40. decimal30female2Sample Standard deviation:9.83*Round to two
decimals21female2Q124*Round to one
decimal38female2Q338*Round to one
decimal30Male35female41MaleOgive:5Ogive:Polygon:26maleP
olygon520Male33Male28Female23MaleTotal:2519Male
Student Ages Ogive
1929394959110212325
Student Ages Polygon
Frequency1025354555191122
Week 5AgeGenderPoints95% Confidence Interval for Average
Age of Online College Students:38Male41FemaleSample
Mean:32.3621maleSample St. Dev:9.83Normal
Distribution29Female1Sample Size:T-
Distribution38male56Female2Distribution:24male30Male2Critic
al Value:*2 decimals56Female35Male2Margin of Error:*2
decimalsCalculation:35Male1Lower Bound:*2
45. Basic Chemical Reactions Underlying 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
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61. 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)
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67. 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
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72. 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
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85. *
Metabolism
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*
Oxidation-reduction or redox reactions
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Makeup of a protein enzyme
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Effect of enzymes on chemical reactions
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Enzymes fitted to substrates-overview
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The process of enzymatic activity
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Effects of temperature, pH, and substrate concentration on
enzyme activity
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Denaturation of protein enzymes
86. *
Competitive inhibition of enzyme activity
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Allosteric control of enzyme activity
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Feedback inhibition-overview
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Summary of glucose catabolism
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Glycolysis-overview
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Substrate-level phosphorylation
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Formation of acetyl-CoA
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The Krebs cycle
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87. *
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An electron transport chain
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One possible arrangement of an electron transport chain
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*
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Pentose phosphate pathway
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Entner-Douoroff pathway
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Representative fermentation products and the organisms that
produce them
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88. Protein catabolism in microbes
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*
*
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Photosynthetic structures in a prokaryote
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*
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Reaction center of a photosystem
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Photosynthesis: photophosphorylation-overview
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Simplified diagram of the Calvin-Benson cycle
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Role of gluconeogenesis in the biosynthesis of complex
89. carbohydrates
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Biosynthesis of fat
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Synthesis of amino acids via amination and transamination
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Biosynthesis of nucleotides
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Integration of cellular metabolism
Microscopy, Staining, and Classification
Microscopy, Staining, and Classification
General principles of microscopy
90. 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
Microscopy, Staining, and Classification
The electromagnetic spectrum
Microscopy, Staining, and Classification
91. 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
Microscopy, Staining, and Classification
92. 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
93. 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
94. 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
95. The Convex Lens
f = focal length
Lens
Air
Air
Glass
strength of lens related to
magnification
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Refractive Properties of Lenses
Flat glass
Convex lens (less round)
Convex lens (more round)
Concave lens
96. Microscopy, Staining, and Classification
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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99. 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
100. Line of vision
Ocular lens
Path of light
Prism
Body
Objective
lenses
Specimen
Condenser
lenses
Illuminator
101. 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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103. 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.
104. 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
105. 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
109. 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
110. 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)
112. 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.
113. *
Transmission electron microscope (TEM)
Specimen is coated with plastic and cut really thin 20-100 nm
thick slices.
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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
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114. 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
115. about organisms
Make predictions based on knowledge of similar organisms
Classification and Identification of Microorganisms
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
116. Whitaker proposed taxonomic approach based on five kingdoms:
Animalia, Plantae, Fungi, Protista, and Prokaryotae (widely
accepted)
Classification and Identification of Microorganisms
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
Classification and Identification of Microorganisms
117. 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
118. Classification and Identification of Microorganisms
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
125. External Structures of Bacterial Cells
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
134. 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
153. 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
Carbon-13 (13C) has 6 protons and 7 neutrons
Carbon-14 (14C) has 6 protons and 8 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
156. 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
161. Chemical Bonds
Ionic bonds
Occur when two atoms with vastly different electronegativities
come together (e.g., sodium and chlorine ions)
Atom or group of atoms that have either a full negative charge
or a full positive charge is called an ion
Positively charged ions are called cation, whereas negatively
charged ions are called anion
Cations and anions attract each other and form ionic bonds (no
electrons shared, but opposite electrical charges attract each
other)
Typically form crystalline ionic compounds known as salts
(e.g., sodium chloride and potassium chloride)
When cations and anions dissociate (ionize) from one another
and surrounded by water molecules (or are hydrated), they are
called electrolytes because they can conduct electricity through
the solution