Introduction to Bacteria stomach are now

eating what you ate

What are bacteria?
for breakfast
• Single celled organisms
• Some are warriors (pathogens)
• Very small
– They attack other living
• Need a microscope to see things

• Can be found on most materials and • Example: The

surfaces bacteria on your face
can attack skin
– Billions on and in your body causing infection and
right now acne
What do they look like? Where do you get a pathogen?
• Three basic shapes • Contact with people who are sick
– Rod shaped called bacilli – Direct or indirect
(buh-sill-eye)
• Food, Water, or other Surfaces
– Round shaped called cocci that are contaminated
(cox-eye)
What is a pathogen?
– Spiral shaped
• Bacteria that make you sick
• Some exist as single cells, others
cluster together – Why do they make you sick?

Bacteria are ALIVE! • To get food they need

to survive and
• What does it mean to be alive? reproduce
– They reproduce (make more – How do they make you sick?
of themselves)
• They produce
– They need to eat poisons (toxins) that
How do bacteria reproduce? result in fever,
headache, vomiting,
• Grow in number not in size and diarrhea and
– Humans grow in size from destroy body tissue
child to adult A Closer Look – Where do you get a
• Make copies of themselves by pathogen
dividing in half • Are all bacteria pathogens?
– Human parents create a child • No, most are harmless

• Some are even helpful

How do bacteria eat? – Examples of helpful bacteria:
• Some make their own food from • Lactobacillus: makes
sunlight—like plants cheese, yogurt, &
• Some are scavengers buttermilk and produces
vitamins in your intestine
– Share the environment
around them • Leuconostoc: makes
pickles & sauerkraut
• Example: The
bacteria in your
 • Pediococcus: makes • Bacteria are living organisms
pepperoni, salami, &
• Most are harmless
summer sausage
• A few are pathogens that make you
A Closer Look – Helpful Bacteria
sick
What are some common pathogens?
• You can reduce the risk of getting
• Pathogenic E. coli sick by washing your hands and
handling food properly.
(like O157:H7)

– Found in ground beef,

contaminated fruits and ANTIBIOTICS
vegetables
DIFFERENT CLASSES
• Salmonella
• B-Lactams - inhibit bacteria cell wall
– Found in raw meats, poultry, biosynthesis
eggs, sprouts, fruit and a) amoxicillin
vegetables b) flucloxacillin
c) cefalexin
• Listeria
• Aminoglycosides - inhibit the
– Found in deli foods, lunch synthesis of proteins by bacteria
meats, smoked fish and a) Streptomycin
vegetables b) Neomycin
c) Kanamycin
d) Paromomycin
Examples of Pathogens • Glycopeptides - inhibit bacteria cell
wall biosynthesis
• Pediococcus - used in production of a) Vancomycin
fermented meats b) Teicoplanin
• Lactobacillus casei – found in • Ansamycins - inhibit the synthesis
human intestines and mouth to of RNA by bacteria
improve digestion a) Geldanamycin
• Leuconostoc cremoris – used in the b) Rifamycin
production of buttermilk and sour c) Naphthomycin
cream • Quinolones - interfere with bacteria
• Lactobacillus bulgaricus – used in DNA replication
the production of yogurt a) Ciprofloxacin
How can I avoid pathogens? b) Levofloxacin
c) Trovafloxacin
• Wash your hands often so you • Streptogramins - inhibit the
won’t transfer bacteria to your mouth synthsis of proteins by bacteria
or food a) Pristinamycin IIA
b) Pristinamycin IA
– Warm water with soap for 20
• Lipopeptides - disrupt multiple cell
seconds, rub hard between
membrane functions
fingers and nails
a) Daptomycin
• Cook food thoroughly to kill any b) Surfactin
pathogens that may be in your food • Sulfonamides - prevent bacteria
growth and multiplication
• Store food properly to limit
a) Prontosil
pathogen growth
b) Sulfanilamide
– Cold temperatures (40F) c) Sulfadiazine
d) Sulfizoxacole
Review
 • Chloramphenicol - inhibits • To increase standardization, NCBI
synthesis of proteins has developed and maintains a
o No longer a first line drug in curated database of AMR genes and
any developed country makes them available both as raw
• Tetracyclines - inhibits synthesis of data and with an interactive web
proteins by bacteria interface.
a) Tetracycline
• To make AMR-related data more
b) Doxycycline
widely available, NCBI is collecting
c) Lymecycline
genetic and antibiotic susceptibility
d) Oxytetracycline
data.
• Macrolides - inhibits protein
synthesis by bacteria • To make more effective use of
a) Erythromycin bacterial genomic data, NCBI has
b) Clarithromycin developed AMRFinderPlus to
c) Azithromycin identify AMR genes in bacterial
• Oxazolidinones - inhibits synthesis genomes.
of proteins by bacteria
• To assist researchers and public
a) Linezolid
health officials, NCBI has developed
b) Posizolid
the Isolate Browser and MicroBIGG-
c) Tedizolid
E to allow researchers to identify
d) Cycloserine
bacterial genomes with AMR genes.
Antimicrobial Resistance

Why it matters
Top Dangerous Antibiotic-Resistant
• Antibiotics have been a staple of Bacteria
modern medicine's toolkit to fight
1. Neisseria gonorrhoeae
illnesses, but antibiotic treatment
has become less reliable as  Resistant to: Cephalosporins,
antimicrobial resistance (AMR) has azithromycin, fluoroquinolones
evolved in many bacterial
pathogens, causing the need for  Danger: STD that’s becoming nearly
costly new treatments to be untreatable — called “super
developed, while antimicrobial gonorrhea” 😬
resistant organisms continue to take  Spread: Sexual contact
thousands of lives per year.
 Status: WHO High Priority
• AMR is a growing concern that
affects a wide variety of people,
including those within the medical
2. Acinetobacter baumannii
community, public health officials,
food producers, pharmaceutical  Resistant to: Carbapenems (last-
develops, and the general public. resort antibiotics)
• Multi-drug resistant S. enterica  Nickname: "Iraqibacter"
• In response to the rising threat of  Infections: Pneumonia, wound
AMR, the White House developed infections, bloodstream infections
the National Action Plan for
 Status: WHO Critical Priority
Combating Antibiotic-Resistant
Bacteria in 2015. As part of the
National Action Plan, NCBI is
partnered with several outside 3. MRSA (Methicillin-Resistant
agencies, including the FDA, CDC, Staphylococcus aureus)
USDA, WHO, PHE, and others to  Resistant to: Methicillin, and often
take the following steps: others
  Infections: Skin, lungs, blood  Problem: Resistance is spreading in
normal E. coli strains too
 Common in: Hospitals and the
community  Status: WHO Critical Priority (when
resistant)
 Status: WHO High Priority
8. Mycobacterium tuberculosis

 Resistant to: Isoniazid, rifampicin,

4. Burkholderia cepacia fluoroquinolones (MDR/XDR-TB)
 Resistant to: Many standard  Spread: Through air
antibiotics (hard to treat)
 Danger: Long, hard treatment &
 Infections: Lungs of people with high death risk
cystic fibrosis, immunocompromised
patients  Status: WHO Critical Priority

 Fun fact: Can survive in

disinfectants 😬
9. Klebsiella pneumoniae
 Status: Not on WHO top list but
 Resistant to: Carbapenems, 3rd
dangerous in hospitals
gen cephalosporins
5. Pseudomonas aeruginosa
 Infections: Lungs, blood, UTIs
 Resistant to: Carbapenems and
 Superbug strain: NDM-1 producer
others
 Status: WHO Critical Priority
 Infections: Pneumonia, UTIs,
sepsis, burn wound infections

 Biofilm builder: Makes it extra hard 10. Streptococcus pneumoniae

to kill
 Resistant to: Penicillin, macrolides
 Status: WHO Critical Priority
 Infections: Pneumonia, meningitis,
otitis media
6. Clostridium difficile (C. diff)  Spreads: Coughing/sneezing
 Unique case: Not antibiotic-  Status: WHO Medium Priority
resistant, but thrives because of
antibiotic use

 Infections: Severe diarrhea and HOW ANTIBIOTIC RESISTANCE

colitis SPREADS:

 Risk: When gut flora is wiped by 👯‍♀️1. Person to Person (Literal hawaan)
antibiotics  Touching someone who’s carrying
 Status: Not on resistance list, but resistant bacteria (even if they’re not
still a major threat sick)

 Through hands, coughing, sneezing,

sharing stuff, even just living in the
7. Escherichia coli (E. coli) same house
 Resistant types: ESBL-producing,  Especially bad in hospitals,
carbapenem-resistant schools, crowded areas
 Infections: UTIs, sepsis, food 🚑 2. In Healthcare Settings (Where the
poisoning sickest go)
  MRSA, VRE, CRE = hospital
regulars 💀
🔄 6. Bacteria "Sharing" Resistance
 Spreads through: (Horizontal Gene Transfer)
o Contaminated equipment  Bacteria are generous — they
(like catheters, ventilators) literally give each other resistance
genes through:
o Unwashed hands of staff or
patients o Conjugation (bacterial
“mating”)
o Improper disinfection
o Transformation (picking up
free DNA)
🥩 3. Through Food (Yes, your chicken
o Transduction (via viruses)
can carry it)

 Animals given antibiotics can carry

resistant bacteria ⚠️TL;DR:
 These bacteria can be in: Resistance can spread through people,
animals, food, water, the environment —
o Raw meat, unpasteurized
and even between bacteria themselves 😤.
milk, or unwashed veggies
It’s everywhere if we’re not careful.
o Contaminated water used in
MAJOR CLASSES OF ANTIBIOTICS
farming
1. β-Lactams (Penicillins,
 Cooking can kill them, but poor food
Cephalosporins, Carbapenems,
handling? Big risk.
Monobactams)

 🛠 MOA: Inhibit cell wall synthesis

💩 4. Fecal-Oral Route (Gross but real) by binding to PBPs (penicillin-
binding proteins) → bacteria can't
 Bacteria like E. coli, Shigella, build walls → they burst!
Salmonella can spread from poop to
mouth through:  🧬 Resistance:

o Dirty hands o β-lactamase enzymes:

Break down the drug (e.g.,
o Dirty water ESBL, AmpC, KPC, NDM)
o Poor sanitation o Altered PBPs: e.g., MRSA
 A major issue in places with limited has a modified PBP (PBP2a)
clean water or sewage treatment. o Efflux pumps or reduced
permeability (esp. Gram-
negatives)
🔁 5. Environmental Spread

 Resistant bacteria can end up in:

o Wastewater from hospitals

and farms
2. Glycopeptides (e.g., Vancomycin)
o Soil and rivers
 🛠 MOA: Inhibit cell wall synthesis
o Even dust
by binding to D-Ala-D-Ala terminal of
 So yeah… resistance doesn’t stay peptidoglycan
where it starts.
 🧬 Resistance:
 o D-Ala-D-Lac modification
(in VRE): Vancomycin can't
bind 🦠 VIRUSES

o Thickened cell wall in some 🔹 What is a virus?

MRSA strains  A non-cellular particle made of
genetic material (DNA or RNA) and
a protein coat (capsid).
3. Aminoglycosides (e.g., Gentamicin,
 Can only replicate inside a host
Amikacin)
cell—basically hijacks living cells to
 🛠 MOA: Inhibit protein synthesis at make more of itself.
the 30S ribosomal subunit →
🧠 Think of viruses as microscopic USBs
misreading mRNA
with dangerous files. They plug into living
 🧬 Resistance: cells and force them to read (and replicate)
the virus code.
o Aminoglycoside-modifying
enzymes (acetylation,
phosphorylation)
🧬 STRUCTURE OF A VIRUS
o Ribosomal mutations
 Nucleic Acid Core: Contains either
o Efflux pumps DNA or RNA, never both.

4. Macrolides (e.g., Erythromycin,  Capsid: Protein shell that protects

Azithromycin) the core.

 🛠 MOA: Bind to 50S ribosomal  Some viruses have an envelope

subunit, block protein elongation (membrane-like layer from the host
cell).
 🧬 Resistance:
Visual: Like a lollipop—head = capsid with
o Methylation of 23S rRNA
DNA/RNA, stick = tail fibers.
(erm genes)

o Efflux pumps (mef genes)

🔁 VIRAL REPLICATION CYCLES
o Enzymatic degradation
Lytic Cycle

 Virus injects its DNA → takes over

5. Fluoroquinolones (e.g., Ciprofloxacin, cell → makes more viruses → cell
Levofloxacin) bursts (dies).
 🛠 MOA: Inhibit DNA gyrase and  Fast & destructive.
topoisomerase IV → no DNA
replication Lysogenic Cycle

 🧬 Resistance:  Virus DNA hides in host DNA (called

a prophage).
o Mutations in gyrA/parC
genes  Stays dormant until triggered →
switches to lytic.
o Efflux pumps
🧠 Lytic = attack now. Lysogenic = sleeper
o Plasmid-mediated cell mode.
resistance (qnr genes)
💉 VACCINES

 Attenuated: Live but weakened

📘 MICROBIOLOGY REVIEWER: Viruses & viruses (grown on chicken embryos).
Bacteria (Grade 11 Level)
  Inactivated: Heat-killed viruses. 🔬 TYPES OF BACTERIA (BASED ON
SHAPE)
🧠 Vaccines train your immune system like a
rehearsal—"hey, if you see this guy again,  Cocci: Spheres
destroy him."
 Bacilli: Rods

 Spirilla: Spirals
🔁 RETROVIRUSES
 Flagella: Tail-like propellers for
 Use RNA instead of DNA. movement

 Have an enzyme called reverse

transcriptase to convert RNA →
💊 GRAM STAINING
DNA.
 Gram-positive: Thick cell wall,
 Example: HIV
stains purple
🧠 Retroviruses are basically reverse UNO
 Gram-negative: Thin cell wall,
cards—flipping the genetic code game.
stains pink
Visual: Retrovirus = envelope + capsid +
🧠 It’s like giving bacteria a personality test—
RNA + reverse transcriptase.
how they stain tells you about their wall and
how to treat them.

🧫 BACTERIA

🔹 Prokaryotes HOW BACTERIA GET ENERGY

 No nucleus How They

Type Example
Eat
 Tiny but everywhere
Make their
 Split into 2 main kingdoms:
own food
Autotrophs Cyanobacteria
o Eubacteria: Common using
bacteria sunlight

o Archaebacteria: Use
Extremophiles (survive crazy chemicals to
Chemotrophs Archaebacteria
hot, salty, or toxic places) make
energy

Eat other
🦠 STRUCTURE OF A BACTERIAL CELL Heterotrophs E. coli
organisms
 Cell Wall: Protection

 Plasma Membrane: Controls what

enters/leaves
🫁 BACTERIAL RESPIRATION
 Capsule: Slimy layer for extra
protection Type Oxygen Usage
 Flagella/Cilia: Movement Obligate
Die in oxygen
 Pili: For sticking or conjugation Anaerobes

Visual: Jellybean with tails and fuzzy hair = Facultative Can live with/without
bacteria Anaerobes oxygen

Need oxygen to
Obligate Aerobes
survive
🧠 Think of bacteria as picky roommates—  Bacteria = prokaryotes (no
some love air, some don’t. nucleus), found everywhere, can be
good or bad.

 They reproduce fast, survive

🧬 BACTERIAL REPRODUCTION
tough conditions, and come in all
1. Binary Fission shapes.

 One cell splits into two identical ones  Gram staining helps ID their type for
(like copy-paste). treatment.

2. Conjugation  Some bacteria make their own

food; others eat stuff.
 Bacteria “mate” by swapping DNA
(like giving cheat codes).  Bacteria breathe differently
depending on the type.
3. Spore Formation
 Relationships: they can be helpful
 When conditions are bad, bacteria (mutualism), harmful (parasitism), or
form endospores—super tough just chillin' (symbiosis).
survival pods.

CHAPTER 3 TOOLS OF THE

🤝 BACTERIA & OTHER ORGANISMS LABORATORY: THE METHODS FOR
STUDYING MICROORGANISMS
What
Relationship Example
Happens 🧪 THE “6 I’s” OF MICROBIOLOGY

E. coli in your These are the core steps used to collect,

Mutualism Both benefit
gut grow, isolate, and study
microorganisms:
One benefits,
Parasitism Tuberculosis
one harmed

Long-term Any close 1. Inoculation

Symbiosis
relationship bacterial pair
 What it means: Introducing a
sample (like saliva, blood, or urine)
onto a growth medium
🌱 NITROGEN FIXATION
 Goal: Give microbes the right
 Converts atmospheric nitrogen environment to grow
(N₂) into a usable form for plants.
 Tool used: Inoculating loop, swab,
 Super important in agriculture. pipette
🧠 Bacteria help plants eat nitrogen—like  Example: Swabbing your throat and
turning clouds into fertilizer. streaking it on agar

💡 TL;DR SUMMARY 2. Incubation

 Viruses = non-living particles that  What it means: Letting the

need hosts to reproduce. inoculated media sit in a controlled
environment (temp, O2)
 Retroviruses are viruses that do
reverse transcription (HIV).  Goal: Allow microbes to multiply and
form colonies
 Vaccines help train your body to
fight viruses.  Common conditions: 35–37°C,
24–48 hours
  Example: Bacteria incubated
overnight in a warm incubator
🧫 SPECIMEN COLLECTION

Collecting a sample the right way is 💯

3. Isolation crucial. Here's the tea:

 What it means: Separating

individual species from a mixed
✨ Why it's important:
sample
 Poor collection = wrong results (false
 Goal: Get pure colonies
positives/negatives)
 Technique: Streak plate method
 Some bacteria die quickly or are
 Example: Isolating E. coli from a easily contaminated
stool sample

✅ Key Guidelines:
4. Inspection
1. Collect before starting antibiotics
 What it means: Observing colonies'
appearance (color, shape, size, 2. Use sterile tools (swabs,
texture) containers)

 Goal: Spot differences & potential ID 3. Label properly (name, time, type of
clues sample)

 Tool: Naked eye, microscope 4. Transport immediately or store

correctly (refrigerate if needed)
 Example: Yellow circular colonies =
maybe Staphylococcus aureus 5. Avoid contamination from skin,
tools, or environment

5. Information gathering
📦 Examples of Specimens:
 What it means: Running
biochemical tests, staining, or Sample Collected
Notes
genetic tests Type From

 Goal: Collect data for identification Throat Back of For strep throat,
swab throat diphtheria, etc.
 Example: Gram staining, catalase
test, antibiotic susceptibility testing Avoid first few
Midstream
Urine drops — sterile
pee
needed

Blood 2+ samples from

Vein
6. Identification culture different sites

 What it means: Pinpointing the NOT saliva —

exact name of the organism Sputum Deep cough needs lung
secretions
 Goal: Determine if it’s harmful,
normal flora, or needs treatment Wound Clean edges first
Infection site
 Outcome: Diagnosis + proper swab before swabbing
treatment plan

 Example: Confirming it's MRSA

🧼 Final Tip:
through tests
Always follow aseptic technique to keep it field; used for live and preserved
clean and avoid cross-contamination. stained specimens
Gloves on, swabs ready, and label
• Dark-field – brightly illuminated
everything like a boss
specimens surrounded by dark field;
THE MICROSCOPE used for live and unstained
specimens
Key characteristics of a reliable
microscope are: • Phase-contrast – transforms subtle
changes in light waves passing
• Magnification – ability to enlarge
through the specimen into
objects
differences in light intensity, best for
• Resolving power – ability to show observing intracellular structures
detail
Fluorescence Microscope
Magnification in most microscopes results
• Modified microscope with an
from an interaction between visible light
ultraviolet radiation source and filter.
waves and the curvature of a lens.
• Uses dyes that emit visible light
– The objective lens forms the
when bombarded with shorter UV
magnified real image
rays - fluorescence
– The real image is projected to the
• Useful in diagnosing infections
ocular where it is magnified again to
form the virtual image Scanning Confocal Microscope
• Total magnification of the final • Uses a laser beam of light to scan
image is a product of the separate the specimen.
magnifying powers of the two lenses
• Integrates images to allow focus on
Resolution - the capacity to distinguish or multiple depths or planes.
separate two adjacent objects and depends
on Electron Microscopy

– The wavelength of light that forms the • Forms an image with a beam of
image along with characteristics of the electrons that can be made to travel
objectives in wavelike patterns when
accelerated to high speeds
• Quantifying Resolution
• Electron waves are 100,000 times
• Visible light wavelength is 400 nm– shorter than the waves of visible
750 nm light
• Numerical aperture of lens ranges • Electrons have tremendous power to
from 0.1 to 1.25 resolve minute structures because
resolving power is a function of
• Shorter wavelength and larger
wavelength
numerical aperture will provide
better resolution • Magnification between 5,000X and
1,000,000X
• Oil immersion objectives resolution
is 0.2 μm 2 Types of Electron Microscopes
• Magnification between 40X and • Transmission electron
2000X microscopes (TEM) – transmit
electrons through the specimen.
Variations on the Optical Microscope
Darker areas represent thicker,
• Bright-field – most widely used; denser parts and lighter areas
specimen is darker than surrounding indicate more transparent, less
dense parts.
 • Scanning electron microscopes a) Inoculation – introduction of a
(SEM) – provide detailed three- sample into a container of media to
dimensional view. SEM bombards produce a culture of observable
surface of a whole, metal-coated growth
specimen with electrons while b) Isolation – separating one species
scanning back and forth over it. from another
c) Incubation – under conditions that
Specimen Preparation for
allow growth
Optical Microscopes
d) Inspection
• Wet mounts and hanging drop e) Information gathering
mounts – allow examination of f) Identification
characteristics of live cells: size,
Isolation
motility, shape, and arrangement
• If an individual bacterial cell is
• Fixed mounts are made by drying
separated from other cells and has
and heating a film of specimen. This
space on a nutrient surface, it will
smear is stained using dyes to
grow into a mound of cells— a
permit visualization of cells or cell
colony. A colony consists of one
parts.
species.
Staining
– Streak plate technique
• Dyes are used to create contrast by
– Pour plate technique
imparting color
– Spread plate technique
• Basic dyes – cationic, positively
charged chromophore Inspection

• Positive staining – surfaces of • If a single species is growing in the

microbes are negatively charged container, you have a pure culture
and attract basic dyes but if there are multiple species than
you have a mixed culture.
• Staining
• Check for contaminants (unknown
• Acidic dyes – anionic, negatively
or unwanted microbes) in the
charged chromophore
culture.
• Negative staining – microbe repels
Ways to Identify a Microbe:
dye, the dye stains the background
• Cell and colony morphology or
• Simple stains – one dye is used;
staining characteristics
reveals shape, size, and
arrangement • DNA sequence

• Differential stains – use a primary • Biochemical tests to determine an

stain and a counterstain to organism’s chemical and metabolic
distinguish cell types or parts characteristics
(examples: Gram stain, acid-fast
• Immunological tests
stain, and endospore stain)
Media: Providing Nutrients in the
• Structural stains – reveal certain
Laboratory
cell parts not revealed by
conventional methods: capsule and Media can be classified according to
flagellar stains three properties:

1. Physical state – liquid, semisolid,

and solid
The 6 I’s of Culturing Microbes
2. Chemical composition – synthetic
(chemically defined) and complex
 3. Functional type – general purpose, be fermented, converted to acids,
enriched, selective, differential, and a pH indicator to show this
anaerobic, transport, assay, reaction
enumeration

Physical States of Media

CHAPTER 4 A SURVEY OF
a) Liquid – broth; does not solidify PROKARYOTIC CELLS AND
b) Semisolid – contains solidifying MICROORGANISMS
agent
Characteristics of Cells and Life
c) Solid – firm surface for colony
formation All living things (single and
multicellular) are made of cells that share
– Contains solidifying agent
some common characteristics:
– Liquefiable and nonliquefiable
– Nutrient broth – liquid medium – Basic shape – spherical, cubical,
containing beef extract and cylindrical
peptone
– Nutrient agar – solid media – Internal content – cytoplasm,
containing beef extract, peptone, surrounded by a membrane
and agar – DNA chromosome(s), ribosomes,
Chemical Content of Media metabolic capabilities

• Synthetic – contains pure organic Two basic cell types: eukaryotic and
and inorganic compounds in an prokaryotic
exact chemical formula Characteristics of Cells
• Complex or nonsynthetic – • Eukaryotic cells: animals, plants,
contains at least one ingredient that fungi, and protists
is not chemically definable
– Contain membrane-bound
• General purpose media – grows a organelles that
broad range of microbes, usually compartmentalize the
nonsynthetic cytoplasm and perform
• Enriched media – contains complex specific functions
organic substances such as blood, – Contain double-membrane
serum, hemoglobin, or special bound nucleus with DNA
growth factors required by fastidious chromosomes
microbes
• Prokaryotic cells: bacteria and
Examples of Enriched Media archaea
a) Selective media: contains one or – No nucleus or other
more agents that inhibit growth of membrane-bound organelles
some microbes and encourage
growth of the desired microbes Characteristics of Life
b) Differential media: allows growth of • Reproduction and heredity –
several types of microbes and genome composed of DNA packed
displays visible differences among in chromosomes; produce offspring
those microbes sexually or asexually
Some media can be both Selective & • Growth and development
Differential
• Metabolism – chemical and physical
Miscellaneous Media life processes
• Carbohydrate fermentation
medium – contains sugars that can
 • Movement and/or irritability –  Note: Can be transferred between
respond to internal/external stimuli; bacteria (via conjugation)
self-propulsion of many organisms
🧫 6. Ribosomes (70S)
• Cell support, protection, and storage
 Function: Protein synthesis
mechanisms – cell walls, vacuoles,
granules and inclusions  Smaller than ours (we have 80S),
which is why some antibiotics can
• Transport of nutrients and waste
target them without hurting us
Structure of a bacterial cell
🧃 7. Capsule (not always present)
🧱 1. Cell Wall
 Function: Sticky, protective outer
 Function: Provides shape, layer
protection, and prevents bursting
 Bonus: Helps evade immune
 Made of: Peptidoglycan (unique to system + stick to surfaces
bacteria!)
 Made of: Polysaccharides or
 Gram + vs Gram -: proteins

o Gram-positive: Thick wall, 🏃‍♀️8. Flagella (if present)

purple in Gram stain
 Function: Movement — helps
o Gram-negative: Thin wall + bacteria swim
outer membrane, pink in
 Structure: Tail-like structure made
Gram stain
of flagellin
🧫 2. Cell Membrane (Plasma Membrane)
👋 9. Pili / Fimbriae
 Function: Controls what goes in/out
 Function: Attachment to surfaces or
of the cell
other bacteria
 Structure: Phospholipid bilayer with
 Pili (longer): used in conjugation
proteins
(DNA exchange)
 Bonus: Site for energy production
 Fimbriae (shorter): used to cling to
(no mitochondria in bacteria!)
host cells
🧬 3. Cytoplasm

 Function: Jelly-like fluid where all

🥶 10. Endospores (only in some bacteria
cellular activities happen
like Bacillus & Clostridium)
 Contains: Enzymes, nutrients,
 Function: Survival mode — highly
ribosomes, and the nucleoid
resistant to heat, drying, chemicals

 Note: Can stay dormant for YEARS

📍 4. Nucleoid 😱

 Function: Holds the bacterial DNA

 Structure: A single, circular 🧠 TL;DR:

chromosome (no membrane = no
true nucleus) Bacteria may look simple, but their structure
is built for survival: cell wall + membrane,
🧬 5. Plasmids DNA in nucleoid, ribosomes, sometimes
capsules, pili, flagella, and even
 Function: Extra DNA that gives
endospores.
superpowers like antibiotic
resistance External Structures
 • Appendages • Internal flagella, enclosed in
the space between the outer
– Two major groups of appendages:
sheath and the cell wall
• Motility – flagella and axial peptidoglycan
filaments (periplasmic flagella)
• Produce cellular motility by
• Attachment or channels – contracting and imparting
fimbriae and pili twisting or flexing motion

• Glycocalyx – surface coating • Fimbriae

• Flagella • Fine, proteinaceous, hairlike

bristles emerging from the
– 3 parts: cell surface
a) Filament – long, thin, helical • Function in adhesion to other
structure composed of cells and surfaces
protein flagellin
• Pili
b) Hook – curved sheath
– Rigid tubular structure made of pilin
c) Basal body – stack of rings protein
firmly anchored in cell wall
– Found only in gram-negative cells
– Rotates 360o
• Function to join bacterial cells for
– Functions in motility of cell partial DNA transfer called
through environment conjugation
• Flagellar Arrangements • Glycocalyx
– Monotrichous – single – Coating of molecules external to the
flagellum at one end cell wall, made of sugars and/or
– Lophotrichous – small proteins
bunches emerging from the – Two types:
same site
1. Slime layer - loosely organized
– Amphitrichous – flagella at and attached
both ends of cell
2. Capsule - highly organized,
– Peritrichous – flagella tightly attached
dispersed over surface of cell
• Functions of the Glycocalyx
• Flagellar Responses
1. Protect cells from dehydration
Guide bacteria in a direction in response to and nutrient loss
external stimulus:
2. Inhibit killing by white blood cells
1. Chemical stimuli – chemotaxis; by phagocytosis, contributing to
positive and negative pathogenicity
2. Light stimuli – phototaxis
3. Attachment - formation of
Signal sets flagella into motion clockwise or biofilms
counterclockwise:
• Biofilm on a catheter
1. Counterclockwise – results in
smooth linear direction – run • The Cell Envelope
2. Clockwise – tumbles
• External covering outside the
cytoplasm
• Periplasmic Flagella
• Composed of two basic
layers:
 • Cell wall and cell • Lipid portion (endotoxin) may
membrane become toxic when released during
infections
• Maintains cell integrity
• May function as receptors and
• Two different groups of
blocking immune response
bacteria demonstrated by
Gram stain: • Contain porin proteins in upper
layer – regulate molecules entering
1. Gram-positive bacteria:
and leaving cell
thick cell wall composed
primarily of Structures of Gram-Positive and Gram-
peptidoglycan and cell Negative Bacterial Cell Walls
membrane
Yesss Nath!! Time to compare Gram-
2. Gram-negative Positive vs. Gram-Negative bacterial cell
bacteria: outer cell walls 🔬🦠 — these two are like cousins with
membrane, thin very different vibes.
peptidoglycan layer, and
Gram- Gram-
cell membrane
Feature Positive Negative
Structure of Cell Walls (+) (–)
• Determines cell shape, prevents ✅ Thick ❌ Thin
lysis due to changing osmotic Peptidoglycan
(multi- (single
pressures Layer
layered) layer)
• Peptidoglycan is the primary ✅ Present
component: (wall &
Teichoic Acids ❌ Absent
• Unique macromolecule lipoteichoi
composed of a repeating c acid)
framework of long glycan
✅ Present
chains cross-linked by short
Outer Membrane ❌ Absent (extra
peptide fragments
protection)
•
✅ Clearly
Gram-Positive Cell Wall ❌ Usually defined
Periplasmic Space small or (between
– 20-80 nm thick peptidoglycan
absent membranes
– Includes teichoic acid and
)
lipoteichoic acid: function in cell
wall maintenance and enlargement ✅ Present
during cell division; move cations LPS
(contains
across the cell envelope; stimulate a (Lipopolysaccharid ❌ Absent
endotoxin
specific immune response e)
⚠️)
– Some cells have a periplasmic
space, between the cell membrane ✅ Present
and cell wall (lets stuff
❌ No pass
Gram-Negative Cell Wall Porin Proteins
porins through
• Inner and outer membranes and outer
periplasmic space between them membrane)
contains a thin peptidoglycan layer
Penicillin ✅ More ❌ Less
• Outer membrane contains Sensitivity sensitive sensitive
lipopolysaccharides (LPS) (no outer (outer
barrier) membrane
blocks
 Gram- Gram- Gram-
Feature Gram-Negative
Feature Positive Negative Positive
(+) (–)
acids, es (LPS),
drugs) n lipoteichoic lipoproteins,
acids phospholipids
Gram Stain Color 💜 Purple 💖 Pink
Overall ~20–80 nm
~8–11 nm (thin)
Thickness (thick)
🔍 Breakdown of Each: Outer
❌ Absent ✔ Present
✅ Gram-Positive Cell Wall Membrane

 Thick peptidoglycan (20–80 nm Periplasmi

Narrow Extensive
thick) c Space

 Teichoic acids: Help maintain More Less permeable

structure and bind ions Permeabilit permeable (outer membrane
y to (no outer blocks many
 Strong & rigid but no outer
Molecules membrane substances;
membrane, so it’s more vulnerable
barrier) requires porins)
to antibiotics

❌ Gram-Negative Cell Wall

 Thin peptidoglycan (2–3 nm)

The Gram Stain
 Outer membrane made of:
• Differential stain that distinguishes
o LPS (Lipopolysaccharide)
cells with a gram-positive cell wall
→ Contains Lipid A =
from those with a gram-negative cell
endotoxin ⚠️(causes
wall
fever/shock)
• Gram-positive - retain
o Porins: Allow passage of
crystal violet and stain purple
small molecules
• Gram-negative - lose crystal
 More complex, but also more violet and stain red from
resistant to drugs and detergents safranin counterstain

• Important basis of bacterial

🧠 TL;DR: classification and identification

 Gram-Positive = thick, simple, • Practical aid in diagnosing infection

stains purple and guiding drug treatment
 Gram-Negative = thin, complex, Nontypical Cell Walls
stains pink & has LPS (toxic alert 🚨)
• Some bacterial groups lack typical
Comparison of Gram-Positive and Gram- cell wall structure, i.e.,
Negative Cell Walls Mycobacterium and Nocardia
Gram- • Gram-positive cell wall
Feature Gram-Negative
Positive structure with lipid mycolic
acid (cord factor)
Number of 1 (Thick 2 (Thin
Major peptidoglyca peptidoglycan + • Pathogenicity and
Layers n layer) outer membrane) high degree of
resistance to certain
Chemical Peptidoglyca Peptidoglycan, chemicals and dyes
Compositio n, teichoic lipopolysaccharid
 • Basis for acid-fast – Used in genetic engineering -
stain used for readily manipulated and
diagnosis of infections transferred from cell to cell
caused by these
• Bacterial Ribosome
microorganisms
– Made of 60% ribosomal RNA
• Some have no cell wall, i.e.,
and 40% protein
Mycoplasma
– Consist of two subunits: large
• Cell wall is stabilized by
and small
sterols
– Prokaryotic differ from
• Pleomorphic
eukaryotic ribosomes in size
Cell Membrane Structure and number of proteins

• Phospholipid bilayer with embedded – Site of protein synthesis

proteins – fluid mosaic model
– Found in all cells
• Functions in:
Bacterial Internal Structures
• Providing site for energy
• Inclusions and granules
reactions, nutrient
processing, and synthesis – Intracellular storage bodies
– Vary in size, number, and
• Passage of nutrients into the
content
cell and discharge of wastes
– Bacterial cell can use them
• Cell membrane is selectively when environmental sources
permeable are depleted

Inside the Bacterial Cell • Cytoskeleton

• Cell cytoplasm: • Many bacteria possess an

internal network of protein
• Dense gelatinous solution of
polymers that is closely
sugars, amino acids, and
associated with the cell wall
salts
• Endospores
• 70-80% water
• Inert, resting, cells produced by
• Serves as solvent for
some G+ genera: Clostridium,
materials used in all
Bacillus, and Sporosarcina
cell functions
• Have a 2-phase life cycle:
• Nucleoid
– Vegetative cell -
• Chromosome
metabolically active and
– Single, circular, double- growing
stranded DNA molecule that
– Endospore – when exposed
contains all the genetic
to adverse environmental
information required by a cell
conditions; capable of high
• Plasmids resistance and very long-
term survival
– Free small circular, double-
stranded DNA • Sporulation - formation of
endospores
– Not essential to bacterial
growth and metabolism • Hardiest of all life
forms
 • Withstands extremes • Variation in cell shape and size
in heat, drying, within a single species
freezing, radiation,
• Some species are noted for their
and chemicals
pleomorphism
• Not a means of
reproduction Bacterial Arrangements
• Germination - return to • Arrangement of cells is dependent
vegetative growth on pattern of division and how cells
remain attached after division:
Sporulation cycle
• Cocci:
The sporulation cycle (also called
endospore formation) is the survival mode • Singles
of certain bacteria like Bacillus and • Diplococci – in pairs
Clostridium when they're under stress (like • Tetrads – groups of
heat, dryness, or starvation) four
• Irregular clusters
• Chains
• Cubical packets
(sarcina)

• Bacilli:
Endospores
• Diplobacilli
• Dehydrated, metabolically inactive
• Chains
• Thick coat
• Palisades
• Longevity verges on immortality, 250
million years Classification Systems for Prokaryotes
• Resistant to ordinary cleaning
1. Microscopic morphology
methods and boiling
2. Macroscopic morphology – colony
• Pressurized steam at 120oC for 20-
appearance
30 minutes will destroy
3. Bacterial physiology
• Bacterial Shapes, 4. Serological analysis
Arrangements, and Sizes 5. Genetic and molecular analysis
• Vary in shape, size, and Bacterial Taxonomy Based on Bergey’s
arrangement but typically described Manual
by one of three basic shapes:
• Bergey’s Manual of Determinative
• Coccus – spherical Bacteriology – five volume resource
covering all known prokaryotes
• Bacillus – rod
– Classification based on
• Coccobacillus – very
genetic information –
short and plump
phylogenetic
• Vibrio – gently curved – Two domains: Archaea and
Bacteria
• Spirillum – helical, comma, – Five major subgroups with 25
twisted rod, different phyla
• Spirochete – spring- Bergey’s Classification Scheme
like

Pleomorphism
It’s a system of bacterial taxonomy Gracilicutes, Firmicutes, Tenericutes,
(classification) that groups bacteria based Mendosicutes
on a combo of:

 Morphology (shape, size,

arrangement) 📌 Why It’s Important:

 Staining reactions (like Gram stain)  It helps microbiologists identify

unknown bacteria
 Metabolism (aerobic vs anaerobic,
fermentative, etc.)  Useful in medical microbiology for
diagnosing pathogens
 Genetic analysis (like rRNA
sequencing)  Essential in research and biotec

 Biochemical properties (enzymes, Major Taxonomic Groups of Prokaryotes

sugars they use, etc.) • Domain Archaea – primitive,
Developed by David Hendricks Bergey, it’s adapted to extreme habitats and
officially compiled in a set of books called: modes of nutrition

📚 Bergey’s Manual of Systematic • Domain Bacteria:

Bacteriology – Phylum Proteobacteria –
Gram-negative cell walls

– Phylum Firmicutes – mainly

Gram-positive with low G + C
content
📖 Main Classification in Bergey’s Manual – Phylum Actinobacteria –
Gram-positive with high G +
It’s divided into Volumes that group bacteria
C content
into phyla, and then further into genera and
species. Here’s a simplified breakdown of Diagnostic Scheme for Medical Use
the major groups based on the older but
commonly taught system: • Uses phenotypic qualities in
identification
Descriptio
Group Example – Restricted to bacterial
n
disease agents
Gram-
– Divides bacteria based on
Gracilicutes Escherichia coli negative
cell wall structure, shape,
cell walls
arrangement, and
Gram- physiological traits
Staphylococcus
Firmicutes positive cell
aureus Species and Subspecies
walls
• Species – a collection of bacterial
Mycoplasma cells which share an overall similar
Tenericutes No cell wall
pneumoniae pattern of traits in contrast to other
Archaea bacteria whose pattern differs
Mendosicute Methanobacteriu with significantly
s m unusual • Strain or variety – a culture derived
cell walls from a single parent that differs in
structure or metabolism from other
cultures of that species (biovars,
🧠 Mnemonic to Remember: morphovars)

"Gracie Firmly Tends Mendo" • Type – a subspecies that can show

differences in antigenic makeup
 (serotype or serovar), susceptibility • Rickettsia rickettisii –
to bacterial viruses (phage type) and Rocky Mountain spotted
in pathogenicity (pathotype) fever
• Unusual Forms of
Prokaryotes with Unusual
Medically Significant
Characteristics
Bacteria
• Free-living nonpathogenic bacteria
– Chlamydias
• Photosynthetic bacteria – use
• Tiny
photosynthesis, can synthesize
• Obligate intracellular
required nutrients from inorganic
parasites
compounds
• Not transmitted by
1. Cyanobacteria (blue-green arthropods
algae) • Chlamydia trachomatis –
2. Green and purple sulfur severe eye infection and
bacteria one of the most common
3. Gliding, fruiting bacteria sexually transmitted
diseases
• Chlamydia pneumoniae –
lung infections

Cyanobacteria (blue-green algae)

– Gram-negative cell walls Archaea: The Other Prokaryotes

– Extensive thylakoids with • Constitute third Domain Archaea

photosynthetic chlorophyll pigments • More closely related to Eukarya than
and gas inclusions to Bacteria
• Contain unique genetic sequences
Green and Purple Sulfur Bacteria in their rRNA
• Photosynthetic • Have unique membrane lipids and
cell walls
• Contain photosynthetic pigment
bacteriochlorophyll Archaea

• Do not give off oxygen as a product • Live in the most extreme habitats in
of photosynthesis nature, extremophiles

Gliding and Fruiting Bacteria • Adapted to heat, salt, acid pH,

pressure, and atmosphere
– Gram-negative
– Glide over moist surfaces • Includes: methane producers,
hyperthermophiles, extreme
Unusual Forms of Medically Significant halophiles, and sulfur reducers
Bacteria

• Obligate intracellular parasites

– Rickettsias

• Very tiny, gram-negative

bacteria
• Most are pathogens
• Obligate intracellular
pathogens
• Cannot survive or multiply
outside of a host cell