Organisms Too Small To Be Seen by The Unaided Eye

UST College of Science
MODULE 1 Domain Archaea

● Distinguished from Bacteria by unique rRNA gene
Microbiology: Is defined as the study of sequences
● Lack peptidoglycan in cell walls
organisms too small to be seen by the ● Have unique membrane lipids
unaided eye. ● Some have unusual metabolic characteristics
● Many live in extreme environments.
Is an ancient biological science in which identi cation

and characterization of microorganisms and their
interactions with the surrounding environment are Domain Eukarya
studied. ● Protists - generally larger than Bacteria and Archaea
○ Algae - photosynthetic
Why Microbiology Matters? ○ Protozoa - may be motile, “hunters, grazers”
○ Slime molds - two life cycle stages
● Keeps the planet healthy
○ Water molds - devastating disease in plants
○ Plays a major role in recycling essential
● Fungi
elements
○ Yeast - unicellular
● Agriculture and Food
○ Mold - multicellular
○ Enables farmers to increase yield and

productivity in a sustainable way
● Combating diseases
○ Etiology and epidemiology, control and
prevention
● Industry and biotechnology
○ Antibiotics and vaccines as well as other
pharmaceutical products
○ Genetic engineering

Earth: Home to 1 Trillion Microbial
Species

Types of Microbial Cells
● Prokaryotic cells lack a true membrane-delimited
nucleus
○ This is not absolute (Planctomycetes are an
exception.)
● Eukaryotic cells have a membrane-enclosed nucleus, are
more complex morphologically, and are usually larger
than prokaryotic cells.

Classi cation Schemes
● Three domain systems based in
comparison of ribosomal RNA genes, divides
microorganism into
○ Bacteria (true bacteria) PROKARYOTIC
○ Archaea
○ Eukarya (eukaryotes) BACTERIA ARCHAEA

● Typically 0.2 - 5 μm ● Typically 0.2 - 5 μm
Domain Bacteria ● Heterotrophic. ● Heterotrophic.
● Usually single-celled Some are Some are
● Majority have cell wall with peptidoglycan phototrophic (e.g. phototrophic
● Most lack a membrane-bound nucleus Cyanobacteria) ● Not generally
● Ubiquitous and some live in extreme environments ● Some are associated associated with
● Cyanobacteria produce signi cant amounts of oxygen. with diseases diseases
● Major inhabitants of ● Associated with
the human extreme
microbiome environments

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What are FUNGI?

EUKARYOTIC
● Eukaryotes
● Microscopic Fungi: Yeast and Molds (10-100 μm)
FUNGI PROTIST
● Macroscopic Fungi: Mushrooms
● Yeast and Molds ● Protozoa, ● Nutrition: Heterotrophic
● Variable 10 - 100 μm Microscopic algae, ● Some are associated with diseases
● Heterotrophic slime molds, water
● Some are associated molds
with diseases ● Variable 10 - 100 μm
● Heterogenous ● Heterotrophic.
group, with Some are
macroscopic forms, phototrophic What are PROTISTS?
ie. mushroom ● Some are associated ● Eukaryotes, mostly unicellular
with diseases ● Microscopic Protists: Protozoa, microscopic algae,
● Heterogenous slime molds, water molds (10-100 μm)
group, with ● Macroscopic: Seaweeds
macroscopic forms, ● Nutrition: Chemoheterotrophic, photoautotrophic
ie. seaweed ● Can be free-living or as parasites
ACELLULAR
VIRUSES
● Typically 20 - 200 nm. Giant viruses up to 1 μm
● Need host for survival
● Some are associated with diseases What are VIRUSES?
● Heterogenous in structure despite being acellular ● Acellular
● Size:20-200 nm, giant viruses up to 1 μm
What are BACTERIA? ● Needs host for survival, do not multiply outside the host
● Prokaryotes ● Some are associate with diseases (can infect all cell
● Size: 0.2-5 μm types)
● Shape: cocci, bacilli, spiral, comma-shaped, pleomorphic
● Nutrition: Heterotrophic, some phototrophic
● Some are associated with diseases.
● Basic structure
○ Genetic materials are localized in the nucleoid
○ Motility: agella
○ Attachment: Fimbriae and Pili Other acellular infectious agents
○ Survival strategy: Endospore
Viroids - simpler than viruses
● Consists only of small single-stranded, circular RNA
● Needs host for survival
● Associated with plant diseases

Satellite Viruses - subviral pathogens that are entirely dependent
What are ARCHAEA? upon the replication machinery of their helper viruses
● Prokaryotes ● May infect animals, protists and plants
● Size: 0.2-5 μm ● May alter symptoms caused their helper virus
● Shape: cocci, bacilli, spiral, star/branched-shaped,
pleomorphic Prions - multiply by converting normal protein molecules into
● Nutrition: Heterotrophic, some phototrophic pathogenic ones by inducing the normal molecules to change their
● Associate with extreme environments. shape
● Associated with animal diseases

How did it start?
Based on chemical and fossil evidence, microbes are ancient and
were the only inhabitants of our planet for billions of years.

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Sustainable Agriculture and

Industry/Energy Source
● Sewage treatment
● Source of biofuel
● Composting recycle vital soil nutrients
● Biocontrol agents
● Food security using genetic engineering
● Bioterrorism

Important Events in Microbiology

History of Microbiology
● Development of ideas about microbes
○ Germ theory of disease (relationship between
microbes and diseases of plants, animals, and
humans)
○ Controversy on spontaneous generations
○ Immunology
○ Microbial ecology (unique physiology,
enrichment culture)
○ Industrial microbiology (fermentations,
pasteurization)
● Development of tools used to study them
○ Microscopes
○ Culture techniques
○ Molecular genetics
○ Genomics

Fermentation is the oldest and most popular
technology used by humankind, dating back to the
Neolithic period. Its exploitation was mostly used in dairy
products, baking, wine making, and brewing.

Food

● Alcoholic beverages from barley, berries, etc.
Basic and Applied Microbiology
● Soy sauce from soybeans
● Basic aspects are concerned with achieving a deeper
● Creates the aroma, avor and rich color of chocolates
understanding of the workings of the microbial cell
● Angkak (red yeast rice) - may lower cholesterol
○ Microbial physiology

○ Microbial ecology
Various milk products are made with microbes
○ Genetics and molecular biology

○ Taxonomy and Systematics of various groups of
Baking bread requires yeast; sour dough, uses a special strain
microbes
of yeast.
● Applied aspects are concerned with practical problems

○ Medical microbiology
Medicine ○ Food microbiology
● Bacteria are grown on bioreactor to harvest vitamins ○ Industrial microbiology
● Fungi tapped as source of novel drugs
● Used to develop vaccine and even cosmetic products

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Major Fields in Microbiology

● Medical microbiology
Notable Persons in History

○ Diseases of humans and animals
Oswald Avery
● Public health microbiology
● Oswald Avery and his colleagues set out to discover
○ Control and spread of communicable diseases
which constituent in the heat-killed virulent
● Immunology
pneumococci was responsible for transformation.
○ How the immune system protects a host from
● The publication of these studies by Avery, C. M.
pathogens
MacLeod, and M. J. McCarty in 1944 provided the rst
● Agricultural microbiology
evidence that DNA carried genetic information.
○ Concerned with the impact of microorganisms
Martinus Beijerinck
on agriculture
● Martinus Beijerinck was one of the great general
○ Food safety microbiology
microbiologists who made fundamental contributions
○ Animal and plant pathogens
not only to virology but to microbial ecology as well.
● Microbial ecology
● He isolated aerobic nitrogen- xing bacteria (Azotobacter
○ Relationship of organism with their
spp.), a root nodule bacteria also capable of xing
environment
nitrogen (genus Rhizobium), and sulfate-reducing
○ Less than 1% of the Earth’s microbial
Bacteria.
population has been cultured
● Beijerinck and Winogradsky also developed enrichment
● Industrial microbiology
culture techniques and selective media, which have been
○ Fermentation
of great importance in microbiology.
○ Antibiotic production
Charles Chambeerland
○ Production of cheese, bread, etc.
● Paved way for the discovery of viruses and their role in
● Microbial physiology
diseases
○ Studies metabolic pathways of microorganisms
● Constructed a porcelain bacterial lter in 1884.
● Molecular biology, microbial genetics, and
● Invented the autoclave
bioinformatics
● Water puri cation device used to discover virus
○ Nature of genetic information and how it
● Developed Pasteurella vaccine
regulates the development and function of cells
● Chamberland Filter - lter had pores that were smaller
and organisms.
than bacteria, thus making it possible to pass a solution
○ Microbes are a model of the system of
containing bacteria through the lter, and having the
genomics.
bacteria completely removed from the solution.

Ferdinand Cohn
Molecular and Genomic Methods
● Discovered that the heat-resistant bacteria recognized by
● Led to a second golden age of microbiology (rapid
English physicist, John Tyndall were species capable of
expansion of knowledge)
producing bacterial endospores.
● Discoveries
● Cohn later played an instrumental role in establishing a
○ Restriction endonucleases (Arber and Smith)
classi cation system for bacteria based on their
○ First novel recombinant molecule (Jackson,
morphology and physiology.
Symons, Berg)
● First to classify algae as plants
○ DNA sequencing methods (Woese, Sanger)
Anton De Barry
○ Bioinformatics and genomic sequencing and
● He is a founding father of plant pathology as well as the
analysis
founder of modern mycology.

● He was the rst one who proved that fungi could infect
Careers in Microbiology
and attack healthy plants. Before that time, it was
● Microbiologists are important in industry
generally assumed that fungi appeared only after the
○ Manufacturing
plant had become diseased in some way or another.
■ Food and beverage
● We owe to him the terms heteroecism, autoecism,
■ Pharmaceuticals
teleutospores and aecidiospores, saprophytism and
■ Cosmetics and personal hygiene
parasitism, and symbiose.
products
Paul Ehrlich
○ Testing Laboratories
● The modern era of chemotherapy began with Paul
● Microbiologists can be Researchers in various elds
Ehrlich’s work on drugs against African sleeping sickness
● Microbiologists can have a career in academe
and syphilis.
● Microbiologists as policy makers
● Ehrlich was fascinated with dyes that speci cally bind to
● Microbiologists as technical specialists.
microbial cells. He reasoned that one of the dyes could
be a chemical that would selectively destroy pathogens
without harming human cells.
● In 1909 Paul Ehrlich introduced an arsenic derivative,
arsphenamine or salvarsan, as therapy.
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● Co-discoverer of antibodies, antigens, and chemotherapy Esther Lederberg

for disease ● Esther Lederberg was a major pioneer of bacterial
● Together with Behring, they demonstrated that genetics. She discovered the lambda phage, a bacterial
protection could be transferred from one animal to virus which is widely used as a tool to study gene
another using serum alone regulation and genetic recombination.
Alexander Fleming Joshua Lederberg
● Alexander Fleming accidentally rediscovered the rst ● Joshua Lederberg discovered bacterial recombination
true antibiotic, Penicillin in 1928. and started a new eld of research.
● Penicillin was rst discovered in 1896 by Ernest ● A pioneer in the eld of bacterial genetics, who shared
Duchesne. the 1958 Nobel Prize for Physiology or Medicine.
Fanny Hesse ● discovered that bacteria can mate and exchange genes,
● Is the wife of Walther Hesse. not just clones
● She provided agar as a better solidifying agent than Joseph Lister
gelatin as gelatin can be digested by many microbes and ● Lister successfully introduced carbolic acid (now known
can also be melted at temperatures above 28°C. as phenol) to sterilise surgical instruments and to clean
● Agar was not attacked by most bacteria. Furthermore, it wounds.
did not melt until reaching a temperature of 100°C and, ● Applying Louis Pasteur's advances in microbiology,
once melted, did not solidify until reaching a Lister championed the use of carbolic acid as an
temperature of 50°C; this eliminated the need to handle antiseptic, so that it became the rst widely used
boiling liquid. antiseptic in surgery.
Robert Hooke Louis Pasteur
● Credited with publishing the rst drawings of ● Louis Pasteur was a French chemist and microbiologist
microorganisms in the scienti c literature. whose work changed medicine. He proved that germs
● In the year 1665, he published a highly detailed drawing cause disease; he developed vaccines for anthrax and
of the fungus Mucor in his book Micrographia. rabies; and he created the process of pasteurization.
Edward Jenner ● To expound on that, his discovery led to the knowledge
● The rst scienti c attempts at arti cial immunizations that microbes were responsible for souring alcohol and
were made in the late eighteenth century by Edward came up with the process of pasteurization, where
Jenner (1749–1823). bacteria are destroyed by heating beverages and then
● He investigated the basis for the widespread belief of the allowing them to cool. His work in germ theory also led
English peasants that anyone who had vaccinia (cowpox) him and his team to create vaccinations for anthrax and
never contracted smallpox. rabies.
Robert Koch ● Debunked spontaneous generation/Showed that
● Identi ed Mycobacterium tuberculosis as the causative fermentation, spoiling, and contamination was due to
agent of tuberculosis. microbes
● The rst direct demonstration that bacteria cause disease ● Proved germ theory of disease
came from the study of anthrax by the German ● showed that sterilization or ltration can maintain
physician Robert Koch. organic material in sterile condition without microbial
● His criteria for proving the causal relationship between a growth
microorganism and a speci c disease are known as Richard Petri
Koch’s postulates. ● In 1887, Julius Petri invented a simple pair of nesting
- Pathogens accounts for features of disease and glass dishes, ideal for keeping specimens of growing
must be found in every case of disease bacteria sterile—the 'Petri dish.
- Pathogen is not found in other non diseases as Ronald Ross
non pathogen, bacteria must be isolated from ● British doctor who received the Nobel Prize for
the host with the disease in pure culture Physiology or Medicine in 1902 for his work on malaria.
- After being isolated and passed in pure culture, ● His discovery of the malarial parasite in the
pathogen can induce disease gastrointestinal tract of the Anopheles mosquito led to
- Same pathogen must be re-isolated from the the realization that malaria was transmitted by Anopheles,
experimental animal. and laid the foundation for combating the disease.
Elie Metchniko Ignaz Semmelweis
● The rst immune system cells were discovered when Elie ● Discovered the cause of purple (puerperal) fever which is
Metchniko (1845–1916) found that some white blood some form of “putrid matter” from autopsies carried on
cells could engulf disease-causing bacteria. He called the hands of the physician handling pregnant women
these cells phagocytes and the process phagocytosis ● Discovered antisepsis. Found that washing hands with a
(Greek phagein, eating). dilute, chlorinated lime after performing autopsies
● Provided initial description of innate immunity helped reduce mortality rate of purple fever
● Con rmed that phagocytosis by neutrophils and
macrophages was an essential part of innate immune
response in humans
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John Snow
● Founding Father of Epidemiology
● Was able to identify the source of Cholera that it is
waterborne or foodborne (contaminated water)
● Highest number of cholera cases near river
Edward Tatum
● Proved that human’s genetic code, genes, govern the
information of enzyme
● Discovered the occurrence of genetic
recombination, or “sex,” between Escherichia coli
bacteria of the K-12 strain
● One gene, one enzyme
Anton Van Leeuwenhoek
● Father of Microbiology Types of Light Microscopes
● Laid the foundations of plant anatomy ● Bright-Field Microscope
● First to observe microorganisms ○ Uses viable / non-viable cells; shows the
● Discovered protozoa specimens dark on a bright background.
● Contributes to the development of microscopes. ● Dark-Field Microscope
Emil Von Behring ○ Not culturable organisms; shows the
● Development of serum from immune horses against specimens bright on a dark background.
diphtheria and tetanus ● Phase-contrast
● Founder of Immunology ○ Used to view transparent specimens without
● Savior of children staining them; can be used to view living cells.
Selman Waksman ● Polarization Microscopy
● Discovered streptomycin which was the rst ○ Looking at di erent crystal formations; shows
antimicrobial agent developed after penicillin and the the specimens bright on a dark background.
rst antibiotic e ective in treating tuberculosis ● Fluorescence
Chaim Weizmann ○ Makes use of exciter and bio lters.
● Father of industrial fermentation ● Compound Microscope
● Discovered how to use bacterial fermentation ○ Has two magnifying lenses
● Acetone-butanol-ethanol fermentation process that
produces acetone Compound Light Microscopes
Sergei Winogradsky - Uses two lenses. The eyepiece or the ocular lens coupled
● Invented Winogradsky column with the objective lenses.
● Discovered chemosynthesis - Enhances the image better with the use of the two lenses.
● Founded microbial ecology, where the interactions of - Either monocular or binocular.
microbes in cycles with their natural environments - Limit of resolution: 0.2 μm (micrometers) or 200 nm
● Discovered and isolated nitrogen xing bacteria in soil (nanometers)
that make nitrates available to green plants
Antonio Luna Electron Microscopes
● Contributed to the leading Pharmacy scienti c journals. ● Uses electron beams
● First environmental science research in the Philippines ● Electromagnets function as lenses.
which included the bacteriological studies of Pasig River
water. Types of Electron Microscopes
● Pasig River is un t for drinking water ● SEM (Scanning Electron Microscope)
● therapeutic and chemical properties of Sibul Spring ○ Forms an image through radiation that has
water and the rst study on Philippine forensic science, passed through a specimen - resolution 7nm or
where he did a study on using human blood as evidence less; air-dried material can be examined directly.
in judicial proceedings. ○ Produces excellent images of the surface of cells
and small organisms.
MODULE 2 ○ Excellent for studying surface morphology of
organisms, or any other suitable material under
study.
Microscopes: Seeing the invisible. ○ Electron beams scan over the surface of the
Microscopes were invented for us to be able to view these sample.
small organisms. ○ Based on scattered e- / produces images by
detecting secondary e- which are emitted from
Light Microscopes were the rst invented and most commonly the surface due to excitation by primary
used microscopes. electron beam.
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● SEM (Scanning Electron Microscope)

○ Lower resolution than TEM (2nm - average;
Staining: Enhances the viewing
0.2nm - special) experience of specimens under
○ Depth of eld: High observation.
○ Magnifying power: 100,000x
○ Specimen contrast: by electron adsorption

○ Produced 3D black & white images. Staining Specimens
○ Uses sputter coating (coating of ● Fixation - process by which internal and external
electrically-conducting material; eg. gold). structures of specimens are preserved and xed in
position; inactivates enzymes disrupting morphology
● TEM (Transmission Electron Microscope) and toughens cell structures.
○ Produces very clear images. ● Heat xation - bacteria/archaea; a lm/smear of cells is
○ Wavelength 100,000 times shorter than the gently heated (destroys proteins in subcellular structures
visible light. which may distort appearance)
○ Electron dense areas are darker. ● Chemical xation - chemical xatives penetrate cells and
○ Negative Staining and Shadowing are utilized. react with cellular components, usually proteins and
○ Freeze-etching procedure. lipids - used to protect ne cellular substructure and
○ To study the ultrastructure of a cell & its morphology.
components. ● Dyes and Simple Staining
○ Can see objects as small as a protein molecule / ○ Chromophore Groups
at nano level. ○ Cells bind via ionic, covalent, or hydrophobic
○ Provides details about internal composition of bonds.
cells / any suitable material under study. ● Ionizable dyes - basic (e ective under basic conditions)
○ Electron beams pass through the samples. and acidic (e ective under acidic conditions when
○ Based on transmitted electrons / produces proteins etc. carry a positive charge)
images by detecting primary e- transmitted
from the sample. Staining Methods
○ High resolution (10nm - average; 0.5nm - ● Simple Staining
special) ○ Begin with a heat- xed emulsion
○ Depth of eld: Moderate ○ Cover the smear with a stain (use a staining
○ Magnifying power: 5 million x tray/beaker to catch excess stain)
○ Specimen contrast: by electron scattering. ○ Grasp the slide with a slide holder
○ Produced 2D Black and White images. ○ Rinse the slide with water
■ Dispose excess stain
● Electron Cryotomography ○ Gently blot dry in a tablet of bibulous
○ Freezing; creating an image.
paper/paper towels. Do not rub.

Scanning Probe Microscopy ● Negative Staining
● Scanning Tunneling Microscope ● Di erential Staining
○ 100 million x magni cation ○ Gram staining
○ Needle-like probe on specimen ■ Di erentiating cells based on their
■ Probe lowered for electron clouds to cell wall structures.
touch the surface of atoms of a ○ Acid fast staining
specimen; if a voltage is applied, and a ■ Uses acidi ed alcohol to identify
highly sensitive ow of electron acid-fast characteristics (colo remains:
occurs. acid-fast).
■ Tip is moved back and forth over the ○ Endospore staining
specimen. ■ Heat is used to drive dye into
● Atomic Force Microscope endospore; hard to stain, though
○ Probe moves over the surface while keeping when stained, it is highly resistant to
distance between probe and surface constant. decolorization.
○ Can be used to study surfaces that don’t ○ Capsule staining
conduct electricity very well. ■ Negative staining .w/India ink or
nigrosine dye (cell/capsule remain
light because they’re hard to
penetrate).
○ Flagella staining
■ Coating agella with mordants (i.e.
tannic acid and potassium alum) then
staining with a dye.
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Staining: Gram Staining Bacterial Cell Organization

● Developed by Hans Christian Gram, a Danish ● Common Features
Microbiologist / Bacteriologist. ○ Cell envelope
● Primary Stain. ■ Plasma membrane
● Applicable only to bacteria. ■ Cell wall
● It divides the bacterial group to gram (+) and gram (-). ■ Capsule or Slime Layer
● Treatment with iodine solution (iodine acts as mordant - ○ Cytoplasm
helps bind dye to a target molecule). ○ External Structures
● Washing with alcohol.
● Gram (+) retain primary stain; Gram (-) becomes Common Bacterial Structures and Their Functions
colorless.
Plasma membrane
Bacterial Cell Structure ● Encompasses the cytoplasm
● Absolute requirement for all living things
● Bacteria and Archaea have long been clustered together
● Selectively permeable barrier, mechanical boundary of
as prokaryotes.
cell, nutrient and waste transport, location of many
● Stanier and van Niel (1962) - described prokaryotes in
metabolic processes (respiration, photosynthesis),
terms of what they lacked: membrane-bound organelles
detection of environmental cues for chemotaxis.
as well as nucleus, a cytoskeleton and internal

membranous structures (i.e. ER and Golgi apparatus).
Lipid Bilayer
● Planctomycetes causes con ict: membrane-bound
○ Amphipathic lipids
genetic material and organelle called anammoxosome.
■ Polar ends (hydrophilic - interact with
○ Anoxic ammonia oxidation - important in
water)
the nitrogen cycle
■ Non-polar tails (hydrophobic -

insoluble in water)
Shape, Arrangement and Size
■ Phospholipid bilayer
Most common: Cocci and Rods
○ Peripheral Membrane Protein
● Cocci (s., coccus) - spheres
■ Loosely attached; can be easily
○ In pairs / diplococci (ex: Neisseria)
removed.
○ In chain (ex: Streptococcus)
○ Integral Membrane Protein
○ Grape-like cluster (ex: Staphylococcus)
■ Amphipathic (embedded within the
○ Tetrads - 4 cocci in a square (ex: Micrococcus)
membrane); carry out important
○ Cubic con guration of 8 cocci (ex: Sarcina)
functions.
● Bacilli (s., bacillus) - rods
● Transporter
○ Varies in length-to-width ratio and
● Receptor
arrangement
● Enzyme
○ Coccobacillus - short rods (ex: Acinetobacter)
● Anchor
● Comma-shaped (ex: Vibrios)
○ Bacterial Lipids
● Rigid, spiral-shaped (ex: Spirilla)
■ Saturation levels of membrane lipids
● Flexible, spiral-shaped (ex: Spirochetes)
re ect environmental conditions such
● Stalked (ex: Caulobacter crescentus)
as temperature.
● Pleomorphic - organisms that are variable in shape.
■ Bacterial membranes lack sterols

(present in eukaryotes) but do not
Size - Shape Relationship
contain sterol-like molecules,
Does size matter?
hopanoids.
The smaller the microorganism, the bigger
■ Stabilize membrane.
the surface to volume ratio. The bigger the ratio, the
○ Nutrient Uptake
more e cient the nutrient uptake.
■ They only take what they need.
Large size and odd shape may be a protective
■ Macroelements (macronutrients) -
mechanism against predation.
required in relatively large amounts.

● C, O ,H ,N ,S , and P -
Prokaryotic Cells
found in organic molecules
● Cells that do not have a true nucleus or any
(proteins, lipids,
membrane-bound organelles.
carbohydrates, and nucleic

acids).
Eukaryotic Cells
● K, Ca, Mg, and Fe (cations)
● Cells with a true nucleus as well as membrane bound
- serve in a variety of roles
organelles.
including assisting enzymes

and biosynthesis and energy

conservation.
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■ Trace elements (micronutrients) - Microcompartments

required in trace amounts. ● Large polyhedrons formed by one or more proteins
● Mn, Zn, Co, Mo, Ni, and ● Enclosed within protein shell are one or more enzymes
Cu. ● Include ethanolamine utilization (Eut)
● Often supplied in microcompartments, propanediol utilization (Pdu)
water/media components; compartments and carboxysomes
ubiquitous in nature. ● Carboxysomes are present in cyanobacteria and carbon
● Part of certain enzymes, aid dioxide xing bacteria
in catalyzing reactions - Polyhedral coat is composed of 6 di erent
● Maintain protein structure. proteins and is 100 nm in diameter
■ Growth Factors - Carbonic anhydrase converts carbonic acid to
● Molecules that cannot be carbon dioxide; carboxysomes shell prevents
synthesized by the cells. carbon dioxide from escaping; it stores it.
● Organic compounds Nucleoid
● Must be supplied by the ● The location of chromosomes and associated proteins
environment if the cell is to ● Bacterial chromosome: circular or linear
survive and reproduce. double-stranded DNA molecule
● Classes include: ● Supercoiling and nucleoid proteins (di erent from
● Amino acids - needed for histones) aid in folding
protein synthesis ● Usually not membrane-bound except for phylum
● Purines and pyrimidines - Planctomycetes
needed for nucleic acid ● Localization of genetic material (DNA)
synthesis.
● Vitamins - function as Plasmids
enzyme cofactors. ● Extrachromosomal, small, circular, double stranded
■ Methods for Uptake of Nutrients DNA molecule
● Microbes can only take in ● Exist and replicate independently of chromosome
dissolved particles across ● Important in genetic recombination and gene cloning
selectively permeable ● Confers selective advantage to the organism
membranes. ● Classi cation via mode of existence, spread, and
■ Transport Mechanisms function.
● Passive di usion
● Facilitated di usion Periplasmic space
● Primary and secondary ● In typical Gram (-) bacteria, contains hydrolytic enzymes
transport and binding proteins for nutrient processing and uptake;
● Group translocation in typical Gram (+) bacteria, may be smaller or absent.

Gas vacuole Cell wall
● An inclusion that provides buoyancy for oating in ● Protection from osmotic stress; helps maintain cell
aquatic environments. shape.
● May contribute to pathogenicity.
Ribosomes ● Mainly made up of Peptidoglycan (murein)
● Site of protein synthesis ○ Rigid structure lying just outside the cell
● Made of complex protein and RNA molecules plasma membrane.
● Bacterial ribosomes are composed primarily of ribosomal ○ Peptidoglycan structure - Mesh-like polymer of
RNA (rRNA) molecules identical subunits forming long strands.
● Bacterial ribosome = 70S ribosomes ■ Two alternating sugars
(50S and 30S subunits) ● N-acetylglucosamine
● Small subunit contains the 16S rRNA, (NAG)
● Large subunit consists of 23S and 5S rRNA ● N-acetylmuramic acid
(NAM)
Inclusions ■ Alternating D- and L- amino acids
● Granules, crystals, or globules ■ Stands are Cross-linked:
● Made of organic or inorganic material that are stockpiled ● Peptidoglycan strands have
by the cell for future use a helical shape
● Storage of carbon, phosphate, and other substances; site ● Peptidoglycan chains are
of chemical reactions (microcompartments); movement. cross-linked by peptides for
● Some are enclosed by a single-layered membrane strength
○ Membranes vary in composition ● Interbridges may form
○ Some made of proteins; others contain lipids
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● Peptidoglycan sace - Slime Layers

interconnected networks ● Not easily observed under the microscope.
● Various structures occur ● Slime may facilitate motility.
○ Two types of bacteria based on Gram stain
■ Gram-positive (+): purple stain, thick Cytoskeleton
peptidoglycan ● Bacterial Cytoskeleton (Homologous to eukaryotic
■ Gram-negative (-): pink or red stain; cytoskeleton)
thin peptidoglycan + outer ○ Actin laments - made from actin
membrane ○ Microtubules - made from tubilins
○ Mechanism of Gram Stain Reaction ○ Intermediate laments - one or more members
■ Gram stain reaction due to nature of of the di erent classes of proteins
cell wall ● Functions (similar to eukaryotes):
■ Shrinkage of the pores of ○ Participate in cell division
peptidoglycan layer of Gram (+) cells ○ Localize proteins
■ Constriction prevents loss of crystal ○ Determine cell shape
violet during decolorization step ● Best Studied Bacterial Cytoskeletal Proteins
■ Thinner peptidoglycan layer and ○ FtsZ - common in most bacteria
larger pores of Gram (-) bacteria do ■ Tubulin homologue (eukaryote)
not prevent loss of crystal violet ■ Forms ring during septum formation
■ Alcohol may also remove/extract in cell division
some lipids from the outer layer of ○ MreB - many rods; not found in cocci
Gram (-) cell wall, making crystal ■ Actin homologue
violet dye removal easier. ■ Determine cell shape in rods; helps in
● Cell walls protects cell from osmotic lysis chromosome segregation, motility,
○ Hypotonic environments: cell polarity
■ Solute concentration outside the cell ○ CreS (crescentin) - rare, maintains curve shape
less than inside the cell. ■ Lamin and keratin homologue
■ Water moves into the cell and the cell ■ Caulobacter crescentus
swells.
■ Cell wall protects from lysis Intracytoplasmic Membranes
● Observed in many photosynthetic bacteria such as
○ Hypertonic environments: cyanobacteria
■ Solute concentration outside the cell ● Observed in many bacteria with high respiratory activity
is greater than inside the cell. such as nitrifying bacteria
■ Water leaves the cell ● Function: provide larger surface for more e cient
■ Plasmolysis occurs. metabolic activity
● Components Outside the Cell wall
○ Outermost layer in the cell envelope Fimbriae (s., mbria) and pili (s., pilus)
○ Glycocalyx - network of polysaccharides; aids ● Function: Attachment to surfaces, DNA uptake
in attachment to solid surfaces ● Short, thin, hairlike, protein appendages (upto 1,000
■ Capsules cell)
■ Slime layers (ex. bio lms)
○ S-layers (Surface protein layer) Sex pili (s., pilus) - Type IV pili
■ Functions: ● Motility and gene transfer
■ Protect from ion and pH uctuations ● Longer, thicker, less numerous (1 to 10/cell)
■ Maintains shape and rigidity ● Genes for formation on plasmids
■ Promotes adhesion to surfaces ● Required for conjugation
■ Protects from host defenses ● Bacteria conjugation and bacterial transformation
■ Potential use in nanotechnology
Flagella
Capsules ● Swimming and swarming motility
● Well organized and not easily removed from the cell. ● Ultrastructure composed of three parts:
● Usually composed of polysaccharides (others, proteins) ○ Filament extends from the cell surface to the
● Visible in light microscopy. tip
● Protective advantages: Resistance to phagocytosis, ○ Basal body is a series of rings that drive
Protect from desiccation, exclude viruses and detergents. agellar motor
○ Hook links lament to basal body
Slime Layers
● Similar to capsules except di used, unorganized, and
easily removed.
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Patterns of Flagella Bacterial Motility

● Monotrichous - single agellum ● Spirochete motility
● Polar Flagellum - one or more agella arising from one or ○ Multiple agella form axial bril which winds
both poles of the cell around the cell
● Amphitrichous - One agellum coming from each end ○ Flagella remain in a periplasmic space inside the
of the cell (or two agella in total) outer sheath
● Lophotrichous - Several agella form a tuft that comes ○ Corkscrew shape exhibits exing and spinning
from one or both ends of the cell. movements
● Peritrichous - evenly spread on the whole cell surface ● Twitching and gliding motility
○ Observed when cells are on solid surfaces
Endospore ○ May involve type IV pili and slime
● A survival strategy ○ Twitching (social motility)
● Complex, dormant structure formed by some bacteria ■ Pili at the ends of the cell
● Various locations within the cell ■ Short, intermittent, jerky motions
● Resistant to adverse environmental conditions ■ Pili extend and retract
(including heat, radiation, chemicals, desiccation) due ■ Group of cells move together in a
to: coordinated fashion
○ Calcium (complexed with dipicolinic acid) ○ Gliding (adventurous motility)
○ Small, acid-soluble, DNA-binding proteins ■ Smooth movements
(SASPs) ■ Single cells move independently
○ Dehydrated core ● Chemotaxis
○ Spore coat and exosporium ○ Move toward chemical attractants such as
● Survival under harsh environmental conditions. nutrients; away from harmful substances
● Endospore structure ○ Move in response to temperature, light,
○ Spore surrounded by thin covering called oxygen, osmotic pressure, and gravity
exosporium
○ Thick layers of protein from the spore coat
○ Cortex - beneath the coat, thick peptidoglycan
Archaeal Cell Structure
● Features in common with Bacteria:
○ Core has nucleoid and ribosomes
○ Genes for metabolism
● Sporulation
● Other elements are unique to Archaea.
○ Process of endospore formation
○ Unique rRNA gene structure
○ Occurs over several hours
○ Capable of methanogenesis
○ Normally commences when growth ceases
● Highly diverse with respect to morphology, physiology,
because of lack of nutrients
reproduction, and ecology
○ Complex multistage process
● Best known for growth in anaerobic, hypersaline, pH

extremes, and high-temperature habitats.
● Formation of Vegetative Cell

○ Activation
Taxonomy
■ Prepares endospores for germination
● Phyla
■ Often results from treatments like
○ Crenarchaeota
heating
○ Euryarchaeota
○ Germination
○ Thaumarchaeota
■ Environmental nutrients are detected

(by germinant receptors)
Archaeal Morphology
■ Spore swelling and rupture of the
● Much like bacteria, cocci and rods are common shapes
spore coat
● Other shapes can also exist
■ Increased metabolic activity
○ No spirochetes or mycelial forms discovered yet
○ Outgrowth
○ Branched / at shapes
■ Emergence of vegetative cell
● Sizes vary (typically 1 to 2 x 1 to 5 μm for rods, 1 to 3 μm

in diameter for cocci)
Bacterial Motility
● Smallest observed is 0.2 to 0.4 μm in diameter
● Flagellar movement
● Largest (so far) is a multicellular form that can reach 30
○ Flagellum rotates like a propeller
mm in length.
● Swarming

○ Occurs on moist surfaces as a type of group

behavior by bacteria

○ Most swarmers have peritrichous agella

○ Production of molecules that aid movement is

typical

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Archaeal Cell Envelopes The Nucleoid

● Di er from bacterial envelopes in the molecular makeup ● Usually not membrane bound (there are few exceptions)
and organization ● Location of single circular chromosome and associated
○ S-layer may be only component of the cell wall proteins.
○ Some lace cell wall ● Some evidence for polyploidy in some archaeons
○ Capsules and slime layers are rare ● Nucleoid-Associated Proteins (NAPs) and Histones -
compacting chromosomes (Euryarchaeota)
Archaeal Membranes ● NAPs (no histones) only for Crenarchaeota
● Composed of unique lipids
○ Isoprene units ( ve carbon, branched) Archaeal External Structures
○ Ether linkages rather than ester linkages to ● Pili
glycerol ○ Some composed of pilin protein and
● Some have monolayer structure instead of bilayer homologous bacterial type IV pili proteins
structure ○ With central lumen
● Lipids: Polar phospholipids, sulfolipids, glycolipids, and ○ May be involved in archaeal adhesion
unique lipids are found in archaeal membranes mechanisms
● Cannulae
Archaeal Membranes and Lipids ○ Hollow, tubelike structures on surface of
● Glycerol diether lipids thermophilic archaea in genus Pyrodictium
○ Two hydrocarbons are attached to glycerol (3) ○ Function unknown
● Diglycerol tetraether lipids ○ May be involved in formation of networks of
○ Two glycerol residues are linked by two long multiple daughter cells.
hydrocarbons (1 & 2) ● Hami
○ Not well understood
Archaeal Cell Walls ○ ‘Grappling hook’ appearance suggests…
● Lack peptidoglycan ○ Involvement in cell adhesion mechanism.
● Most common cell wall is S-layer
● May have protein sheath external to S-layer Archaeal Flagella
● S-layer may be outside membrane and separated by ● Flagella (archaellum)
pseudomurein ○ Thinner than bacterial agella.
● Pseudomurein may be the outermost layer - similar to ○ Composed of more than one type of agellin
Gram (+) microbes. protein.
○ Filament is not hollow.
Archaeal Cells and Nutrient Uptake ○ Hook and basal body are di cult to
● Archaeal cells use many of the same nutrient uptake distinguish.
exhibited by bacterias. ○ More related to type IV bacterial pili.
○ Passive di usion ○ Growth occurs at the base, not the tip.
○ Facilitated di usion ○ Rotation propels the cell, driven by ATP
○ Active transport (primary and secondary) Hydrolysis.
○ Group translocation
■ The phosphoenolpyruvate: sugar MODULE 3
phosphotransferase system (PTS)

group translocation mechanism has
been found in some archaea. Eukaryotic Cell Structure
● Prominent members of ecosystems.
Ribosomes ● Useful as model systems and industry.
● Bacterial and archaeal ribosomal RNA = 70S ● Some are major human pathogens.
○ 16S in small subunit
○ 23S and 5S in large subunit Two groups of Eukaryotes commonly possess microbial
○ At least one archaeon has additional 5.8S members:
rRNA (also seen in eukaryotic large subunit) ● Protists
● Proteins in ribosomes vary ● Fungi
○ More protein than in bacteria
○ Archaea more similar to eukarya than to Highly diverse in morphology.
bacteria, but there are some that are unique to

archaea

○ Archaeal ribosomes are impervious to

antibiotics.

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Common Features of Eukaryotic Cells ● Cell wall

● Membrane-delimited nuclei ○ Unlike the peptidoglycan in the cell wall of
● Membrane-bound organelles that perform speci c Bacteria and Archaea, many eukaryotes lack or
functions. have a chemically distinct cell wall.
● Large membrane surfaces allow greater respiratory and ○ Photosynthetic algae: cellulose, pectin
photosynthetic activities. ○ Fungi: cellulose, chitin, or glucan
● Intracytoplasmic membrane complex serves as a ● External coverings (eg. glycocalyx)
transport system.
● More structurally complex and generally larger than Cellular transport
bacterial or archaeal cells. ● Passive di usion
● Facilitated di usion
Structure of Two Representative Eukaryotic Microbes ● Primary and secondary Active Transport
● Endocytosis

Eukaryotic Cytoplasm
● The most important part of the cell as it is the location
of important biological processes.
● Composed of cytosol (liquid portion) and organelles.
○ Cytosol - liquid component of the cytoplasm;
many organelles are located here.
● Location of many metabolic processes.
● Endocytic and Secretory Pathway
○ Endoplasmic reticulum (Smooth ER and
Rough ER)
○ Golgi apparatus
○ Lysosomes

● For Genetic Control

○ Nucleus
Common Eukaryotic Structures and Their Functions
○ Ribosomes
Eukaryotic Cell Envelopes
● For Energy Conservation
● Plasma membrane
○ Mitochondria
○ Is a lipid bilayer
○ Chloroplast
■ Sphingolipids

■ Sterols (eg. cholesterol and ergosterol)
Cytoskeleton
■ Phospholipids
● Composed of actin laments, intermediate laments and
○ Microdomains (“lipid rafts”) participate in a
microtubules.
variety of cellular processes.
● Provides cell structure and movement.
○ Mechanical cell boundary.
● Helps cells maintain their shape and internal
○ Selectively permeable barrier with transport
organization.
systems.
● Provides mechanical support that enables cells to carry
○ Mediates cell-cell interactions and adhesion to
out essential functions like division and movement
surfaces.
● Vast networks of interconnected laments.
○ Secretion and Signal transduction.
○ Actin laments (micro laments) - involved
○ Other structures embedded in the Plasma
in amoeboid movement, endocytosis,
Membrane:
cytokinesis, and the movement of some
■ Integral membrane proteins
structures within the cell
■ Other lipids
○ Intermediate laments - structural functions;
the role in eukaryotic microorganisms is
unclear
○ Microtubules - form the spindle apparatus
that separates chromosomes during mitosis
and meiosis; motility (cilia and agella) and
support (rigid pseudopodia).
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○ Synthesis of secreted proteins by ER-associated

ribosomes.
● Smooth endoplasmic reticulum (Smooth ER)
○ Devoid of ribosomes
○ Synthesis of lipids by ER-associated enzymes.

Eukaryotic Ribosomes
● Organelle for Genetic Control
● Protein synthesis
● More mass than the 70S bacterial and archaeal
ribosomes.
● 80S in size: 60S + 40S subunits
● May be attached to Endoplasmic Reticulum or free in

cytoplasmic matrix.

● 60S is bound subunit to Endoplasmic Reticulum
Endocytic and Secretory Pathway
● Rough ER ribosomes: integral membrane or secreted
● Endocytic Pathway - movement of materials into the
proteins.
cell from the outside.
● Free ribosomes: nonsecretory / non membrane proteins
○ Used by all eukaryotic cells.
○ Some proteins are inserted into organelles.
○ Used to bring materials into the cell.

○ Solutes or particles taken up and enclosed in
Golgi apparatus
vesicles pinched from the plasma membrane.
● Involved in Secretory pathways.
○ Used as a feeding mechanism.
● Membranous organelle made of cisternae stacked on
○ Entry of pathogen (eg. virus) to eukaryotic
each other (rare exceptions will have non-stacked
cells.
cisternae)
○ In most cases, materials are then delivered to
○ Typical example for non-stacked cisternae:
lysosomes for digestion.
Saccharomyces cerevisiae
● Secretory Pathway - from inside of the cell out and
● Dictyosomes = stacks of cisternae
within the cell.
● Involved in modi cation, packaging, and secretion of
○ Used to move material to various sites within
materials.
the cell, as well as to either the plasma
● Lysosome formation
membrane or cell exterior

○ Proteins destined for the cell membrane,

endosomes, and lysosomes or secretion are
Lysosomes
synthesized by ribosomes on rough
● A degradative organelle involved in the Endocytic
endoplasmic reticulum (RER).
pathway.
● Functions:
○ Intracellular digestion
■ Hydrolases - enzymes which
hydrolyze molecules; function best

under slightly acidic conditions.
● Degradation of Proteins in Cells
● Maintain an acidic environment by pumping protons
○ Quality control mechanisms
into their interior
○ Unfolded or misfolded proteins are secreted
● Eukaryotic microbes: lysosomes = vacuoles, phagocytic
into the cytosol and tagged for destruction by
vacuoles, of food vacuoles
ubiquitin polypeptides.
○ Functions:
○ Proteasomes destroy targeted proteins.
■ Storage of calcium ions, phosphate,

and amino acids and components of
Endoplasmic reticulum
the endocytic pathway.
● Involved in the Endocytic pathways.

● An irregular network of branching and fusing
Mitochondria
membranous tubules and attened sacs (cisternae - s.,
● Organelle for Energy Conservation
cisterna)
● Powerhouses of most eukaryotic cells.
● Functions:
● Site of tricarboxylic acid cycle activity also known as the
○ Transports proteins, lipids, and other materials
Krebs cycle.
within the cell.
● Site where ATP is generated by electron transport and
○ Major site of cell membrane synthesis.
oxidative phosphorylation
● Rough endoplasmic reticulum (Rough ER)
● About the same size as bacterial cells
○ Ribosomes attached
● Reproduce by binary ssion similar to bacterial cells.
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● Energy production through the use of the tricarboxylic Chloroplasts

acid cycle, electron transport, oxidative phosphorylation ● Organelle for Energy Conservation.
and other pathways. ● Type of plastid.
● Mitochondrial Structure ○ Pigment-containing organelles observed in
○ Outer membrane plants and protists.
■ Contains porin proteins similar to ● Site of photosynthesis reactions.
Gram (-) bacteria. ● Contains chlorophyll.
○ Inner membrane ● Surrounded by double membrane.
■ Highly folded to form cristae (s., ● Photosynthesis - trapping light energy and forming
crista) carbohydrates from CO₂ and water.
■ Location of enzyme and electron ● Chloroplast Structure
carriers for electron transport and ○ Stroma (a matrix) within the inner membrane.
oxidative phosphorylation. ■ Contains DNA, ribosomes, lipid
○ Matrix enclosed by inner membrane droplets, starch granules, and
■ Contains ribosomes, mitochondrial thylakoids.
DNA, enzyme of tricarboxylic acid ■ Site of dark reactions of
cycle and catabolism of fatty acids. photosynthesis (formation of
carbohydrates from water and CO₂)
○ Thylakoids
■ Site of light reactions of
photosynthesis (ATP and NADPH
production).

Nucleus
● Organelle for Genetic Control
● Repository for genetic information.
● Membrane-bound spherical structure that houses
genetic material of eukaryotic cells (chromosome).
● Contains dense brous material called chromatin.
○ Complex of DNA, histones, and other
proteins.
○ Five types of histones form nucleosomes:
■ H1
Hydrogenosomes ■ H2A
● Small organelle for Energy Conservation in some ■ H2B
anaerobic protists. ■ H3
● Double membrane, no cristae, usually lacks DNA. ■ H4
● ATP is generated by the fermentation process rather ○ Chromatin condenses into chromosomes
than through respiration. during division.
○ CO₂, H₂ and acetate are products

Nuclear Envelope
● Double membrane structure that delimits nucleus.
● Continuous with ER; outer membrane covered with
ribosomes.
● Penetrated by nuclear pores
○ Associated proteins make up the nuclear pore
complex.
○ Pores allow materials to be transported into or
out of the nucleus.

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Nucleolus 80 nm diameter) that are enriched in cholesterol and

● Ribosomal RNA synthesis membrane protein caveolin - vesicles budded from
● Ribosome construction caveolae are called caveolin-coated vesicles.
○ Has been implicated in signal transduction,
Cell wall and pellicle transport of macromolecules and small
● Strengthens and gives shape to the cell. molecules such as folic acid.
○ Toxins such as cholera may enter cells via
Cilia and agella caveolae.
● Structures for Motility ● Macroautophagy involves nonselective digestion and
● Flagella (s., agellum) recycling of cytoplasmic components (including
○ 100 to 200 μm long organelles and mitochondria)
○ Move in undulating fashion generating planar ○ Helps maintain cellular homeostasis.
or helical waves originating at either the base or ○ Also used to destroy pathogens that have
the tip. entered the cell by endocytosis.
○ Types: Tinsel and Whiplash Flagella ● Residual body - lysosome containing undigested
● Cilia (s., cilium) materials.
○ 5 to 20 μm long
○ Beat with two phases:
■ Moving like oars (e ective stroke)
Viruses and Other Acellular Infectious
■ Bend and pull cell forward (recovery Agents
stroke)

● Ultrastructure of Flagella and Cilia
Virology: The study of viruses, a unique
○ Membrane-bound cylinders approximately 0.2 group of infectious agents.
μm in diameter.
○ Axoneme: set of microtubules in a 9+2 Their distinctiveness lies in their simple, acellular
arrangement organization and pattern of multiplication.
○ Movement power by ATP
○ 10 - 40 strokes per second Acellular Agents
● Viruses - protein and nucleic acids
● Viroids - only RNA
● Satellites - only nucleic acids
● Prions - proteins only

Virus
● Can exists extracellularly or intracellularly
● Major cause of disease
○ Also importance as a new source of therapy
○ New viruses
● Important members of aquatic world
○ Move organic matter from particulate to
Vacuole dissolved.
● Temporary storage and transport. ● Important in evolution
● Digestion (Food vacuoles) ○ Transfer genes between bacteria and others
● Water balance (Contractile vacuole) ● Important model systems in molecular biology.

Endocytosis is observed in all eukaryotic cells. Virus can infect all cell types
● Bring cells in from the outside. ● Bacterial viruses called bacteriophages (phages)
● Few archaeal viruses
Types of Endocytosis ● Most are eukaryotic viruses
● Phagocytosis: use of cell surface protrusions to ○ Plants, animals, protists, and fungi
surround and engulf particles. ● Classi ed into families based on:
● Pinocytosis: cells take up solutes. ○ Genome structure
● Clathrin-dependent endocytosis: clathrin-coated pits ○ Life cycle
in the membrane invaginate to form endocytic vesicles. ○ Morphology Genetic relatedness
○ Used to internalize hormones, growth factors,
iron, and cholesterol.
○ Observed in fungi.
● Caveolin-dependent endocytosis: involves caveolae
(cup-shaped invaginations of the plasma membrane, 50 -
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The Structure of Viruses Virus Envelopes and Enzymes

● Virions are tiny (Approximately 10 - 400 nm in ● Many viruses are bound by an outer, exible,
diameter) and most viruses must be viewed with an membranous layer called the envelope
electron microscope. ● Envelope lipids and carbohydrates are usually acquired
● All virions contain a nucleocapsid which is composed from host cell plasma or nuclear membranes.
of nucleic acid (DNA or RNA) and a protein coat ● Envelope proteins are coded by viral genes
(capsid)
○ Enveloped virus Viral Envelope Proteins
○ Non-enveloped / naked virus ● Coded by viral genes
● May project from the envelope surface as spikes or
Size and Morphology of Select Viruses peplomers
Capsids ○ Involved in viral attachment to host cell
● Large macromolecular structures which serve as protein ○ Used for identi cation of virus
coat of a virus. ○ May have enzymatic activity
● Made of protein subunits called protomers. ■ Examples is neuraminidase of
● Protect viral genetic material and aid in its transfer in uenza virus
between host cells. ○ May play a role in nucleic acid replication.
● Capsid symmetry: helical, icosahedral, or complex
Viral Genomes are Structurally Diverse
Icosahedral Capsids ● A virus may have single or double-stranded DNA or
● An icosahedron is a regular polyhedron with with 20 RNA
equilateral faces and 12 vertices ● The length of the nucleic acid also varies from virus to
● Capsomers - assemblages of protomers virus
○ Pentamers (pentons) - 5 subunit capsomers ● Genomes can be linear or circular
○ Hecamers (hexons) - 6 subunit capsomers ○ Some RNA viruses have segmented genomes
● Example: Adenovirus
Viral Multiplication
Capsids of Complex Symmetry ● Mechanism used depends on viral structure and genome
● Neither helical or icosahedral capsids ● Five-step Life Cycle
○ Poxviruses - largest animal virus; ovoid to ○ Attachment (Absorption)
brick-shaped exterior ■ Interactions occur within virion
○ Large bacteriophages - binal symmetry (head surface molecules (ligands) and
resembles icosahedral, tail is helical) receptors (which are on the host’s
surface)
Complex Capsid Symmetry ■ This often causes conformational
● Bacteriophage changes in virion proteins that
○ Binal Symmetry facilitate interaction with secondary
■ Icosahedral head receptors, entry into the host, and
■ Helical tail uncoating.
■ Receptor speci city is partially
Types of Endocytosis responsible for virus preferences for
● Phagocytosis: use of cell surface protrusions to hosts.
surround and engulf particles. ■ Viruses have evolved such that they
● Pinocytosis: cells take up solutes. use host receptors that are essential
● Clathrin-dependent endocytosis: clathrin-coated pits for the host’s functions and are
in the membrane invaginate to form endocytic vesicles. always present
○ Used to internalize hormones, growth factors, ■ Lipid rafts (eukaryotic cells) are
iron, and cholesterol. thought to be involved in virion entry
○ Observed in fungi. ■ Host cell receptor distribution varies
● Macroautophagy involves nonselective digestion and at the cellular level, some are
recycling of cytoplasmic components (including concentrated in lipid rafts
organelles and mitochondria) ■ Distribution at the tissue level plays a
○ Helps maintain cellular homeostasis. role in determining virus tropism and
○ Also used to destroy pathogens that have infection outcome (a virus with
entered the cell by endocytosis. receptors in the lungs will cause lung
● Residual body - lysosome containing undigested disease, etc.)
materials. ■ Plant viruses: exception for receptors
– viruses enter plants through
damaged areas; they are usually

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deposited as plant-eating insects ■ Middle proteins – participate in

devour plant tissues replication of the viral genome or
activation of expression of late genes
○ Entry into the Host and uncoating of ■ Late proteins – usually include capsid
genome proteins and other proteins involved
■ Entire nucleocapsid enters host in self-assembly and release.
cytoplasm
■ Some, such as bacteriophages, only ○ Assembly - late proteins are involved in
have nucleic acid enter mature virion assembly, such as
■ Some bacteria shed their capsid nucleocapsid proteins.
proteins as they enter host cytoplasm ■ Assembly process can be complex
in a process called uncoating with multiple
■ Three modes of entry are usually independently-functioning sub
followed by animal viruses o fusion of assembly lines that converge in later
viral envelope w/host plasma steps to complete nucleocapsid
membrane; o entry by endocytosis; o construction.
release of viral nucleic acid into host ■ Packasome – a complex of proteins
cytoplasm that incorporates DNA into
■ Uncoating is assisted by endosomal bacteriophage prohead o consists of
enzymes and a low pH level. the portal protein and the enzyme
terminase.
○ Synthesis Stage
■ Di ers dramatically among viruses ○ Virion Release
because genome dictates events that ■ Two common mechanisms: lysing the
occur host cell and release by budding.
■ dsDNA viruses have similar synthesis ■ Release by lysis: common with
stages due to the typical ow of bacterial viruses and some non
information in cells; the genetic enveloped animal viruses; involves the
information is stored in DNA and activity of viral proteins, such as
replicated by enzymes called DNA lysozyme, which attacks host
polymerases, recoded as mRNA bacteria’s peptidoglycan and holing,
(transcription) and decoded during which creates holes in host plasma
protein synthesis (translation) membrane.
■ RNA viruses – cellular organisms ■ Budding: frequently observed for
lack the enzymes needed to replicate enveloped viruses – envelope
RNA or synthesize mRNA from an formation and virion release are
RNA genome – RNA viruses must frequently concurrent
carry necessary enzymes in their ■ Host cell may survive following
nucleocapsids, or must have them release via budding, and continue to
synthesized during infection release virions
■ Some viruses bring about ■ Envelopes of animal viruses are
reorganization of host cell derived from host cell membranes
membranes to protect synthesis and through a multistep process.
assembly stages from host defenses ● Virus-encoded proteins are
● Structures called viral incorporated into the
replication complexes are membrane
formed; these appear as ● Nucleocapsid is
vesicles, tubular structures, simultaneously released and
and other forms the envelope is formed by
■ Some viruses carry out synthesis and membrane budding.
assembly in areas unenclosed by ● In several virus families, M
membrane – they concentrate and protein attaches to plasma
form areas called viroplasms o membrane and aids in
viroplasms viral replication complexes budding.
are referred to as virus factories ■ Some viruses do not release into the
■ Genes are regulated – early, middle, environment – they move directly to
and late genes; they encode proteins another host cell.
as early, middle, and late proteins
■ Early proteins – involved in taking
over the host cell
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Types of Viral Infections (Bacteriophage) normally functions to protect against infection

● Virulent phage - multiplication upon entry to host cell; by RNA viruses - during which, dsRNA is
followed by release from host by lysis (ex: T4 phage) detected and cut into fragments and is used to
● Temperate phage - can act like a virulent phage or stay destroy target mRNA molecules or prevent
inside the host without destroying it (ex: Bacteriophage their translation.
lambda) ● Viroids take over by hybridizing to host
○ Prophage - viral nucleic acid that remains mRNA molecules to which they have a
inside the host cell complementary nucleotide sequence, resulting
in the destruction of host mRNA and silencing
the host gene.
○ This may lead to disease in the host
plant

Satellites
● Infectious nucleic acids (DNA or RNA)
○ Satellite viruses encode their own capsid
proteins when helped by a helper virus
○ Satellite RNAs/DNAs do not encode their
own capsid proteins.
● Encode one or more gene products
● Require a helper virus for replication
○ Human hepatitis D virus is a satellite
Viroids ○ Requires human hepatitis B virus
● Infectious agents composed of closed, circular ssRNAs
● Does not encode gene products Prions
● Replication requires host cell ● Proteinaceous infectious particle
● DNA-dependent RNA polymerase ● Causes a variety of neurodegenerative diseases in humans
● Causes plant diseases. and animals
Two families ○ Scrapie in sheep
● Pospiviroidae ○ Bovine spongiform encephalopathy (BSE) or
○ Have circular RNA that exists as a “mad cow disease.”
rod-like shape due to intrastrand base ○ Human diseases: Kuru; Fatal familial insomnia,
pairing, which forms double-stranded Creutzfeldt-Jakob disease (CJD), and
regions with single stranded loops; Gerstmann-Sträussler-Scheinker syndrome
replicate in the nucleus. (GSS)
● How they work is unclear, though the scrapie prion has
● Avsunviroidae been studied.
○ Shaped like a rod with a highly
branched structure at one end, like a
tree trunk with its roots; replicates in
plant plastids such as chloroplasts of
each branch are formed by
intramolecular base pairing of the
RNA that creates a stem loop
structure.

● RNA of viroids does not encode any gene
products, so they cannot replicate themselves;
they use a host cell enzyme called a
DNA-dependent RNA polymerase.
○ DNA-dependent RNA polymerase:
usually functions in the host cell to
synthesize RNA using DNA as a
template during transcription,
though uses viroid RNA as a
template when infected.
● May cause latent infection in plants (no
symptoms), or severe disease.
● Some cause disease by triggering a eukaryotic
response called RNA silencing, which
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Water
● Work to assist enzymes (cofactors)

Macronutrients
● Carbon
○ Most abundant element in all classes of
macromolecules.
● Nitrogen
○ Second major element (proteins, nucleic acids,
etc; in nature can be found in organic and
inorganic (ammonia, nitrate, N₂) forms
● Phosphorus
○ Occurs in nature as organic or inorganic
phosphates - required for the synthesis of
nucleic acid and phospholipids.
● Sulfur
○ Structural component of amino acid (cysteine
and methionine), present in some vitamins and
in coenzyme A
○ Mot cell sulfur comes from inorganic sources
(sulfates or sul des).
● Potassium
○ Required by a variety of enzymes esp. Those
involved in protein synthesis.
● Magnesium
○ Stabilized ribosomes, cell membrane and
nucleic acids; required for the activity of many
enzymes.
● Calcium
○ Helps stabilize bacterial cell walls and
contributes to heat stability of endospores.
● Sodium
○ Not required by all organisms
○ Determines habitat (marine microorganisms)
● Iron
○ Major role in cellular respiration as a key
component of cytochromes and iron-sulfur
proteins involved in electron transport.

MODULE 4 Micronutrients (Trace Elements)

● Cobalt
Nutrition and Metabolism ○ Vitamin B12
○ Transcarboxylase (propionic acid bacteria)
Microbial nutrition and nutritional types: ● Copper
a.) Chemoorganotrophs ○ Certain proteins especially those involved in
b.) Chemolithotrophs respiration or in photosynthesis
c.) Phototrophs ● Manganese
Overview of metabolism: ○ Activator of many enzymes
● Molybdenum
a.) Catabolism
○ Present in various avin-containing enzymes
b.) Anabolism
● Nickel
c.) ATP
○ Most hydrogenases
d.) Redox reactions
○ Coenzyme F₄₃₀ of methanogens
e.) Electron carriers
○ Carbon monoxide dehydrogenase
In the lab, nutrients are provided to microbes by growth ○ Urease
● Zinc
media or culture media
○ Present in enzyme carbonic anhydrase

○ Alcohol dehydrogenase
… in plates, tubes, or flasks and in liquid or solid form
○ RNA and DNA polymerase and many

DNA-binding proteins
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Growth Factors
● Organic compounds that the cell cannot
synthesize.
● Vitamins, amino acids, purines, and
pyrimidines, heme

Microbial cells are highly-ordered and need energy to
maintain their structures and activities of growth

Transport work Consequences of Microbial Growth
● Uptake of nutrients, elimination of wastes, and ● In uence the well-being of plants, animals, and humans
maintenance of ion balances. ● Commercial applications in food and industry
Mechanical work ● Contribute to the global cycling of carbon, nitrogen, and
● Cell motility and movement of structures within cells sulfur in terrestrial and aquatic ecosystems
Chemical work
● Synthesis of biomolecules or cellular material Importance of Microbial Growth
● Chemolithoautotrophs
Sources of Carbon, Energy, and Electrons ○ Contribute to the chemical transformations of
elements (eg. the conversion of ammonia into
Carbon Sources nitrate or sulfur to sulfate) that continually
● Autotrophs occur in ecosystems
○ CO₂ sole or principal biosynthetic carbon ○ Important primary producers in ecosystems
source ● Chemoorganoheterotrophs (chemoheterotrophs)
● Heterotrophs ○ Important in biogeochemical cycle (carbon and
○ Reduced, preformed, organic molecules from nitrogen cycle)
other organism ○ Industrially important microbes (food and
Energy Sources beverage; antibiotics)
● Phototrophs ○ Most pathogenic organisms are COH
○ Light
● Chemotrophs Overview of metabolism
○ Oxidation of organic or inorganic compounds. Metabolism is the total of all chemical reactions in the
cell - It is divided into two parts
Electron Sources
● Lithotrophs
○ Reduced inorganic molecules
● Organotrophs
○ Organic molecules

Major Nutritional Types of Microorganisms

There is logic in metabolism: Catabolism and anabolism are
coupled to each other

Comparison between Catabolism and Anabolism
Catabolism - Breakdown of complex molecules to simple
subunits is accompanied by oxidation steps
● Generates energy and reducing power
● Exergonic

Anabolism - Biosynthesis of complex compounds from simple
building blocks is accompanied by reduction steps.
Fueling Reactions ● Requires energy and reducing power
Convert an Organism’s Carbon, Energy, and Electron ● Endergonic
Sources into Precursor Metabolites, ATP, and Reducing Power

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Both require enzymes in multi-step chemical reactions called The Structure ATP, ADP, and AMP

biochemical pathways. Adenosine 5’triphosphate (ATP)
Role of ATP in Metabolism - Energy currency of the cell
● ATP is formed by exergonic reactions and then used to Structure:
drive endergonic reactions. ● Nitrogen base
● ATP is formed from energy made available during ● 5-carbon sugar (ribose)
chemoorganotrophic, chemolithotrophic-, and ● Phosphate group
phototrophic growth.
● Its breakdown to ADP and phosphate makes chemical, The two red bonds are more easily broken and release considerable
transports, and mechanical work possible. energy that can be used in endergonic reactions.

Reduction-Oxidation (Redox) Reactions
● Transfer of electron between two compounds (an
electron donor to an electron acceptor)
● The more electrons a molecule can give, the more energy
rich it is
● Redox half reactions: GEROA / LEORA
● Conjugate Redox Pair:
Redox reactions in the Electron Transport Chain
● The electron tower arranges redox pairs with the most
● Standard Redox Potential: tendency of a half reaction negative E₀ on top
to lose Electrons (E₀) ● The electron donor will always be higher in the tower
than the acceptor
● Aerobic respiration is represented by the movement of
electrons from glucose (topmost) to oxygen
(bottommost)

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● Electron Transport Chain MODULE 5

○ Series of highly organized electron transfers

○ Avoids random and non-productive reduction
of molecules in the cell Nutrition and Metabolism
○ Thus energy is conserved and more ATPs are
produced. 1. Fueling reactions in Chemoorganotrophs
● Location of Electron Transport Chain ○ Aerobic respiration
○ Bacteria and Archaea ○ Anaerobic respiration
■ Plasma membrane and ○ Fermentation
intracytoplasmic membrane 2. Fueling reaction in Chemolithotrophs
○ Eukarya ○ Sulfur oxidation
■ Inner membrane of mitochondria or ○ Ammonia oxidation
chloroplast 3. Fueling reactions in Phototrophs
Metabolism is Organized into Pathways. ○ Oxygenic
○ Anoxygenic
● Biochemical pathways can be linear, branched, cyclic
○ Rhodopsin-mediated
● Each step is catalyzed by an enzyme
4. Selected anabolic pathways
● Pathways often overlap or feed into each other
○ Calvin cycle
○ Nitrogen xation

Fueling Reactions
Convert an Organism’s Carbon, Energy, and Electron
Sources into Precursor Metabolites, ATP, and Reducing Power

Energy Source
● Chemoorganotroph - organic molecules
● Chemolithotroph - inorganic molecules
● Phototroph - light

Carbon Source
● Biochemical Pathways - sets of linked chemical
● Autotroph - Carbon dioxide
reactions
● Heterotroph - organic molecules
● Substrate - starting molecule in a reaction

● Metabolites - products of chemical reactions
Electron Source
● Pathway Intermediate - metabolites in between
● Organotroph - organic molecules
● Enzyme - catalyze the reaction
● Lithotroph - inorganic molecules

Metabolic pathways are interconnected and form a complex
network
● In the diagram, each black circle represents a metabolite
formed by reactions in the network.
● Each line represents the enzyme-catalyzed reaction
that converts one metabolite into another.
● Anything that hinders enzyme function will hamper the
metabolism and physiology of the cell.

Summary
1. Microorganisms need nutrients for growth:
macronutrients, micro-nutrients, growth factors Chemoorganotrophic Fueling Processes
2. The organisms’ unique sources of energy, carbon, and Energy Source: Organic compound
electrons de ne the major nutritional types of microbes
3. Microbial cells require energy to fuel chemical 1. Aerobic respiration
reactions, transport processes, and mechanical work. ○ Final electron acceptor is oxygen.
4. ATP, the major energy currency in cells, is formed 2. Anaerobic respiration
during chemoorganotrophic, chemolithotrophic, and ○ The nal electron acceptor is a di erent
phototrophic growth. exogenous acceptor such as NO3-, SO42-, CO2,
5. Energy transformations are governed by redox reactions Fe3+, or SeO42-.
and transfer of electrons from donor to acceptor. 3. Fermentation
6. Chemical reactions in cells are organized to form ○ Final electron acceptor is an organic
biochemical pathways that feed into each other. compound.
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● Produces ATP via the activity of the electron transport

Nutritional Type Carbon Energy Source Electron chain high energy electron carriers and chemiosmosis
Source Source ● Uses oxygen as the nal electron acceptor.

Chemoorganoheterotroph Organic Organic Organic e- STEP 1. The Embden-Meyerhof Pathway
chemicals, often donor, often (Glucose to Pyruvate)
carbon
same as the the same as
Carbon source the Carbon ● Most common pathway for glucose
source. degradation to pyruvate
● Found in all major groups of microorganism
● Functions in presence or absence of oxygen
Chemoorganoheterotrophs (chemoheterotrophs) ● Occurs in the cytoplasm
● Important in biogeochemical cycle (carbon and nitrogen ● Two Phases
cycle) ○ Six carbon phase
● Industrially important microbes (food and beverage, ○ Three carbon phase
antibiotics)
● Most pathogenic organisms GLUCOSE → PYRUVATE
(6-carbon) (3-carbon)
Microbial Examples
Respiration
● Aerobic microbes
○ Bacteria, Archaea, protists, and fungi
● Anaerobic bacteria
○ Sulfate-reducing bacteria
○ Nitrate-reducing bacteria
Fermentation
● Anaerobic microbes
○ Many bacteria, yeasts, and molds.

Pathways used by chemoorganotrophs to catabolize organic What is an amphibolic pathway?
energy sources
● This is a metabolic pathway that functions both
These pathways funnel metabolites into the glycolytic catabolically (breakdown) and anabolically (synthesis)
pathways and the tricarboxylic acid cycle, increasing metabolic
e ciency and exibility. Example:
● The enzymes in Embden-Meyerhof pathway
are freely reversible
● During glycolysis (breakdown of glucose) an
enzyme catalyzes the reaction in a catabolic
direction
● During gluconeogenesis (glucose production)
another enzyme catalyze the reverse, anabolic
reaction
● The cell has to “make a decision” which
pathway it will follow depending on its needs.

Glycolytic Pathways: Glucose to Pyruvate

● The Embden-Meyerhof Pathway is only one of the
processes that breakdown glucose

● The Entner-Doudoro Pathway produces pyruvate

from glucose following a di erent route. This is found
Aerobic Respiration
only in some bacteria.
● A process that can completely catabolize an organic
● The Pentose Phosphate Pathway is a major producer
energy to CO2
of reducing power (NADPH) used for anabolic
● 3 Steps
reactions.
a. Glycolytic pathways (ex. Embden-Meyerhof

pathway)
b. Tricarboxylic acid cycle (or Krebs cycle)
c. Electron transport chain with oxygen as the
nal electron acceptor
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Speci cs of Embden-Meyerhof Pathway

Glucose is phosphorylated at the expense of one ATP, creating
glucose 6-phosphate, a precursor metabolite and the starting
molecule for the pentose phosphate pathways.

Isomerization of glucose 6-phosphate (an aldehyde) to fructose
6-phosphate (a ketone and a precursor metabolite)

ATP is consumed to phosphorylate C1 of fructose. The cell is
spending some of its energy currency in order to earn more in
the next part of the pathway.

-----------------------------------------------------------------------
Fructose 1, 6-bisphosphate is split into two 3-carbon molecules,
one of which is a precursor metabolite. DHAP is readily
converted to glyceraldehyde 3-phosphate.

Glyceraldehyde 3-phosphate is oxidized and simultaneously
phosphorylated, creating a high-energy molecule. The electrons
released reduce NAD1 to NADH

ATP is made by substrate-level phosphorylation

Another precursor metabolite is made.

Another precursor metabolite is made.

The oxidative breakdown of one glucose results in the
formation of two pyruvate molecules. Pyruvate is one of the
most important precursor metabolites.

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STEP 2. Tricarboxylic Acid Cycle ● This proton and charge gradient is called the proton
(Pyruvate to CO2) motive force (PMF), a form of energy in the cell
● Also called Citric Acid Cycle and Krebs ● Take note that O2 is the nal electron acceptor.
cycle ● Oxidative phosphorylation is the process by which
● Common in aerobic bacteria, free-living ATP is made as a result of electron transport.
protozoa, most algae, and fungi ● The chemiosmotic hypothesis states that ATP
● Occurs in the cytoplasm of prokaryotes and synthesis is driven by the electrochemical gradient
the mitochondrial matrix in eukaryotes formed through the ETC.
● A source of carbon skeletons for use in ● As the protons ow back into the
biosynthesis cytoplasm/mitochondrial matrix through ATP
● Generates ATP, NADH, and FADH. synthase, it is down the concentration gradient and is
able to drive ATP synthesis.
● 1 ATP is synthesized per 3 protons passing via ATP
synthase.

Summary of TCA Cycle
For each acetyl-CoA molecule oxidized, the TCA cycle generates: Anaerobic Respiration
● 2 molecules of CO2 ● The chemoorganotrophic process whereby an
● 3 molecules of NADH exogenous terminal or nal electron acceptor other
● One FADH2 than O2 is used in electron transport.
● One ATP or GTP (Guanosine triphosphate - ○ Final electron acceptor is not OXYGEN
energy important in protein synthesis) ○ Exogenous materials/compounds such as:

STEP 3. Electron Transport Chain and Oxidative
Phosphorylation

● The ETC is a series of e- carriers, operating together to
transfer e- from NADH and FADH2 to a terminal e-
acceptor, O2
● e- transfer is accompanied by proton movement across
the membrane, generating a proton gradient.
● Generate the most number of ATPs.
● e- transfer is accompanied by proton movement across
the cell membrane or inner mitochondrial membrane.
● It creates a proton gradient and a charge gradient across
the membrane.
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● Uses an ETC forming PMF ● Reduction of pyruvate to lactate

● May use the same catabolic processes of glycolysis and ● Pyruvate is the acceptor of electron coming
TCA as in aerobic respiration. from NADH
● The use of alternative nal electron acceptors has ● Occurs in bacteria, some protists, and animal
ecological consequences in anoxic habitats (ex. Aquatic skeletal muscle
sediment, waterlogged soil) and global cycling nitrogen ● Ex. Lactic acid bacteria in yoghurt
and sulfur ○ Streptococcus thermophilus
● Practical application in wastewater treatment, i.e. ○ Lactobacillus delbrueckii subs.
removal of nitrates. Bulgaricus
● In the absence of oxygen, nitrate is used as the terminal
electron acceptor. Two types of LA fermenters:
● Nitrate is reduced to nitrogen gas (N2) using di erent ● Homolactic fermenters
reductases. ○ Use EM pathway
● Note that PMF is formed ○ Converts most of the pyruvate to lactate using
● Less ATP is formed with anaerobic respiration lactate dehydrogenase
● ATP is formed via oxidative phosphorylation ● Heterolactic fermenters
● Other facultative anaerobic microorganisms carry out ○ Use the PP pathway
denitri cation. ○ Produce lactate + Other products (Ethanol and
CO2)
DISSIMILATORY NITRATE REDUCTION
● Nitrate becomes unavailable for the cell to construct Common Microbial Fermentations
N-containing molecules such as amino acids and 1. Lactic acid bacteria (Streptococcus, Lactobacillus),
nucleotides Bacillus, enteric bacteria (Escherichia, Eneterobacter,
Salmonella, Proteus)
DENITRIFICATION 2. Yeast, Zymomonas
● Process of reducing nitrate and producing gaseous 3. Propionic acid bacteria (Propionibacterium)
nitrogen. 4. Enterobacter, Serratia, Bacillus
5. Enteric bacteria
Fermentation 6. Enteric bacteria
● Does not involve and ETC 7. Clostridium
● A chemoorganotrophic f ueling process in which an 8. Enteric bacteria
organic molecule is oxidized without an exogenous 9. Enteric bacteria
electron acceptor.
● A catabolic by-product such as pyruvate and related Enteric bacteria carry out Mixed Acid Fermentation
compounds serves as the electron acceptor producing ethanol, formic acid, acetic acid, lactic acid CO2, H2.
● No electron transport chain is involved
● NADH is oxidized to NAD ● Fermentations produce valuable commercial products
● Oxygen is not needed such as alcoholic beverages and fermented food.
● Produces ATP via substrate level phosphorylation ● The di erent fermentative capabilities can also be used as
○ The synthesis of ATP by phosphorylation diagnostic characteristics to help identify certain bacteria
coupled with the exergonic breakdown of a (ex. MRVP test: acid production, acetoin production)
high-energy organic molecule

A Close look at Lactic Acid Fermentation
Compounds other than glucose can also be used as carbon

and energy sources by microorganisms

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The catabolic pathways for proteins and lipids funnel Phototrophy

metabolites into the glycolytic pathways and the tricarboxylic acid The use of light energy to fuel a variety of cellular
cycle, increasing metabolic e ciency and exibility. activities but not necessarily CO2 xation
(ex: Photoheterotrophs)
Chemolithotrophy - “Eating Rocks’

The synthesis of ATP by oxidizing reduced inorganic
compounds with an electron transport chain
● Oxygen is a common terminal electron acceptor
● ATP is made via oxidative phosphorylation
● Only members of the Bacteria and Archaea can carry out
chemolithotrophy
● Most are autotrophic, using CO2 as carbon source

Photosynthesis
The process of capturing light energy for the synthesis of
ATP and reducing power (NADPH), which are then used to
reduce and incorporate CO2 into the cell (carbon dioxide
xation)
● The oxygen in our atmosphere has accumulated as a
result of the activities of oxygenic photosynthetic
bacteria, the cyanobacteria
3 Major Groups of Chemolithotrophs ● Today, the atmospheric oxygen and carbon dioxide levels
1. Hydrogen-oxidizing (Alcaligenes, Hydrogenophaga, are modulated by photosynthetic organism, which carry
Pseudomonas spp.) out half of the global photosynthesis (the other half by
2. Sulfur-oxidizing (Beggiatoa, Thiobacillus, Sulfurovum green plants)
riftiae*)
3. Ammonia-oxidizing (Nitrobacter, Nitrosomonas) Phototrophic f ueling reactions

Ammonia Oxidation: Three types of Phototrophy:
Nitri cation ● Oxygenic Photosynthesis
● Oxidation of ammonia to nitrate by nitrifying bacteria ○ Oxygen is generated and released into the
Ammonia →→→→→ nitrite →→→→→ nitrate environment when light energy is converted to
(Nitrosomonas) (Nitrobacter) chemical energy
○ Most important pigment: chlorophyll
Sulf ur Oxidation: ○ Triggers electron ow from the photosynthetic
● Elemental sulfur/H2S/thiosulfate →→→ sulfuric acid pigment to an ETC, which is cyclic or
(Sulfolobus, Thiobacillus, Acidithiobacillus) non-cyclic, forming PMF.
● Anoxygenic Photosynthesis
Reverse Electron Flow in Nitrobacter ○ Molecules other than water are used as an
electron source and therefore O2 is not
produced
○ Pigment: Bacteriochlorophyll
○ Triggers electron ow from the photosynthetic
pigment to an ETC, which is cyclic or
non-cyclic, forming PMF.
● Rhodopsin-based phototrophy
○ Is di erent in that the PMF is formed
directly by the light-absorbing pigment.

Photosynthesis can be oxygenic or anoxygenic

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● Use alternative electron donors: H2S, elemental sulfur,

organic molecule.
● Not all anoxygenic photosynthetic bacteria are able to x
carbon dioxide
● Some are photoorganoheterotroph, using organic
material as carbon source

*It is therefore more appropriate to use the term anoxygenic
Major Pigments
phototrophs
● Chlorophyll is the major photosynthetic pigment

● A large planar molecule with four pyrrole rings with a
Rhodopsin-Based Phototrophy
central magnesium atom associated with the nitrogen
● Rhodopsins are found in certain bacteria (e.g.
atoms of the pyrrole rings
Flavobacteria), and Archaea (Halobacterium salinarum)
● Pyrrole rings are associated with various chemical
● Best studied is the archaerhodopsin of Halobacterium
groups, which is unique for every kind of chlorophyll or
salinarum
bacteriochlorophyll molecule
● Archaerhodopsin has retinal, a kind of carotenoid
● R-group aids in attachment to membranes
● It is a light-driven proton pump
● Absorb light in the red and blue range of the visible
● Membrane-bound
spectrum, green light is transmitted
● PMF drive ATP synthesis

● H. salinarum is a chemoorganotroph that shifts of
Accessory Pigments
phototrophy under high light and low oxygen
● These pigments help trap light energy and transfer it to
conditions
the pair of chlorophylls in the reaction center

● They absorb light in a range di erent from that of
Selected Anabolic Pathways
chlorophyll
1. Calvin-Benson cycle was chosen because of the huge
● They protect the microbes from intense sunlight which
impact of photosynthetic microbes on the levels of
could damage the photosynthetic apparatus
atmospheric CO2 and oxygen
Examples
2. Nitrogen xation was chosen because it is a uniquely
● Phycocyanin - cyanobacteria and red algae
prokaryotic metabolic pathway that impacts the global
● Phycoerythrin - cyanobacteria and red algae
N-cycle.
● Fucoxanthin - diatoms, dino agellate

● Carotenoids - cyanobacteria, protists, plants
Anabolism

The biosynthesis of complex compounds from
Oxygenic Photosynthesis - Photosystem II
simple ones with the input of energy and reducing power
● The photosynthetic apparatus is membrane-bound
● The cell structure is made up of macromolecules that are
○ Cell membrane of prokaryotes
synthesized from simple monomers or precursors
○ Thylakoid membrane in chloroplasts of
metabolites
eukaryotes
● Precursor metabolites are the carbon skeletons used in
● Photosystem II (P680) absorbs light and chlorophylls are
biosynthesis
energized and lose electrons
● The electrons ow from one carrier to another
generating PMF
● Electrons lost from chlorophyll are replaced by electron
from water, mediated by OEC enzyme (Oxygen evolving
complex)
● O2 and protons are waste products

Anoxygenic Photosynthesis
● Involve membres of 5 bacterial phyla:
○ Proteobacteria (purple sulfur and purple
nonsulfur bacteria)
○ Chlorobi (green sulfur bacteria)
○ Chloro exi (green nonsulfur bacteria)
○ Firmicutes (heliobacteria)
○ Acidobacteria
● Major pigments is bacteriochlorophyll
● Associate with the cell membrane or vesicles called
chlorosomes
● Single photosystem
● Mostly are strict anaerobes
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The 12 Precursor Metabolites

● Chemoorganotrophs produce these by the central metabolic pathways
● Autotrophs use CO2 xation and other pathways to make precursor metabolites

CO2 Fixation: Reduction and assimilation of CO2 carbon ○ Recall that carboxysomes are cell inclusions
● Autotrophs use CO2 as their sole or principal carbon enclosed by a protein shell
source ○ 3 Phases of the Calvin-Benson Cycle
● CO2 xation require energy and reducing power i. Carboxylation phase
● Comprises the Dark Reaction of photosynthesis ● CO2 + RUBP
● Autotrophic organism belong to ii. Reduction phase
○ Phototrophs ● PGA to G3P
○ Chemolithotrophs iii. Regeneration phase
● Eukaryotic and most prokaryotic autotrophs use the ● RUBP is reformed
Calvin-Benson cycle 2. Reductive TCA cycle (Aquificae, Proteobacteria,
● There are other pathways for CO2 xation Nitrospirae, Chlorobi)
3. Acetyl-CoA pathway (methanogens)
CO2 xation pathways in autotrophic microorganisms 4. 3-hydroxypropionate bi-cycle (Chloroflexi)
1. Calvin-Benson cycle (algae, most photosynthetic 5. 3-hydroxypropionate/4-hydroxybutyrate pathway
bacteria) (Sulfolobales)
○ Also called the reductive pentose phosphate 6. 4-hydroxybutyrate cycle (Thermoproteales,
cycle and Calvin cycle Desulfurococcales)
○ Occurs in the stroma of chloroplasts of
eukaryotic phototrophs Nitrogen- xation: N2 to NH3
○ Occurs in carboxysomes in cyanobacteria, The reduction of gaseous nitrogen (N2) to ammonia (NH3)
nitrifying bacteria, and sulfur-oxidizers ● Few bacterial and archaea can perform this
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3 Major categories
● Free-living bacteria
○ E.g. Azotobacter, Klebsiella, Clostridium
● Bacteria in symbiotic association with plants such as
legum, forming root nodules
○ E.g. Rhizobium, Bradyrhizobium
● Cyanobacteria
○ E.g. Anabaena, Nostoc, Trichodesmium

MODULE 6

Growth and Control
1. The in uence of environmental factors on growth: salt
concentration, pH, temperature, oxygen requirement,
pressure
2. Quorum sensing and the formation of bio lms
3. Generation or doubling time
4. De nition of terms in microbial control
5. Mechanisms and application of the di erent physical
methods of microbial control
● Heat-moist and dry ltration, HEPA lter,
radiation - UV and ionizing, osmotic pressure,
desiccation of drying, pH
6. Mechanism and antimicrobial applications of
● Phenolics, alcohols, halogens, heavy metals,
quaternary ammonium compounds, aldehydes.
Sterilizing gases
7. Conditions in uencing the e ectiveness of antimicrobial
agent activity
8. E ciency evaluation of chemical agents
● Protein FtsZ assemble into a ring-like structure at the
Control of Microbial Growth center of a cell
● Multiple ssion by cyanobacteria Stanieria forming
How do microbial cells grow? baeocytes
● Most bacterial and archaeal cells reproduce by binary
ssion
● Other strategies:
○ Budding
○ Multiple ssion
○ Spore formation

○ Intracellular o spring
● Molecular mechanisms of bud formation in bacteria are
● Many eukaryotic microbes:
not known
○ Asexual reproduction (mitosis)
● FtsZ are placed near both cell poles
○ Sexual reproduction (meiosis)
○ Often alternate between haploid and diploid
stages in their life cycle

● Spore formation by Streptomyces coelicolor
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● Multinucleoid laments are formed that eventually 1. Salt concentration

divide to form unicleoid spores ● Halophiles
● Spores are dispersed like the lamentous fungi - grow optimally in the presence of NaCi or
other salts at a concentration above about
Eukaryotic Cell Production 0.2M
● Extreme halophiles
- Requires salt concentrations of 2M and 6.2M
- Extremely high concentrations of potassium
- Cell wall, proteins, and plasma membrane
require high salt to maintain stability and
activity

Environmental Factors on Growth
● Most organisms grow in fairly
moderate environmental conditions
● Extremophiles - grow under harsh
conditions that would kill most other
organisms
● Growth range and optimum Solute concentration
condition ● Water activity (aw) - indicates free water for
● Ex. Salmonella the microorganisms to use
Temperature range: 5 - 45°C
Optimum growth temperature of 35
- 37°C

● Osmotolerant - they grow over wide ranges of
water activity but optimally at higher levels
● Xerophiles grow best at low aw

2. pH - is a measure of the relative acidity of a solution and
is de ned as the negative logarithm of the hydrogen ion
concentration (pH 0-14)
● Acidophiles - growth optimum between pH
0-5.5
● Neutrophils - growth optimum between pH
5.5-8
● Alkaliphiles (alkalophiles) - growth optimum
between pH 8.0-11.5
Drastic variations in cytoplasmic pH can harm
microorganisms:
- Damage plasma membrane
- Inhibiting the activity of enzyme and
membrane transport proteins

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Temperature ranges for Microbial Growth

● psychrophiles/cryophiles - 0°C to 20°C
● psychrotrophs/psychrotolerans - 0°C to
35°C
● Mesophiles - 15°C to 45°C
● Thermophiles - 45°C to 85°C
● Hyperthermophiles - 85°C to 113°C

pH Tolerance Mechanisms of Microbes Adaptations of Thermophiles
● Most microbes maintain an internal pH near ● Protein structure stabilized by a variety of
neutrality means
- The plasma membrane is - More H bonds
impermeable to proton - More proline
- Exchange potassium for protons - chaperons
● Acidic tolerance response ● Histone-like proteins stabilize DNA
- Pump protons out of the cell ● Membrane stabilized by variety of means
- Some synthesize acid and heat shock - More saturated, more branched and
proteins that protect proteins higher molecular weight lipids
● Many microorganisms change the pH their - Ether linkages (archaeal membranes)
habitat by producing acidic or basic waste
products 4. Oxygen concentration
● Growth in presence of di erent oxygen
3. Temperature concentrations depends on a microbe’s
● Microorganisms cannot regulate internal temperature, metabolic processes, electron transport chains
therefore easily a ected by external temperature (ETC), terminal electron acceptor used
● E ects enzyme-catalyzed reactions, membrane structure ○ Aerobe - grows in presence of
● Organisms exhibit distinct cardinal growth temperatures atmospheric oxygen (O2) which is
- Minimal 20% O2
- Maximal ○ Obligate aerobe - requires O2
- optimal ○ Anaerobe - grows in the absence of
O2
○ Obligate anaerobe - usually killed in
presence of O2
○ Microaerophile - requires 2-10% O2
○ Facultative anaerobes - do not
require O2 but grow better in its
presence
○ Aerotolerant anaerobes - grow with
or without O2

BIO425
E ects of Di erent Oxygen Levels on Microbe ○ Deinococcus radiodurans -

Growth extremely resistant to large doses of
ionizing radiation
○ Able to piece together its genome
after it is blasted apart by massive
doses of radiation
● Ultraviolet (UV) radiation - short
wavelength (approximately from 10 to 400
nm) and high energy
○ 260 nm - most lethal, the wavelength
most e ectively absorbed by and
damaging to DNA
○ Singlet oxygen - generated when
photosensitizer transfers energy to
oxygen
Basis of Di erent Oxygen Sensitivities - Highly reactive, quickly
● Oxygen reduced to reactive oxygen species destroys the cell
(ROS) - Carotenoids (accessory
○ Superoxide radical pigment) protects the cells
○ Hydrogen peroxide against singlet oxygen by
○ Hydroxyl radical absorbing energy from SO
● Aerobes produce protective enzymes and reverting it to and
○ Superoxide dismutase (SOD) - unexcited state
catalyze the destruction of superoxide
radical Microbial Growth in Natural Environments
○ Catalase - destroys peroxides Bio lms
○ Peroxidase - can be used to destroy - Most microbes grow attached to surfaces (sessile) rather
hydrogen peroxide than free oating (planktonic)
- These attached microbes are members of complex, slime
5. Pressure enclosed communities
● Microbes that live on land and water surface - Bio lms are ubiquitous in nature in water
live at 1 atm - Can be formed on any conditioned surface
● Some bacteria and archaea live in deep sea with - Form a slimy matrix made up of extracellular polymeric
very high pressures substances (proteins, polysaccharides, glycoproteins,
● Barotolerant - adversely a ected by increased glycolipids, DNA)
pressure , but not a severely as non tolerant - Protects microbes, from UV and antibiotics
organisms - Can be found in surfaces submerged in water (rocks on
● Barophilic (piezophilic) organisms - require streams), toilet tiles, teeth
or grow more rapidly in the presence of
increased pressure. Change membrane fatty
acids to adapt to high pressures

6. Radiation
● Ionizing radiation - one of the most
damaging to microorganisms. Very short
wavelength, high energy.
○ 2 forms of ionizing radiation
■ X-rays - arti cially Bio lm Formation
produced
■ Gamma rays - emitted
during natural radioisotope
decay
○ Low levels of ionizing radiation may
produce mutations that indirectly
result in death, whereas higher levels
are directly lethal
○ Breaks hydrogen bonds, oxidizes
double bonds, destroys ring
structures, and polymerizes some
molecules
BIO425
● Microbes reversibly attach to conditioned surface and Interdomain communication

release polysaccharides, proteins, and DNA to form the - Across domain
extracellular polymeric substance (EPS) - Association between plant and fungi
● Additional polymers are produced as microbes - Grows on the roots of the plant
reproduce and bio lm matures - Bene cial impact on plant
- Resistance to unfavorable conditions
Quorum sensing - Resistance to pests
● Density dependent - Droughts and stress
● Allows members of the same species to communicate - Increase absorption of nutrients from soil
with each other - In return the plant will provide the shelter and nutrients
● Acylhomoserine lactone (AHL) is an autoinducer for fungi to grow
molecule produced by many gram-negative organisms
○ Di uses across plasma membrane Culture Media - a solid or liquid preparation used to grow,
○ Once inside the cell, induces expression of transport, and store microorganisms
target genes regulating a variety of functions

Culture Media (Chemical composition)

● De ned or synthetic medium - chemical components
are known. Used to culture photoautotrophs and many
chemoorganoheterotrophs

● Complex media - contain some ingredients of
unknown chemical composition. Used to culture
fastidious microbes

Culture Media (Functional Types)
● General purpose/supportive media - sustain the
growth of many microorganisms
○ Enriched media - forti ed supportive media
(addition of blood and other nutrients)

BIO425
● Selective media - allow the growth of particular Measurement of Growth Rate and Regeneration Time
microorganisms, while inhibiting the growth of others
● Di erential media - distinguish among di erent
groups of microbes and even permit tentative
identi cation of microorganisms based on their
biological characteristics

Microbial Growth Curve in a Closed System

The Mathematics of Growth
● Generation (doubling) time (g)
○ Time required for the population to double in
size
○ Varies depending on species of microorganisms
and environmental conditions
○ Range from 10 minutes for some bacteria to
days for some eukaryotes

Microbial Control
● Growth rate constant (k) ● Physical agents
○ The number of generations per unit time ● Chemical agents
○ Expressed as n/t ● Mechanical removal methods
○ Reciprocal of generation ● Biological agents

De nition of Frequently Used Terms
● Sterilization
○ Destruction or removal of all viable (the
growing, the dividing organism, the
reproducing organisms) organisms, spores and
infectious agents.
○ Makes use of an autoclave to sterilize culture
media and decontaminate culture media as well
as glasswares in the laboratory.
○ Autoclaving - Method or procedure in the lab
in which keeps the culture media free from any
organisms.
○ Makes use of very high temperatures (121°C
to be speci c). Expose the materials in high
temperatures at around 15 - 20 minutes in
high pressure.
BIO425
● Disinfection Moist Heat

○ Killing, inhibition, or removal of disease ● It is established that the moist heat is more e ective than
causing (pathogenic) organism the dry heat.
○ Disinfectants ● Destroys viruses, fungi, and bacteria
■ Agents, usually chemical, used for ● Boiling will not destroy spores and does not sterilize
disinfection ● Degrades nucleic acids, denatures proteins, and disrupts
■ Usually used on inanimate objects membranes
● Sanitization / Sanitation
○ Reduction of microbial population to levels
deemed safe (based on public health standards)
● Antisepsis
○ Prevention of infection of living tissue by
microorganisms
○ Antiseptics
■ Chemical agents that kill or inhibit
growth of microorganisms when
applied to tissue
● Chemotherapy
○ Use of chemicals to kill or inhibit growth of
microorganism within the host tissue Steam Sterilization
● Agent that kill microorganisms or inhibit their ● Carried out above 100°C which requires
growth saturated steam under pressure
○ Cidal agents kill (-cide su x indicating agent ● Uses an autoclave
that kills) ● E ective against all types of microorganisms
■ Germicide kills pathogens and many (including spores)
non-pathogens but not necessarily ● Quality control - indicator strip or an ampule
endospores of Geobacillus stearothermophilus
■ Include bactericides, fungicides,
algicides, and virucides Pasteurization
○ Static agents inhibit growth (-static su x ● Controlled heating at temperatures well below
indicates growth inhibiting agent) boiling
■ Include bacteriostatic and fungistatic ● Used for heat sensitive products (milk, beer,
fruit juice and other beverages)
● Process does not sterilize but does kill
pathogens present and slow spoilage by
destroying spoilage enzymes and reducing the
total microbial load

Tyndallization
● Use steam and intermittent steril
● Also includes 24-hr incubation in between
sterilization to allow germination of spores
● Used for products that may be contaminated
with spores but cannot withstand the high
temperatures of autoclave.

Dry Heat
Physical Control of Microbial Growth
● Oxidizes cell constituents and denatures proteins
1. Heat
● Less e ective than moist heat sterilization, requiring
○ Moist heat
higher temperatures and longer exposure times
○ Dry heat
○ Ex. in dry heat oven, items are subject to
2. Filtration
160-170°C for 2 to 3 hours
3. Radiation
● Advantage over moist heat: does not corrode glassware
○ UV radiation
and metal instruments as moist heat does, and it can be
○ Ionizing radiation
used to sterilize powers, oil, and similar items.
4. Osmotic pressure

5. Desiccation or drying

6. pH

BIO425
Filtration
● Reduces microbial population or sterilizes solutions of
heat-sensitive materials by removing microorganisms
● Also used to reduce microbial populations in air.
● Membrane lters - porous membranes with de ned
pore sizes that remove microorganisms primarily by
physical screening.

Air Filtration
● Surgical masks
● Cotton plugs on culture vessels
● High-e ciency particulate air (HEPA) lters
○ Used in laminar ow biological safety
cabinets

Ultraviolet Radiation
● Wavelength of 260 is most bacterial (DNA absorbs)
● Causes thymine dimers preventing replication and
transcription Phenolics
● UV limited to surface sterilization because it does not ● Commonly used as laboratory and hospital disinfectants
penetrate glass, dirt lms, water, and other substances ● Act by denaturing proteins and disrupting cell
● Has been used for water treatment. membranes
● Tuberculocidal, e ective in presence of organic material
Ionizing Radiation and long lasting
● Gamma radiation penetrates deep into objects ● Disagreeable odor and can cause skin irritation
● Destroys bacterial endospores; not always e ective
against viruses Alcohols
● Used for sterilization and pasteurization of antibiotics, ● Among the most widely used disinfectant and
hormones, sutures, plastic disposable supplies and food antibiotics
● Two most common are ethanol and isopropanol
Other Methods: ● Bactericidal, fungicidal, but not sporicidal
● Osmotic pressure ● Inactivate some viruses
● Desiccation ● Denature proteins and possibly dissolve membrane
● pH lipids

Chemical Growth of Microbial Growth Halogens
● Phenolics ● Any of the ve elements:
● Alcohols ○ Fluorine, chlorine, bromine, iodine, and
● Halogens astatine
● Heavy metals ○ Important antimicrobial agents
● Quaternary ammonium compounds ● Iodine
● Aldehydes ○ Skin antiseptic
● Sterilizing gases ○ Oxidizes cell constituents and iodinates
proteins
○ At high concentrations may kill spores
○ Skin damage, staining, and allergies can be a
problem
○ Iodophore
■ Iodine complexed within organic
carriers
■ Released slowly to minimize skin
burns
● Chlorine
○ Oxidizes cell constituents
○ Important in disinfection of wall supplies and
swimming pools, used in dairy and food
industries.
○ Destroys vegetative bacteria and fungi
○ Chlorine gas is sporicidal
BIO425
○ Can react with organic matter to form E ciency Evaluation of Chemical Agents
carcinogenic compounds
● Phenol Coe cient Test
Heavy Metals ○ Potency of a disinfectant is compared to that of
● E ective but usually toxic phenol
● Combine with and inactive proteins; may also ○ Useful for screening but may be misleading
precipitate proteins ● Use dilution Test
● E.g. ions of mercury, silver, arsenic, zinc and copper ○ Determines rate at which selected bacteria are
destroyed by various chemical agents
Quaternary Ammonium Compounds ● Normal in-use testing
● Detergents that have antimicrobial activity and are ○ Testing done using conditions that
e ective disinfectants approximate normal use of disinfectant
○ Amphipathic organic cleansing agents
● Cationic detergents are disinfectants END of Module 1 - 6 (Prelims)
○ Kill most bacteria, but not M. tuberculosis or
endospores
○ Safe and easy to use, inactivated by hard water
and soap

Aldehydes
● Commonly used agents are formaldehyde and
glutaraldehyde
● Highly reactive molecules
● Sporicidal and can be used as chemical sterilants
● Combine with and inactivate nucleic acids and proteins

Sterilizing Gases
● Used to sterilize heat-sensitive materials
● Microbicidal and sporicidal
● Ethylene oxide sterilization is carried out in
equipment resembling an autoclave
● Beta Propiolactone and vaporized hydrogen peroxide
● Combine with and inactivate DNA and proteins

Conditions In uencing the E ectiveness of Antimicrobial
Agent Activity
● Population size
○ Larger populations take longer to kill than
smaller populations
● Population composition
○ Microorganisms di er markedly in their
sensitivity to antimicrobial agents
● Concentrations or intensity of an antimicrobial agent
○ Usually higher concentrations kill more rapidly
○ Relationship is not linear
● Duration of exposure
○ Longer exposure ⇒ More organisms killed
● Temperature
○ Higher temperatures usually increase killing
● Local environment
○ pH, viscosity, concentration of organic matter,
etc. can profoundly impact e ectiveness
○ Organisms in bio lms are less susceptible to
many antimicrobial agents

BIO425

Organisms Too Small To Be Seen by The Unaided Eye

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UST College of Science

MODULE 1 Domain Archaea

What are FUNGI?

Sustainable Agriculture and

Major Fields in Microbiology

● Co-discoverer of antibodies, antigens, and chemotherapy Esther Lederberg

● SEM (Scanning Electron Microscope)

Staining: Gram Staining Bacterial Cell Organization

■ Trace elements (micronutrients) - Microcompartments

● Peptidoglycan sace - Slime Layers

Patterns of Flagella Bacterial Motility

Archaeal Cell Envelopes The Nucleoid

Common Features of Eukaryotic Cells ● Cell wall

○ Synthesis of secreted proteins by ER-associated

● Energy production through the use of the tricarboxylic Chloroplasts

Nucleolus 80 nm diameter) that are enriched in cholesterol and

The Structure of Viruses Virus Envelopes and Enzymes

deposited as plant-eating insects ■ Middle proteins – participate in

Types of Viral Infections (Bacteriophage) normally functions to protect against infection

● Electron Transport Chain MODULE 5

● Produces ATP via the activity of the electron transport

Speci cs of Embden-Meyerhof Pathway

● Uses an ETC forming PMF ● Reduction of pyruvate to lactate

Compounds other than glucose can also be used as carbon

The catabolic pathways for proteins and lipids funnel Phototrophy

● Use alternative electron donors: H2S, elemental sulfur,

The 12 Precursor Metabolites

● Multinucleoid laments are formed that eventually 1. Salt concentration

Temperature ranges for Microbial Growth

E ects of Di erent Oxygen Levels on Microbe ○ Deinococcus radiodurans -

● Microbes reversibly attach to conditioned surface and Interdomain communication

● Disinfection Moist Heat

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