UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &

Prokaryotic Cell Structure

Ch1: Humans and the Microbial World

● Define spontaneous generation
○ Life arises spontaneously from non-living material
○ Those who contributed to disproving the theory include:
■ Francesco Redi
■ Louis Pasteur
■ John Tyndall

● Describe the key experiments of Redi, Pasteur, and Tyndall in disproving

spontaneous generation.
○ Redi (​1668) → worms found on rotting meat originated from the eggs of
flies not from the decaying meat as proponents of spontaneous generation
○ Pasteur ​(1861) → father of modern microbiology, demonstrated that air
contains microorganisms through experiments of swan-necked flasks in
which if the flask remained upright no microbial growth occurred but if
tipped microorganisms grew
○ Tyndall→ ​proved Pasteur correct by showing that sterilizing broths
required different boiling times and the existence of heat-resistance forms

● Discuss three examples of the role and impact of microbial activity on

earth.
○ Nitrogen fixation
○ Oxygen production
○ Material degradation such as cellulose, sewage and wastewater

● Describe three ancient applications of microbiology.

○ Food production→ ancient Egypt, to ferment cereal grains to make beer,
milk and other fermented products

● Describe three modern applications of microbiology.

○ Food production​→ bacteria added to fermented milk products
○ Biodegradation→​ microorganisms help degrade environmental pollutants
○ Bacteria synthesize commercially valuable products​→ such as
antibiotics, ethanol, insecticides, amino acids as dietary supplements
among others
○ Biotechnology​→ the use of microbiological and biochemcial techniques
to solve practical problems

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

○ Genetic engineering→ ​the introduction of genes into another organism

resulting in disease-resistant plants and the production of medications
such as insulin.

● Define the term medical microbiology.

○ Founded by ​Robert Koch (1875)​ who demonstrated that anthrax was
caused by a spore-forming bacterium
○ Koch’s Postulates→ criteria used to establish that a specific
microorganism causes a specific disease:
■ 1. Microbe present in every case of the disease
■ 2. Isolated from diseased host and grown in pure culture
■ 3. Disease reproduced when microbe is put back into healthy host
■ 4. Same microbe recovered from experimentally-infected host
○ Definition​→ branch of medicine that is concerned with the prevention,
diagnosis and treatment of infectious diseases.
■ Includes clinical research of microbial study for the improvement of
human health

● Discuss the major impacts on human health of the so-called Golden Age of
Microbiology (1876-1918)
○ Most pathogenic bacteria were identified and early work on viruses began
○ Most vaccines were made against the new identified bacteria

● Distinguish between emerging diseases and re-emerging diseases.

○ Emerging diseases→ ​a disease that suddenly becomes prevalent
meaning it is increasing in incidence or geographical range. (ie swine flu,
Lyme disease, Hepatitis C, SARS, AIDS, Mad cow disease, West Nile
encephalitis)
■ Due to:
● Resistance to antimicrobial medications (ie tuberculosis,
malaria)
● Increased travel and immigration (ie malaria, cholera)
● Changes in population (i.e elderly, HIV/AIDS)
● Bacteria may cause chronic diseases (i.e H. pylorI)
○ Re-Emerging diseases→ ​diseases that were previously in check and
under control but are now becoming prevalent mostly due to
uncompliance in vaccination and antimicrobial resistance (i.e measles,
mumps, whooping cough

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 UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Define the term normal microbiota.

○ The collective term of the normal flora or microbes found in the surfaces of
the human body

● Identify the roles of the normal microbiota in maintaining human wellness.

○ Help prevent disease by competing against pathogens
○ Help develop the immune system response
○ Aid in digestion

● Compare and contrast the Bacteria, Archaea and Eucarya.

BACTERIA ARCHAEA EUKARYA

Size 0.3-2 micrometer 0.3-2 micrometer 5-50 micrometers

Nuclear No No Yes
Membrane?

Cell Wall? Peptidoglycan present No peptidoglycan No peptidoglycan

Organelles? No No Yes

Location? All environments Mostly are Almost all

extremophiles environment

Prok/Eukaryotes Prokaryotes Prokaryotes Eukaryotes

DNA Location Nuceloid Nuceloid Nucelous

Reproduction Via binary fission Via binary fission Varies

Movement flagella flagella Varies

● Compare and contrast algae, fungi, and protozoa.

○ Microbial members of domain Eucarya
ALGAE FUNGI PROTOZOA

Cell Organization Single or multicellular Single or multicellular Single-celled

Source of Energy Sunlight Organic compounds Organic compounds

Size Micro or macroscopic Micro or macroscopic Microscopic

Location Water Land Water and land

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 UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

Movement Motile Non-motile Motile

● State the principle distinguishing features between the six types of

microbes including bacteria, fungi, protists, helminths, viruses, and prions.

● Construct a Venn diagram representing the structural relationships

between the six types of microbes.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Compare the relative sizes of the six types of microbes.

○ Eukaryotes are larger than prokaryotes which in turn are larger than
viruses

● Explain how the scientific name of an organism is written.

○ Uses the binomial system of nomenclature. They are always italicized or
underlined.
■ Genus (capitalized)= first word
■ Species name (not capitalized)= second word
■ I. e ​Escherichia coli (E. coli)

● Compare and contrast viruses, viroids, and prions.

VIRUSES VIROIDS PRIONS

Obligate intracellular Obligate intracellular Abnormal fom of a cellular protein

parasites parasites

DNA/RNA + protein coat RNA (no protein protein

coat)

Plant diseases Neurodegenerative diseases

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

Resistant to usual sterilization

procedures
Ch 3: ​Prokaryotic Cell Structure
● Distinguish between magnification, resolution, and contrast in microscopy.
○ Magnification→ ​due to 2 magnifying lenses: the ​objective lens ​which
forms the real image and the ​ocular lens ​which forms the virtual image.
■ The total power of magnification is the product of the power of the
objective and the power of the ocular lens.
○ Resolution→ ​measure of the ability to distinguish two adjacent objects or
points from one another. Also known as ​resolving power.

■ Meaning that a shorter wavelength provides a better resolution

■ Numerical aperture→ ​describes the relative efficiency of a lens in
bending light rays
○ Contrast→ ​determines how easily cells can be seen.
■ Staining increases contrast

● Compare and contrast light microscopes, electron microscopes, and

atomic force microscopes.
○ Light microscopes→ ​most common and important tool in microbiology,
visible light passes through a series of lenses to produce a magnified
image up to 1000x
■ Bright field→ ​illuminates the field of view evenly, most common
type
■ Dark field→ ​light is directed towards the specimen at an angle
making unstained cells appear as bright colors against a dark
background
■ Phase-contrast→ ​uses special optics to amplify the difference
between refractive index of dense material and surrounding
medium making cells and other dense material appear darker
■ Differential interference contrast→ ​two light beams pass through
the specimen and then recombine making the image appear 3D
due to differences in refractive index and because light waves are
out of phase when recombined

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

■ Fluorescence​→ used to observe cells that have been stained or

tagged with fluorescent dyes
● Molecules absorb light at one wavelength (usually UV) and
emit light at longer wavelength
■ Scanning Laser (SLM)​→ used to observe details of the interior of
intact cells by scanning laser beams across specimens constructing
a 3D image of it
● Confocal→ ​lense focuses a laser beam to illuminate a given
point on one vertical plane of the specimen, like a miniature
CAT scan for cells
● Multiphoton→ ​similar to confocal but lower energy is used.
It is less damaging to cells allowing time-lapse images and
because light penetrates deeper it can give interior views of
relatively thick structures

○ Electron microscopes→ ​microscopes that use electrons instead of light

and can magnify images up to 10,000x

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

■ Transmission (TEM)→ ​transmits a beam of electrons through a

specimen, used to observe fine details of cell structure. Depends
on density of region as dense areas are darker than lighter ones.
● Thin-sectioning→ ​used to view internal details but the
process can distort the cells
● Freeze-fracturing→ ​used to observe the shape of
structures within a cell
● Freeze-etching→ ​the frozen surface exposed by fracturing
is dried slightly under vacuum which allows the underlying
regions to be exposed
● Cryo-electron microscopy→​ involves rapidly freezing the
specimen at very low temperatures to create 3D images of
the specimen
● Cryo-electron tomography​→ compiles images taken at
different angles to create 3D images of the specimen
■ Scanning (SEM)→ ​scans a beam of electrons back and forth over
the surface of a specimen, used to observe surface details of cells.
Yields 3D effect.

○ Atomic force microscopy (AFM)→​ ​type of scanning probe microscope

that has a tip mounted so that it can bend in response to the slightest
force between the tip and the sample. Produces detailed images of the
atoms on the surfaces of the atoms since the resolving power is much
higher than that of electron microscopes.

● Describe the different ways for preparing specimens for optical microscopy
○ Wet mount→ ​method of observing a living organism in drop of liquid
using a microscope. A cell is suspended in fluid, a drop of the culture is
then placed on a slide and overlaid with a cover glass.
○ Hanging drop mount→ ​uses a depression slide, Vaseline and coverslip,
The sample is suspended from the coverslip.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

○ Fixed, stained smears→ ​developed by Robert Koch

■ Spread a thin film made from a liquid suspension of cells and
air-drying it
■ Heat the dried smear by a process called heat fixation
■ Some cells are fixed using chemicals

● Distinguish between simple, differential, and special stains.

○ Simple stain→ ​require only a single dye. All cells appear the same color
but can reveal shape, size and arrangement (i.e methylene blue, crystal
violet and safranin).
■ Positive staining: ​uses a basic dye is used to stain cells. Staining
occurs because the basic dye is attracted to the negatively charged
components.
■ Negative staining: ​uses an acidic dye to stain the background
against which the colorless cells can be seen. This avoids the heat
fixing step which can distort the shape of the cells.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

○ Differential stain→ ​used to distinguish one group of bacteria from

another due to the fact that certain bacteria have distinctly different
components by using ​two differently colored dyes to distinguish between
cell types or parts (i.e Gram, acid-fast and endospore stains).
● primary stain→ ​first dye applied, generally stains all cells
● counterstain→ ​stain applied to impart a contrasting color to
bacteria that do not retain the primary stain
○ Special stains→ ​stains specific structures inside or outside of cells

● Describe the techniques used to observe capsules, endospores, and

flagella.
○ Capsule stain→ ​Capsules are ​gel-like layer that surrounds certain
microbes that serves a protective function and often increases an
organism's pathogenicity.
■ Often use negative staining (india ink added to wet mount is the
most common method) to make them visible.
○ Endospore stain→ ​multistep procedure that uses malachite green as a
primary stain and safranin as a counterstain to make endospores​ visible.
■ Endospores​→ ​ a ​special type of dormant cell which are highly
resistant to Gram strain, heat, radiation and disinfectants. Produced
by ​Bacillus ​and ​Clostridium ​species.
○ Flagella stain→ ​the staining agent that adheres to and coats the thin
flagella making them visible with the light microscope. Presence and
distribution can help in identification.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Describe the principles of the Gram stain and the acid-fast stain.
○ Gram-stain→ ​divides bacteria into one or more groups on basis of color
after staining thus reflecting fundamental difference in cell wall structure.
Most widely used staining procedure. ​The steps are as follows:

■ Gram-negative bacteria​→ stain pink as they lose the crystal violet

stain procedure due to their cell walls composition of a thin layer of
peptidoglycan surrounded by an outer membrane
■ Gram-positive bacteria​→ stain purple because the bacteria retain
the crystal violet stain due to their cell wall composition of a thick
layer of peptidoglycan

○ Acid-Fast staining​→ used to detect ​Myobacterium

(causes tuberculosis and leprosy) whose cell wall contains
high concentrations of mycolic acid which prevents uptake
of dyes. Used to presumptively identify clinical specimens.
■ The primary stain is carbolfuschin, a red eye.
■ Decolorizing agent is acid-alcohol
■ Counterstain is methylene blue
■ acid-fast→ ​organisms that retain the dye=
reddish-pink

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● List the benefits of using fluorescent dyes and tags.

○ Some dyes bind to all cells, some bind only to structures
○ Some are changed by cellular processes: distinguish between living and
dead cells
○ Immunofluorescence: ​uses antibody to deliver specific fluorescent tag to
unique microbe proteins

● Describe the five common bacterial shapes.

○ Two most common types: coccus (spherical) and rod or bacillus
(cylindrical)
○ Other shapes:
■ Vibrio (short curved rod), spirillum (spiral) and spirochete (long,
helical cell with a flexible cell wall and endoflagella)
■ Great diversity often found in low nutrient aquatic environments

● Explain the significance of chain, packet, and cluster groupings of bacteria.

○ Cells often stick together following binary fission and form characteristic
groupings such as: (i.e ​Neisseria gonorrhoeae ​(diplococcus)​,
Streptococcus ​(long chains), ​Sarcina ​(cubical packets) and
Staphylococcus ​(grapelike clusters)

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Diagram the typical prokaryotic cell structures

○ External structures
■ Filamentous appendages
● Flagella
● Pili
■ Glycocalyx
● Capsule
● Slime layer
○ Cell envelope
■ (outer membrane)
■ Cell wall
■ Cell membrane
○ Internal structure
■ Cytoplasm
■ Ribosomes
■ Inclusions
■ Nucleoid/chromosomes
■ Actin cytoskeleton
■ Endospore
■ Gas vesicles
■ Granules

● Diagram and describe the structure of the cytoplasmic membrane.

○ Phospholipid bilayer ​embedded with proteins in which hydrophobic tails
face in and hydrophilic tails face out that acts as a semipermeable
membrane
○ Its proteins serve numerous functions such as:
■ Selective gates
■ Sensors of environmental conditions
■ Fluid mosaic model→ ​describes how proteins drift about in the
lipid bilayer

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

○ Provides a site for functions such as: energy reactions, nutrient

processing, synthesis, chemotaxis and anchor for many proteins involved
in these functions.
○ Bacteria and Archaea→ ​have the same general structure with some
minor differences such as distinct different lipid compositions.
■ Archaea→ lipid tails are connected to glycerol by a different type of
chemical linkage and are not fatty acids

● Define the selective permeability of the cytoplasmic membrane and cite

examples of substances which are allowed through or excluded.
○ Selective permeability→ ​only certain substances can cross

● Describe the role of the cytoplasmic membrane in creating the proton

motive force.
○ The ​electron transport chain (ETC) ​which is embedded in the
membrane is a ​group of membrane-embedded electron carriers that pass
electrons from one to another and in the process move protons across the
membrane to create an electrochemical gradient called the​ proton motive
force ​which is harvested to drive cellular processes including ATP
synthesis, transport and motility.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Explain why directed movement of molecules across the cytoplasmic

membrane is necessary for a cell.
○ Because most molecules must pass through proteins functioning as
selective gates ​termed transport systems that allow nutrients and other
molecules to enter the cell and wastes to exit the cell. This interaction is
highly specific.

● Compare and contrast simple diffusion and osmosis.

○ Simple diffusion→ ​movement from high to low concentration.
○ Osmosis→ ​diffusion of water across selectively permeable membrane
due to unequal solute concentrations.
■ Isotonic→ ​environment is equal in solute concentration to the cell’s
internal environment. No net change in cell volume. Generally the
most stable environment for cells.
■ Hypotonic→ ​The solute concentration of the external environment
is lower than that of the cell’s internal environment. Cells without
cell walls swell and can burst.
■ Hypertonic→ ​The environment has a higher solute concentration
than the cytoplasm. Will force water to diffuse out of a cell and the
cell will shrink.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Distinguish between facilitated diffusion, active transport, and group

translocation.
○ Facilitated diffusion→ ​form of passive transport (no energy required)
and it is rarely used by prokaryotes as it is not typically useful in
low-nutrient environments
○ Active transport→ ​moves compounds against a concentration gradient
and therefore requires energy either using:
■ proton motive force​→ as a proton is allowed into the cell another
substance is either brought along or expelled (i.e permease that
transports lactose brings the sugar into the cell along with a proton)
■ ABC transporters​→ use ATP as an energy source. Extracellular
binding proteins deliver a molecule to the transporter.
○ Group translocation→ ​transport process that chemically alters a
molecule during its passage through the cytoplasmic membrane (i.e
phosphorylation)

● Explain the purpose and role of bacterial secretion and the signal sequence
in bacterial secretion.
○ Bacterial secretion→ ​It is the active process that moves certain process
they synthesize out of the cell. This is possible thanks to the signal
sequence.
○ Signal sequence​→ characteristic sequence of amino acids, typically at
one end of the molecule that functions as a tag that directs the secretion
machinery to move the preprotein across the membrane.​ ​During the
transport process, the signal sequence is removed.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Describe the structure and function of peptidoglycan.

○ It is a macromolecule found only in bacteria that provides strength to the
bacterial cell wall. The basic structure is a chain of two alternating
subunits ​N-​acetylglucosamine (NAG) and ​N-​acetylmuramic (NAM)
cross-linked by tetrapeptide chains, peptide bridges through covalent
bonds.
○ Tetrapeptide chains​→ a string of four amino acids.
○ The interconnected glycan chains form a large sheet. Multiple connected
layers create a 3D molecule.
○ It is permeable to sugars, amino acids etc.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Distinguish between the Gram-positive and Gram-negative cell walls.

Gram-Positive Gram-Negative

Color of Gram stained cell Purple Pink

Representative Genera Bacillus, Staphylococcus, Escherichia, Neisseria,

Streptococccus Pseudomonas

Peptidoglycan Thick layer Thin layer

Teichoic acids Present Absent

Outer Membrane Absent Present (bilayer)

Lipolysaccharide (Endotoxin) Absent Present

Porin Proteins Absent (not necessary) Present

Sensitivity to Penicilin More susceptible Less susceptible

Sensitivity to Lysozyme Yes No

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Describe teichoic acids and their significance.

○ Teichoic acids→ ​negatively-charged chains of a common subunit (either
ribitol-phosphate or glycerol-phosphate) to which various sugars and
D-alanine are typically attached.
■ Stick out above the peptidoglycan layer and bind cations (Mg​+​)
■ Function→ not well understood but believed to be a reservoir for
cations that are essential for enzyme function.

● Describe the structure of the outer membrane of Gram-negative cell walls

and the significance of its components,
○ Outer membrane→ ​unique lipid bilayer embedded with proteins joined to
peptidoglycan by lipoproteins. The following elements are found in it:
■ Lipopolysaccharide (LPS) ​→ molecules formed by bonding of
lipid to polysaccharide that make up the outside layer of the outside
membrane.
● Important medically as it signals immune system of invasion
by Gram-negative bacteria. If large amount accumulate in
the bloodstream they can yield a deadly response.
■ Porins→ ​specialized channel-forming proteins that span the outer
membrane and allow the passage of small molecules and ions.
Play a critical role in the disease process of some pathogens.
■ Periplasm→ ​gel-like substance in which all exported proteins
accumulate unless moved across the outer membrane.
● It is found in the periplasmic space between the cytoplasmic
membrane and the outer membrane.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Explain the significance of lipid A and O antigen components of LPS.

○ Lipid A→ ​anchors the LPS molecule in the lipid bilayer. Plays an
important role in the body’s ability to recognize the presence of invading
bacteria as well as responsible for the toxic effects of LPS. Aka an
endotoxin.
○ O antigen→ ​portion of LPS directed away from the membrane.
Composed of a chain of sugar molecules, the number and type varies
among different species which helps them in the identification of certain
species or strains.

● Explain the role of the cell wall in susceptibility to penicillin and lysozyme.
○ Because peptidoglycan is unique to bacteria it makes it susceptible to
compounds that alter its synthesis or alter its structural integrity to a point
where it is unable to prevent cell lysis such as:
■ penicillin→ ​interferes with peptidoglycan synthesis by preventing
cross-linking of adjacent glycan chains
● It is usually more effective against Gram-positive than
Gram-negative bacteria since the outer membrane of the
latter blocks the access of penicillin
■ lysozyme→ ​an enzyme found in tears and saliva breaks the bonds
that link the alternating subunits of the glycan chain thus destroying
the structural integrity of the peptidoglycan molecule.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Explain how the cell wall affects Gram staining characteristics.

○ Gram-negative bacteria​→ stain pink as they lose the crystal violet stain
procedure due to their cell walls composition of a thin layer of
peptidoglycan surrounded by an outer membrane
○ Gram-positive bacteria​→ stain purple because the bacteria retain the
crystal violet stain due to their cell wall composition of a thick layer of
peptidoglycan

● Describe the cell walls of the Archaea.

○ Have a variety of cell walls due to a wide range of environments but no
peptidoglycan instead they have a similar molecule, pseudopeptidoglycan,
arranged in S-layers or sheets of flat protein or glycoprotein subunits that
self-assemble.

● Distinguish the structure and function of capsules and slime layers.

○ They vary in their chemical composition and depend on their microbial
species. Most are composed of polysaccharides and are commonly
referred to as ​glycocalyx ​(sugar shell) ​and function as a mechanism of
either protection or attachment.
■ capsule→ ​gel-like layer that surrounds certain microbes that
serves a protective function and often increases an organism's
pathogenicity.
■ slime layers→ ​type of glycocalyx that is diffuse and irregular.
○ Some allow bacterial cells to adhere to specific surfaces and once
attached can grow as a ​biofilm→ ​a polysaccharide encased community
(i.e dental plaque).

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Describe the structure and arrangements of bacterial flagella, and explain

how they are involved in chemotaxis.
○ Flagella→ ​involved in motility by spinning like propellers to move cells
■ Has 3 basic parts:
● Filament→ ​portion that extends into an external
environment. Made up of identical subunits of protein
flagellin that twist into a helical structure with a hollow core.
● Hook→ ​flexible curved segment, it connects the filament to
the cell surface.
● Basal body→ ​anchors the structure to the cell and the
cytoplasmic membrane.

■ Number and arrangement can be used to characterize bacteria. IE:

● peritrichous→ ​distribution of flagella all around a cell
● polar flagellum→ ​single flagellum at one end of the cell
○ Chemotaxis​→ phenomenon in which motile bacteria sense the presence
of chemicals and respond by moving in a certain direction. Movement
occurs in a series of runs and tumbles.

● Compare and contrast the structure and function of fimbriae and sex pili.
○ Pili→ ​hairlike appendages on many Gram-negative bacteria that function
in conjugation and for attachment. Movement includes: twitching, gliding.
■ Sex pilus→ ​used to join bacteria for DNA transfer during
conjugation (i.e F pilus)
○ Fimbriae→ ​type of pilus that enables cells to attach to a specific surface.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Describe the structure and function of the bacterial chromosome,

plasmids, ribosomes, storage granules, gas vesicles, and endospores.
○ Bacterial chromosome→ ​single, circular double stranded DNA
■ nucleoid​→ geli-like region that contains all of the genetic material
required by the cell
○ Plasmids→ ​small extrachromosomal circular, supercoiled, double
stranded DNA that replicates independently of the chromosome. Often
codes for antibiotic resistance
○ Ribosomes→ ​involved in protein synthesis by facilitating the joining of
amino acids during the process of translation; composed of protein and
ribosomal RNA. Composed of different subunits which is medically
important because antibiotics affecting 70S do not affect the 80S
ribosome.
■ prokaryotic→ 70S= 30S + 50S subunits
■ eukaryotic→ 80S
○ storage granules→ ​an accumulation of high-molecule weight polymer
synthesized from a nutrient that a cell has in excess for energy storage
and pH balance theoretically
○ gas vesicles→ ​produced in some aquatic bacteria. They are small, rigid
protein bound compartments that provide buoyancy to the cell.
○ endospores→ ​unique type of dormant cell produced by certain bacterial
species such as ​Bacillus, Clostridium. ​They are extremely resistant to
heat, desiccation, chemicals, UV light etc

● Describe the significance and processes of sporulation and germination.

○ sporulation→ ​endospore formation triggered by carbon, nitrogen
limitation (aka starvation conditions) which triggers an 8 hour process. It is
not a means of cell reproduction because one ​vegetative cell ​(typical,
active multiplying cell) gives rise to one endospore.
■ 1) Vegetative growth stops and DNA is duplicated
■ 2) A septum forms dividing the cell asymmetrically
■ 3) The larger compartment engulfs the smaller one forming a
forespore ​within a mother cell
● Forespore​ becomes the core of the endospore.
■ Peptidoglycan containing material is laid down between the two
membranes that surround the forespore, forming the core wall and
the cortex. These endospore layers prevent damage by excluding
molecules such as lysozyme.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

● Cortex ​maintains the core in a dehydrated state protecting

from heat
● Core ​has small proteins that bind and protect DNA and is
rich in ​calcium dipicolinate ​which seems to play an
important role in antibiotic resistance.

○ germination→ ​process by which an endospore or other resting cell

becomes a vegetative cell. It is triggered by heat and chemical exposure.
■ After exposure the endospore takes on water and swells
■ The spore coat and cortex crack open and a vegetative cell grows
out

● Describe the structure and function of the eukaryotic plasma membrane,

comparing and contrasting it with the prokaryotic cytoplasmic membrane.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

○ It is an asymmetric lipid bilayer embedded with proteins similar to the

prokaryotic cytoplasmic membrane but the layer facing the cytoplasm
differs from that facing the outside of the cell.
○ The proteins in the outer layer serve as ​receptors ​which bind specific
molecules termed as ​ligands. ​These are important in cell communication.
○ Contain ​sterols​ which provide strength to an otherwise fluid structure.
■ In mammals→ cholesterol
■ In fungi→ ergosterol
○ Lipid rafts→ ​allow the cell to detect and respond to signals. Used by
many viruses to enter and exit cells.
○ The electrochemical gradient is maintained via sodium or proton pumps.

● Compare and contrast the roles of eukaryotic channels and carriers.

○ carriers→ ​protein found in cell membrane that transport certain
compounds across membranes via facilitated diffusion and active
transport
○ channels→ ​pore-forming membrane protein that allows specific ions to
diffuse in and out of the cell
○ aquaporins​→ pore-forming membrane proteins that specifically allow
water to pass through

● Distinguish the processes of endocytosis and exocytosis.

○ endocytosis→ ​process by which cells take up materials from the
surrounding environment by forming invaginations in its membrane
■ pinocytosis→ ​aka cell drinking, ​ ​the process by which cells take in
liquid and small particles from the surrounding environment by
internalizing and pinching off pieces of their own membrane
■ receptor mediated endocytosis→ ​type of pinocytosis that allows
cells to internalize extracellular ligands that bond to the cell’s
receptors

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

○ phagocytosis→​ used by protozoa​, ​process by which cells ingest

particulate matter by surrounding and enveloping those materials by using
armlike extensions called ​pseudopods
○ exocytosis→ ​process by which eukaryotic cells expel material in which
membrane-bound vesicles inside the cell fuse with the plasma membrane
releasing their contents to the external medium

● Explain the role of the endoplasmic reticulum in secretion.

○ The rough ER is studded with ribosomes which are responsible for
synthesizing proteins. As the protein in made it is threaded through the
membrane and into the ER where the protein can be transported by
vesicles to the outside of the cell.

● Describe the structure and function of the eukaryotic organelles:

○ nucleus→ ​contains the genetic information.
Composed of:
■ nuclear envelope→ ​double membrane
that separates the nucleus from the
cytoplasm that surround the nucleus
■ nuclear pores→ ​gaps in the nuclear
envelope that allow large molecules to
pass
■ nucleolus→ ​region within the nucleus
where ribosomal RNAs are synthesized
○ mitochondria→ ​ATP-generating powerhouses
bounded by two lipid bilayers: the ​outer
membrane ​is smooth and the​ inner membrane ​is highly folded, forming

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

invaginations called ​cristae ​which increase the surface area. Division is

by binary fission and has its own DNA.
■ mitochondrial matrix​→ gel-like material enclosed by the
mitochondrial inner membrane that contains DNA, ribosomes
necessary for protein synthesis
■ endosymbiont theory​→ theory that the ancestor of mitochondria
and chloroplasts were bacteria that had been residing within other
cells in a beneficial partnership.

○ ribosomes→ ​structures involved in protein synthesis

○ endoplasmic reticulum (ER)→ ​complex system of flattened, sheets,
sacs and tubes
■ Rough endoplasmic reticulum (RER) → ​site where proteins not
destined for the cytoplasm are synthesized
■ Smooth endoplasmic reticulum (SER) → ​functions in lipid
synthesis and degradation and calcium ion storage

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

○ Golgi apparatus→ ​consists of a series of membrane-flattened

compartments that serve as the site where macromolecules synthesized
in the ER are modified before they are transported to other destinations

○ cytoskeleton→ ​the dynamic filamentous network that provides structure

and shape to eukaryotic cells. It is composed of:
■ microfilaments (aka actin filaments) → ​allow movement;
composed of polymers of actin that polymerize and depolymerize
■ intermediate filaments→ ​they allow cells to resist physical
stresses by​ ​providing mechanical support and functioning like ropes
■ microtubules→ ​long hollow structures made of protein subunits
called tubulin. Provide the framework for organelle and vesicle
movement. Form the following structures:
● mitotic spindles→ ​machinery that separates duplicated
chromosomes as cells divide
● flagella→ ​long whiplike structure composed of microtubules
in a 9+2 (9 pairs surrounded by 2 individual ones)
arrangement that provides a mechanism of locomotion using
ATP as a source of energy. Propel via whiplike motion or
thrash back and forth to pull cell forward.
● cilia→ ​short, projecting hairlike structure of locomotion. (i.e
mucociliary escalator→ epithelial cells that line the
respiratory tract).

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

○ chloroplasts→​ found only in plants and algae. Function as a site of

photosynthesis by which they harvest sunlight to generate ATP.
Composed of a two lipid bilayers and contain DNA and ribosomes.
■ endosymbiotic theory→ evolved from cyanobacteria

○ lysosomes→ ​organelles that contain degradative enzymes

■ endosomes and phagosomes fuse lysosomes allowing the
degradation of material that is taken up by the cell
■ autophagy​→ old organelles and vesicles can also fuse with them
to digest the cell’s own contents
○ peroxisomes→ ​organelles in which oxygen is used to help break down
lipids and detoxify certain chemicals by generating hydrogen peroxide.
Protects cell from toxic effects.

● Compare and contrast structural similarities and differences between

prokaryotic and eukaryotic cells.

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

PROKARYOTIC EUKARYOTIC

Size 0.3-2 microm in diameter 5-50 microm in diameter

Cell Division Chromosome replication Chromosome replication and

followed by binary fission mitosis followed by division

Chromosome In nucleoid In nucleus

Location

Cell Membrane Relatively symmetric with Highly asymmetric; lipid

respect to the lipid content of composition of outer layer differs
the bilayers to that of inner layer

Cell Wall Single-circular DNA Multiple, linear DNA molecules

wrapped around histones

Flagella Composed of protein subunits; Made up of 9+2 arrangement of

attached to the cell envelope microtubules; covered by an
extension of the plasma
membrane

Membrane-bound Absent Present

organelles

Nucleus Absent Present

Ribosomes 70S= 50S + 30S 80S= 60S + 40S

Degradation of Function of enzymes Function of lysosomes

extracell subs

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UNIT 1-Module 1-Ch1,3: Humans and the Microbial World, The Molecules of Life, Microscopy &
Prokaryotic Cell Structure

Motility Flagella Cilia and Flagella

Protein secretion Secretion systems transport Secreted proteins are moved to

proteins across the cytoplasmic the lumen of the RER→ Golgi for
membrane processing and packaging

Strength & Rigidity Peptidoglycan in cell wall cytoskeleton

Transport Primarily active transport and Facilitated diffusion, active

group translocation transport, ion channels

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