Chapter 2 Microbiology

What is spontaneous generation?

Microorganism come into existence “spontaneously” from thin air

What was John Needham’s experiment?

Sterile broth left open to see spontaneous generation

What was Needham’s hypothesis?

Microorganisms come into existence “spontaneously” from thin air

How did Pasteur disprove Needham using the heated air experiment?

Showing that air itself does not cause spontaneous generation, but rather carries pre-existing microbes

What was Pasteur’s Swan-Neck flask experiment?

Showing that microbial life comes from pre-existing life, not spontaneous generation, by showing that sterilized nutrient broth remained sterile as long as airborne microbes were trapped in the flask's bent neck

What is the Germ Theory of Disease?

Microorganisms (germs) are capable of living in the body and can cause illness

What was Pasteur’s Yeast experiment?

Showing that yeast are living microorganisms responsible for alcoholic fermentation

What are the steps to the yeast experiment?

1. Poured grape juice into flask that already had yeast cells

2. Heated the juice to kill the yeast cells

3. Plugged the flask with cotton and let it sit no fermentation appeared

4. Then he added yeast back in the same juice

5. Wine was made

What was Pasteur’s conclusion from the yeast experiment?

Yeast was not just present - it was necessary for fermentation. Something alive was making the change

What was the thought behind the bacteria experiment?

Could microbes cause disease too?

What are the steps to Pasteur’s bacteria experiment?

1. Heated grape juice to kill everything

2. Then in a sterile way, he added yeast in only

Result: wine, no sourness but… if he didn’t control for bacteria the wine turned sour

What was Pasteur’s conclusion from the bacteria experiment?

It wasn’t just yeast that could change liquids. Bacteria could spoil wine. Something similar might happen in the body.

What are Koch’s postulates?

Koch’s work formed a repeatable method - a kind of detectives blueprint for identifying the true cause of disease

1. Find the suspect

2. Isolate it

3. Recreate the disease

4. Recover it again

What disease was killing the cows that Koch observed?

Anthrax

What was the first step in Koch’s experiment?

Koch drew blood from a dead cow, examined it under a microscope, saw tiny rod-shaped organisms - bacteria

What was the second step in Koch’s experiment?

He grew the bacteria by placing a drop of blood onto a solid nutrient jelly. After a few days, distinct colonies appeared - each a clone of a single bacterium

What was the fourth step in Koch’s experiment?

Koch then takes one colony from the dish and injects it into a healthy mouse. Within a week that mouse dies, showing signs of Anthrax.

How did Koch confirm his observations?

To be sure it’s Anthrax, he looked under a microscope (again) and saw the bacteria matched what he found in the original cow

What is the metric system?

The universal language of science

Why is measurement important in biology?

1. Understanding life at the smallest level is key

2. Microorganisms are too small for our eyes

How long is a centimeter?

Roughly 2/5th of an inch

How long is a millimeter?

1mm = 1/1000 m = 10^-3 m

How long is a micrometer?

1μm = 1/1000 mm = 10^-6 m

How long is a nanometer?

1nm = 1/1000 μm = 10^-9 m

How are measurements used in biotechnology?

1. Most biotech tools work in the micrometer and nanometer range

2. Instruments like microscopes, Spectrophotometer, PCR machines

3. Precision matters. A small mistake in measurement can make a failed discovery or missed experiement

What are eukaryotic cells used for in biotechnology?

1. Stem cell research

2. Gene therapy

3. Producing complex biological vaccines

4. Developing cancer treatments

What is a nucleus?

Holds DNA in organized strands (chromosomes) inside nucleus: chromatin - DNA + proteins during non-division

What is the mitochondria?

ATP

What are ribosomes?

Proteins

What is the endoplasmic reticulum?

Moves protein around

What is the golgi apparatus?

Packages proteins

What are lysosomes?

Digest unwanted stuff

What are the key features of prokaryotic cells?

1. No nucleus - DNA floats freely in cell

2. DNA is usually circular, not in strands

3. No membrane bound organelles

4. Do have ribosomes but smaller, simpler

How are prokaryotic cells used in biotechnology?

1. Genetic engineering

2. Produce insulin

3. Human growth hormone, enzymes

4. Designing antibiotics, target prokaryotic features

What are viruses?

• Made of nucleic acids (DNA and RNA)

• Cannot live or grow without infecting a host cell

• Causes diseases like

  • Influenza

  • Chicken pox

  • HIV/AIDS

How are viruses used in biotechnology?

• Used in gene therapy to deliver corrected genes

• Phage therapy explores using viruses to kill bacteria

What are algae?

• Like cyanobacteria but eukaryotic (more complex cells)

• Uses photosynthesis

• Source of Omega-3 oil fatty acids

How are algae used in biotechnology?

Used in bioengineering for renewable energy sources

What are protozoa?

• Single celled but more complex

• Some cause disease

  • Malaria

  • Sleeping

  • Sickness

How are protozoa used in biotechnology?

• Used to study cell motility

• Important models for drug testing

What are cyanobacteria?

• AKA - blue - green algae

• Uses photosynthesis

How are cyanobacteria used in biotechnology?

Studied for bio-fuel production; can be engineered to fix nitrogen for sustainable farming

What are fungi?

Eukaryotic organisms that include microorganisms such as yeasts, moulds and mushrooms.

How are fungi used in biotechnology?

Molds like penicillin gave us antibiotics; yeast help ferment beer, wine, and bread

What is bacillus?

Rod shaped

What is coccus?

Spherical shaped → often found alone, in pairs, chains, clusters

What is staphylococcus?

Forms clusters like grapes, causes food poisoning, skin infections

What is spiral?

Curved or twist

How do spirochete move?

Moves like corkscrew

Why does bacterial shape matter?

1. Identification: shape help diagnose injections

2. Pathogenicity: shape affects how bacteria causes diseases

Why does biotechnology care about the shape of bacteria?

Industrial uses: some bacteria better for genetic engineering

What is the flagella?

• Long whip-like tail use for movement

• Spins like tiny motors to push bacteria through fluids

• Not all bacteria have them; those that do often show directional movement

• In biotech: flagellar genes can be used as markers in genetic tracking

What is the cell wall?

• Made of complex carbohydrates like peptidoglycan

• Provides shape and protection

• Gram-stain depends on differences in cell wall structure

• In biotech: enzymes like lysosome target the wall used in molecular biology for breaking cells

What is the cytoplasm?

• Gel-like interior of the cell

• Contains enzymes, nutrients, ions, and organelles

• Where all metabolic reactions happen

What is the plasma mebrane?

• A double layer of phospholipids and proteins

• Controls what enters and leaves cell

• Site of many enzymes and metabolic pathways

• Antibiotic target membrane functions

What are plasmids?

• Small circular DNA molecules independent of the main nucleoid

• Carrying non-essential but beneficial genes

• Engineered plasmids are used to transform bacteria in recombinant DNA work

What is the nucleoid?

• The command center contains a singular, circular DNA

• No nucleus envelope, floats in cytoplasm

• In biotech: genetic info here is the focus of bacterial cloning, CRISPR, and plasmid insertion

What are pili?

Hair-like structures used for

• attachment to surfaces

• genetic exchange (conjugation)

• used in horizontal gene transfer- basis for genetic engineering

How are bacterial structure targeted in biotechnology?

• We hijack plasmids

• We engineer their ribosomes

• open their membranes to introduce genes

• Use their capsule and pili in vaccines and therapeutic design

What is the cell envelope?

Includes everything from the outside moving inward

• Capsule

• Cell wall

• Cell membrane 

What are the functions of the cell capsule?

• Found in some bacterial cell (notch)

• Made up of polysaccharides (sugars) and sometimes protein fibers

• Function

  • helps bacteria adhere to sticky surfaces (dental plague)

  • shields against immune cells

  • acts like a biological cloak, masking bacteria from detection

• In biotech: capsules help evade immune system - important for vaccine development; genetic engineering sometimes removes the capsule genes, to make it safer for lab use

What is the cell wall made up of?

Peptidoglycan

What is peptidoglycan?

 A sugar protein meshwork that gives the cell wall strength

Describe the peptidoglycan layer on gram-negative bacteria?

Thin peptidoglycan layer

Describe the peptidoglycan layer on gram-positive bacteria?

Thick peptidoglycan layer

What is the cell membrane made up of?

• Also called plasma membrane

• Composed of phospholipid bilayer

What do proteins on the cell membrane do?

• Float near surfaces

• Others span the membrane like a gate

Why does bacteria need to be stained?

• Unstained bacteria are invisible to naked eye

• Stains adds contrast, essential for observation, identification, and differentiation

Describe the Simple Stain Technique.

• Painting the bacteria a single color to make them stand out

• Use a basic dye like crystal violet

• Dye has a positive charge bacterial cytoplasm has negative

• Bacteria absorb color

Describe the Negative Stain Technique.

• Don’t stain bacteria, just the background

• Bacteria repel the dye, so they stay unstained

• Useful for observing shape and size with minimal distortion

What are the steps for gram-staining?

1. Apply crystal violet, stains all bacteria purple

2. Add Iodine, locks the color inside the cell

3. Decolorize with Ethanol (95%)

   1. gram positive- retain the dye

   2. gram negative - bacteria lose it (colorless)

4. Counterstain with Safranin

   1. gram negative - bacteria take up red and appear pink/red

   2. gram positive - stay purple

Result: 

• Purple - gram positive (thick peptido)

• red/pink - gram negative (thin peptido)

How is gram-staining used in biotechnology?

Gram staining affects how we manipulate or transform bacteria

• gram negative E. coli is widely used for cloning, but requires special methods for DNA uptake

What are the two ways life propagates itself?

• Sexual reproduction (not seen in bacteria)

• Asexual reproduction (this is how bacteria multiply)

What is binary fission?

A cell divides into two

What happens during the growth phase?

• Elongates slightly

• Metabolism active, cell builds up energy

What happens during DNA replication?

• DNA replication begins

• Circular DNA  is copied

• Now bacteria has two identical DNA loops

What happens during organelle reproduction and cytoplasmic division?

• Organelles replicate and cytoplasmic separation

What happens during membrane pinching?

• Cell membrane starts to constrict inwards

What happens during cell division?

• Cell splits into two daughter cells

• Each is genetically identical, each is alive and ready to again

What does generation time mean?

• Time between one division and the next

• Depends on the species and conditions

• In this example: 40 min to replicate

Why do bacteria form spores?

Natures vault:

• They are called endospore. Inside the bacterium locks away its most precious belongings: DNA, enzymes

What triggers spore formation?

When the environment becomes harsh, the bacteria halts growth and begins sporulation 

What happens during the DNA preparation stage of spore formation?

DNA is copied, one copy stays with the parent, the other one goes to forming the spore

What happens when spore septum is formed?

A membrane pinches inward and enclosed

DNA + cytoplasm

What happens when the core wall forms?

Inner membrane becomes the core wall

What happens when the cortex develops?

A thick layer of special peptidoglycan forms around the core

• This gives the spore resistance

What is the exosporium?

The (outermost) layer appears made of -glyco and -lipo proteins

Why are bacterial spores important in biotechnology?

• Spores resist extremes

  • heat, chemicals, pressure

  • They’ve been found in ancient mummies

• Problem and a solution

  • In food biotech:

    • sterilization must destroy spores

  • In pharmaceuticals production: spores must be eliminated

  • In industrial microbiology: spores may be used for dormant starter cultures

What are the two ways bacteria get nutrients?

• Autotrophy - making raw food from chemicals

• Heterotrophy - using premade organic materials

What is autotrophy?

Autotrophy - making raw food from chemicals

What is heterotrophy?

Heterotrophy - using premade organic materials

How are autotrophic bacteria used in biotechnology?

Many industrial processes use autotropic bacteria

• Carbon capture

• Wastewater treatment

How do autotrophs create their own food?

Autotrophy “self” grow/nutrition

Create own food using:

• Inorganic molecules

• Energy from sunlight

What are saprobes?

Eat dead matter

What are parasites?

Live off hosts

What do heterotrophs eat?

Glucose → quick energy

Larger carbs → structural use

Lipids → broken down fatty acids (e.g. cell walls)

Proteins → 

• Digested into amino acids

• used to build new proteins

How are heterotrophs used in biotechnology?

Many bacteria used in biotechnology are heterotrophs

• (e.coli used for gene cloning feeds on glucose)

• work horses in biotech turning sugars into proteins, drugs, vaccines

What are obligate anaerobes?

• Require O2

• Found near top test tube

What are microphiles?

• Need O2

  • only little

• Sit below surface

What are facultative bacteria?

• Adaptable

• Prefer O2 but will shift