanisms of active transport
Group translocation
Eukaryotic Cells
Have nucleus and nuclear membrane surrounding their DNA
Have internal membrane-bound organelles (compartmentalize
cellular functions that act like tiny organs)
Eukaryote cells are larger compared to prokaryotes (10-100 μm
in diameter)
Have more complex structures than prokaryotes
Comprised of algae, protozoa, fungi, animals, and plants

Nucleolus
Cilium
Ribosomes
Cytoskeleton
Cytoplasmic
membrane
Smooth endoplasmic
reticulum
Rough endoplasmic
reticulum
Transport vesicles
Golgi body
Secretory vesicle
Centriole
Mitochondrion
Lysosome
Nuclear pore
Nuclear envelope

Typical eukaryotic cell
*
External structure of Eukaryotic cells
Glycocalyces

Eukaryotic cells lacking cell walls have sticky carbohydrate,
glycocalyces anchored to their cytoplasmic membranes
Never as organized as prokaryotic capsules
Helps animal cells adhere to each other
Strengthens cell surface
Provide protection against dehydration
Function in cell-to-cell recognition and communication
Eukaryotic cell walls
Eukaryotic cell walls
Fungi, algae, and plants have cell walls but no glycocalyx
Composed of various polysaccharides but not peptidoglycan of
most bacteria

Cell wall protects cells from the environment and provide shape
and support against osmotic pressure
Cellulose found in plant cell walls and fungal cell walls are
composed of polysaccharide, including cellulose, chitin, and/or
glucomannan
Algal cell walls composed of cellulose, agar, carrageenan,
silicates, algin, calcium carbonate or combination of these
Some protozoa have cell walls composed of various
polysaccharides (cellulose and glucomannan)
A Eukaryotic cell wall
External structures of Eukaryotic cells
Flagella
Structure and arrangement

Differ structurally and functionally from prokaryotic flagella
Within the cytoplasmic membrane (Flagella are inside the cell,
not extensions outside the cell)
Shaft composed of tubulin arranged to form microtubules
Filaments anchored to cell by basal body AND no hook
May be single or multiple (generally found at one pole of cell)
Do not rotate, but undulate rhythmically
Eukaryotic Flagella and Cilia (movement)
External structures of Eukaryotic cells
Cilia
Some eukaryotic cells move by means of hair-like structures
called cilia

Shorter and more numerous than flagella (cover the surface of
the cell)
In comparison, no prokaryotic cells have cilia
Cilia in multi-cellular eukaryotes are used to move substances
in the local environment past the surface of the cell
Coordinated beating propels cells through their environment
Cilia beat rhythmically and this propels cells through their
environment
Eukaryotic Cilia
Eukaryotic cytoplasmic membranes
Eukaryotic cytoplasmic membranes

All eukaryotic cells have cell membrane
Is a fluid mosaic of phospholipids and proteins which act as
recognition molecules, enzymes, receptors, carriers or channels
Contains steroid lipids (sterols) such as cholesterol in animal
cells to help maintain membrane fluidity
Sterols at high temperature stabilize phospholipid bilayer by
making it less fluid and at low temperatures they prevent
phospholipid packing, making membrane more fluid
Controls movement of materials into and out of cell
Contain regions of lipids and proteins called membrane rafts
Eukaryotic cytoplasmic membranes are used for passive
(diffusion, facilitated diffusion, osmosis) and active processes
of transport
Eukaryotic membranes do not perform group translocation, but
perform endocytosis (also called phagocytosis if solid substance
is brought into the cell and pinocytosis if liquid substance is
brought into the cell). Exocytosis enables substances to be
exported out of the cell

Eukaryotic Cytoplasmic Membrane
Cytoplasm of Eukaryotes
Cytoplasm of Eukaryotic cells
More complex than that of either bacteria or archaea
Most distinctive difference is the presence of numerous
membranous organelles in eukaryotic cells (e. g., Gologi body,
rough/smooth endoplasmic reticulum)
Non-Membranous organelles
Ribosomes: Larger than prokaryotic ribosomes (80S versus 70S)
and composed of 60S and 40S subunits. Many eukaryotic
ribosomes are attached to the membranes of the endoplasmic
reticulum

Cytoskeleton: composed of extensive internal network of fibers
and tubules
Function in cytoplasmic streaming and in movement of
organelles within the cytoplasm
Enables contraction of the cell, provides the basic shape of
many cells and anchors organelles
Centrioles and Centrosome: Centrioles play a role in mitosis
(nuclear division), cytokinesis (cell division), and in the
formation of flagella and cilia. Centrosome – region of
cytoplasm where centrioles are found
Cytoplasm of Eukaryotes
Mitochondria and chloroplasts
Mitochondria:
Spherical to elongated structures found in most eukaryotic cells
Have two membranes composed of phospholipid bilayer. Inner
membrane is folded into numerous crystae, where most of the
cell’s ATP is produced
Interior matrix contains small “prokaryotic” 70S ribosomes and
circular molecule of DNA (contains genes for some RNA

molecules and for a few mitochondrial polypeptides)
Chloroplasts:
Light-harvesting structures found in photosynthetic eukaryotes
Have two phospholipid bilayer membranes, DNA and have 70S
ribosomes
Mitochondrion
Chloroplast
Comparison of prokaryotic and eukaryotic organelles

Comparison of prokaryotic and eukaryotic cells
Lecture prepared by Mindy Miller-Kittrell, University of
Tennessee, Knoxville
M I C R O B I O L O G Y
WITH DISEASES BY TAXONOMY, THIRD EDITION
Chapter 2
The Chemistry of Microbiology
The Chemistry of Microbiology
Learning some basic concepts of chemistry will enable us to
understand fully the variety of interactions between
microorganisms and their environments, including, humans,
animals and plants.

Atoms and atomic structure
Matter – anything that takes up space and has mass
Atoms – the smallest chemical units of matter
Electrons – negatively charged subatomic particles circling a
nucleus
Nucleus – structure containing neutrons and protons
Bohr model of atomic structure
Figure 2.1
Atoms and atomic Structure
Atoms and atomic structure (continued)

Neutrons – uncharged particles
Protons – positively charged particles
Element – composed of a single type of atom
Atomic number – equal to the number of protons in the nucleus
Atomic mass (atomic weight) – sum of masses of protons,
neutrons, and electrons
Isotopes
Isotopes
Every atom of an element has the same number of protons, but
atoms of a given element can differ in the number of neutrons in
their nuclei
Atoms that differ in the number of neutrons in their nuclei are

isotopes. Examples are the three naturally occurring isotopes of
Carbon
Carbon-12 (12C) has 6 protons and 6 neutrons
Stable isotopes (equal ratio of protons and neutrons)
Unstable isotopes (un-equal ratio of protons and neutrons).
Unstable isotopes release energy during radioactive decay
Isotopes that undergo radioactive decay are radioactive isotopes
Radioactive isotopes play important roles in microbiological
research, medical diagnosis, treatment of disease and
sterilization of medical equipment and medical
supplies/materials
Isotopes of carbon

Figure 2.2
Atom and atomic structure
Electron configurations
Only the electrons of atoms interact, so they determine atom’s
chemical behavior
Electrons occupy electron shells or form clouds in an atom
Each electron shell can hold only a certain, maximum number of
electrons (e.g., the first shell can accommodate a maximum of 2
electrons and the second no more than 8 electrons (more on this,
please refer to periodic table, Fig. 2.4 page 29 in text)
Valence electrons – electrons in the outermost shell that interact
with other atoms

Electron configurations
Figure 2.3
Bohr diagrams of the first 20 elements
Figure 2.4
Chemical Bonds
Chemical bonds
Chemical bonds – atoms combine by sharing or transferring
valence electrons
Outer electron shells (valence shells) are stable when they
contain eight electrons (except for the first electron shell, which
is stable with only two electrons)
When an atom’s outer shells are not filled with 8 electrons, they
either have room for more electrons to gain or have extra
electrons to lose or are stable when outer electron shells

contain eight electrons
Atoms’ outer most electrons are valence electrons and outer
most shell of an atom is valence shell
An atom’s valence is its combining capacity and is positive if
its valence shell has “extra” electrons to give up, and negative
if its valence shell has spaces to fill in (e.g., Calcium with 2
electrons in its valence shell has a valence of +2, whereas
Oxygen atom with 2 spaces to fill in its valence shell, has a
valence of -2)
Molecule – two or more atoms held together by chemical bonds
Compound – a molecule composed of more than one element
Chemical Bonds
Chemical bonds (continued)
There are three principal types of chemical bonds (plus
hydrogen bonds–weak forces that combine with polar covalent
bonds)

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