Chapter 2: Microbiology

What is spontaneous generation?

The Theory that living things can arise from non-living matter

What was John Needham's experiment?

He boiled broth, sealed it in flasks, and observed microbial growth, concluding that microbes could arise spontaneously (though his results were later shown to be flawed)

What was Needham's hypothesis?

Life can spontaneously arise from non-living matter

How did Pasteur disprove Needham using the heated air experiment?

He boiled nutrient broth in a swan-neck flask, which allowed air in but trapped dust and microbes. No microbial growth occurred, proving that microbes come from other microbes, not spontaneously

What was Pasteur's Swan-Neck flask experiment?

Nutrient broth was boiled in a swan-neck flask that let air in but trapped dust. No microbial growth appeared, showing that life doesn’t spontaneously arise from non-living matter

What is the Germ Theory of Disease?

The idea that many diseases are caused by microorganisms (germs) rather than by spontaneous generation or imbalances in the body

What was Pasteur's Yeast experiment?

He showed that yeast ferments sugar into alcohol only when alive, proving that fermentation is caused by living organisms, not spontaneous chemical processes

What are the steps to the yeast experiment?

Prepared sugar solutions in flasks.

Added yeast to some flasks; left others without yeast.

Boiled some solutions to kill any existing organisms.

Allowed the flasks to sit and observed fermentation.

Noted that only flasks with living yeast produced alcohol, proving fermentation requires living organisms.

What was Pasteur's conclusion from the yeast experiment?

Fermentation is carried out by yeast, not by spontaneous chemical processes

What was the thought behind the bacteria experiment?

To determine whether bacteria appeared spontaneously or came from pre-existing bacteria

What are the steps to Pasteur's bacteria experiment?

Filled flasks with nutrient broth.

Boiled the broth to kill any existing microbes.

Used swan-neck flasks that allowed air in but trapped dust and microbes.

Left flasks exposed to air for a period of time.

Observed that no microbial growth occurred, proving microbes come from other microbes, not spontaneously

What was Pasteur's conclusion from the bacteria experiment?

Microorganisms come from other microorganisms, not spontaneously from non-living matter

What are Koch's postulates?

The microorganism must be found in all sick organisms but not in healthy ones.

The microorganism must be isolated and grown in pure culture.

The cultured microorganism should cause the disease when introduced into a healthy organism.

The same microorganism must be re-isolated from the newly sick organism.

What disease was killing the cows that Koch observed?

Anthrax was killing the cows he studied

What was the first step in Koch's experiment?

Observe sick animals and identify the microorganism present in all diseased individuals but absent in healthy ones

What was the second step in Koch's experiment?

Isolate the microorganism and grow it in a pure culture

What was the fourth step in Koch's experiment? 18. How did Koch confirm his observations?

Re-isolate the same microorganism from the newly infected host to confirm it caused the disease

How did Konch confirm his observations?

He introduced the isolated microorganism into healthy animals, observed that they developed the same disease, and then re-isolated the same microorganism from them

What is the metric system?

A standardized system of measurement based on powers of ten, used worldwide (except US in general) for length, mass, volume, and temperature

Why is measurement important in biology?

It allows scientists to collect accurate, consistent, and comparable data for experiments, observations, and analysis

How long is a centimeter?

1/100th of a meter

How long is a millimeter?

1/1000th of a meter

How long is a micrometer?

1/1,000,000th of a meter

How long is a nanometer?

1/1,000,000,000th of a meter

How are measurements used in biotechnology?

They ensure precision and accuracy in experiments, such as measuring liquids, cell counts, DNA concentrations, and enzyme activity, which is essential for reproducible and reliable results.

What are eukaryotic cells used for in biotechnology?

They are used to produce complex proteins, study human diseases, test drugs, and develop vaccines, since they have organelles and processes similar to those in humans

What is a nucleus?

The control center of a eukaryotic cell that stores DNA and directs cell activities

What is the mitochondria?

Produces ATP through cellular respiration

What are ribosomes?

Cell structures that make proteins by assembling amino acids according to genetic instructions

What is the endoplasmic reticulum?

A network of membranes in a cell that helps make and transport proteins (rough ER) and lipids (smooth ER)

What is the golgi apparatus?

A cell organelle that modifies, sorts, and packages proteins and lipids for storage or transport out of the cell

What are lysosomes?

Cell organelles that contain enzymes to break down and recycle waste, damaged organelles, and foreign substances

What are the key features of prokaryotic cells?

No nucleus (DNA is in a nucleoid region)

No membrane-bound organelles

Small and simple structure

Usually single-celled organisms (like bacteria)

Have a cell membrane and often a cell wall

How are prokaryotic cells use in biotechnology?

They are used to produce proteins, enzymes, and antibiotics, for genetic engineering, and to study basic cellular processes because they are simple and grow quickly

What are viruses?

Tiny infectious agents that can only reproduce inside living cells; they consist of genetic material (DNA or RNA) surrounded by a protein coat

How are viruses used in biotechnology?

They are used as tools to deliver genes in gene therapy, create vaccines, study gene function, and develop viral vectors for research and medicine

What are algae?

Simple, photosynthetic organisms that can be single-celled or multicellular, found mostly in water, and produce oxygen and organic compounds through photosynthesis

How are algae used in biotechnology?

They are used to produce biofuels, dietary supplements, pharmaceuticals, cosmetics, and as model organisms for research on photosynthesis and genetics

What are protozoa?

Single-celled, eukaryotic organisms that often move using cilia, flagella, or pseudopodia and can be free-living or parasitic

How are protozoa used in biotechnology?

They are used to study cell biology, host-pathogen interactions, drug testing, and as model organisms for research on diseases like malaria

What are cyanobacteria?

Photosynthetic bacteria, also called blue-green algae, that produce oxygen and can fix nitrogen, playing an important role in ecosystems

How are cyanobacteria used in biotechnology?

They are used to produce biofuels, nutritional supplements, fertilizers, and as model organisms for studying photosynthesis and nitrogen fixation

What are fungi?

Eukaryotic organisms, including yeasts, molds, and mushrooms, that absorb nutrients from their environment and play key roles in decomposition and fermentation

How are fungi used in biotechnology?

They are used to produce antibiotics, enzymes, alcohol, food products (like bread and cheese), and as model organisms in research

What is bacillus?

A genus of rod-shaped, mostly aerobic bacteria, some of which can form spores and are used in biotechnology and medicine

What is coccus?

A type of bacterium that has a spherical or round shape

What is staphylococcus?

A genus of round (coccus) bacteria that often form clusters like grapes; some species can cause infections, while others are harmless

What spiral?

A type of bacterium that has a twisted or spiral shape; includes forms like spirilla and spirochetes

How do spirochete move?

Using axial filaments (endoflagella) that wrap around their body, allowing them to rotate and corkscrew through liquids

Why does bacterial shape matter?

Shape affects how bacteria move, attach to surfaces, acquire nutrients, and interact with their environment, which can influence their survival and pathogenicity

Why does biotechnology care about the shape of bacteria?

Bacterial shape affects growth patterns, protein production, motility, and how they respond to genetic engineering, making it important for designing experiments and industrial processes

What is the flagelle?

long, whip-like structures that help cell movement

What is the cell wall?

A rigid outer layer found in bacteria, fungi, algae, and plants that provides structure, protection, and support to the cell.

What is the cytoplasm?

The gel-like substance inside a cell that surrounds the organelles and is the site for many cellular processes

What is the plasma membrane?

A thin, flexible barrier around the cell that controls what enters and leaves, maintaining the cell’s internal environment

What are plasmids?

Small, circular pieces of DNA found in bacteria (and some eukaryotes) that can replicate independently and often carry useful genes, like antibiotic resistance

What is the nucleoid?

The region in a prokaryotic cell where the circular DNA is located, not enclosed by a membrane

What are pilli?

Hair-like structures on the surface of bacteria that help them attach to surfaces and sometimes transfer DNA between cell.

How are bacterial streuctures tarheted in biotechnonlogy?

cell wall: target of antibiotics

Plasmids: used as vectors to insert new genes in genetic engineering

ribosomes: targeted by antibiotics to block protein synthesis

Pili/flagella: Studied to understand adhesion and mobility for medical and industrial applications.

Cytoplasm: Used for metabolic engineering to produce proteins, enzymes, and biofuels.

What is a cell envelope?

The protective outer layers of a bacterial cell, made up of the plasma membrane, cell wall, and (in some bacteria) an outer membrane

What is the capsule?

A sticky, protective outer layer around some bacteria that helps them avoid the immune system, stick to surfaces, and prevent drying out

What are the functions of the cell capsule?

Protects bacteria from being engulfed by immune cells.

Helps bacteria stick to surfaces and host tissues.

Prevents the cell from drying out (desiccation).

Provides an extra layer of defense against antibiotics and toxins.

What is the cell wall made up of?

In most bacteria, it is made up of peptidoglycan (a mesh of sugars and amino acids); in plants, it’s made of cellulose; in fungi, chitin; and in algae, various polysaccharides.

What is peptidoglycan?

A strong, mesh-like polymer made of sugars and amino acids that forms the bacterial cell wall, giving it shape and protecting it from bursting

Describe the peptidoglycan layer on gram-negative?

Very thin compared to Gram-positive bacteria.

Located between the inner plasma membrane and an outer membrane.

Surrounded by an outer membrane containing lipopolysaccharides (LPS), which add extra protection.

Describe the peptidoglycan layer on gram-positive?

Very thick (much thicker than in Gram-negative).

Contains teichoic acids that help maintain structure and anchor the layer to the cell membrane.

outside the plasma membrane with no outer membrane.

What is the cell membrane made up of?

made up of a phospholipid bilayer with embedded proteins, and sometimes cholesterol (in eukaryotes) for stability

What do proteins on the cell membrane do?

Transport of molecules in/out

Cell signaling & communication

Acting as enzymes

Providing structural support

Cell recognition (like ID tags)

Why does bacteria need to be stained?

Bacteria are tiny and often transparent, so staining makes them visible under a microscope and helps differentiate types (e.g., Gram-positive vs. Gram-negative).

Describe the simple stain technique?

Uses one type of dye to color bacteria, making them easier to see under a microscope. It highlights cell shape, size, and arrangement but does not differentiate types of bacteria.

Describe the Negative Stain Technique?

Stains the background instead of the bacteria, leaving the cells clear and visible. It’s used to observe cell size, shape, and capsules without heat-fixing, which preserves delicate structures

What are the steps for gram-staining?

Apply crystal violet (primary stain) to the bacterial smear.

Add iodine (mordant) to form a crystal violet-iodine complex.

Wash with alcohol or acetone (decolorizer) to remove the stain from Gram-negative cells.

Counterstain with safranin so Gram-negative bacteria appear pink/red.

Observe under a microscope: Gram-positive bacteria appear purple, Gram-negative bacteria appear pink/red.

How is gram-staining used in biotechnology?

Helps identify bacterial species for research or industrial use.

Determines whether bacteria are Gram-positive or Gram-negative, which affects antibiotic selection.

Used in quality control in food, pharmaceuticals, and microbial production.

Aids in studying bacterial structure and behavior for genetic engineering or fermentation processes.

What are the two ways life propagates itself?

asexual reproduction and sexual reproduction

What is binary fission?

The DNA is copied.

The cell grows larger.

The cell divides into two, each with a complete copy of the DNA.

What happens during the growth phase?

Rapid cell division occurs — the number of bacteria increases exponentially.

Metabolic activity is high — bacteria are actively synthesizing DNA, RNA, proteins, and other molecules.

Nutrients are abundant — resources like carbon, nitrogen, and energy sources are sufficient to support fast growth.

Population doubles at a constant rate — this doubling time is characteristic of the species and conditions.

What happens during DNA replication?

Unwinding the DNA – The enzyme helicase unwinds the double helix, separating the two strands and forming a replication fork.

Stabilizing the strands – Single-strand binding proteins keep the separated strands from rejoining.

Synthesizing new strands – DNA polymerase adds complementary nucleotides to each original (template) strand:

Adenine (A) pairs with Thymine (T)

Cytosine (C) pairs with Guanine (G)

Leading and lagging strands – One new strand (leading strand) is made continuously, while the other (lagging strand) is made in short fragments called Okazaki fragments, which are later joined by DNA ligase.

Result – Two identical DNA molecules, each with one original strand and one newly synthesized strand (this is called semi-conservative replication).

What happens during organelle reproduction and cytoplasmic division?

Organelle reproduction ensures all cell components are ready.

Cytoplasmic division splits the cell into two independent, functional daughter cells.

What happens during membrane pinching?

membrane pinching physically divides one cell into two during cell division.

What happens during cell division?

Two genetically identical daughter cells, each capable of surviving and functioning independently

What does generation time mean?

generation time = time required for one complete cell division or population doubling

Why do bacteria form spores?

bacteria form spores to survive extreme or unfavorable conditions and ensure their species persists

What triggers spore formation?

when survival is threatened, bacteria form spores to protect their DNA and essential cellular components until conditions improve

What happens during the DNA preparation stage of spore formation?

During the DNA preparation stage of spore formation, the bacterium copies, condenses, and protects its DNA so it can survive in the dormant spore.

What happens when spore septum is formed?

The spore septum separates the forespore from the mother cell.

What happens when the core wall forms?

The core wall forms around the forespore, protecting its DNA and giving the spore structure

What happens when the cortex develops?

The cortex develops around the core, providing heat and chemical resistance to the spore

What is the exosporium?

The exosporium is the outermost protective layer of a spore that helps shield it from harsh environmental conditions

Why are bacterial spores important in biotechnology?

spores’ durability and stability make them valuable for industrial, medical, and research applications

What are the two ways bacteria get nutrients?

Autotrophy – they make their own nutrients from inorganic substances (like CO₂) using energy from sunlight or chemical reactions.

Heterotrophy – they obtain nutrients by consuming organic molecules made by other organisms, living on decaying matter or inside hosts.

What is autotrophy?

Autotrophy is when an organism produces its own food from inorganic substances using energy

What is heterotrophy?

Heterotrophy is when an organism obtains food by consuming other organisms or organic matter

How are autotrophic bacteria used in biotechnology?

Autotrophic bacteria are used in biotechnology to produce chemicals, biofuels, and biodegradable plastics and to fix carbon or clean pollutants through bioremediation

How do autotrophs create their own food?

Autotrophs make food by using energy to convert CO₂ into organic molecules

What are saprobes?

Saprobes are organisms that feed on dead or decaying organic matter

What are parasites?

Parasites are organisms that live on or inside a host and benefit at the host’s expense

What do heterotrophs eat?

Heterotrophs eat organic matter, such as other organisms, decaying material, or host tissues

How are heterotrophs used in biotechnology?

Heterotrophs are used in biotechnology to produce antibiotics, enzymes, vaccines, and fermented food

What are obligate anaerobes?

Obligate anaerobes are organisms that cannot survive in the presence of oxygen

What are facultative bacteria?

Facultative bacteria are bacteria that can grow with or without oxygen, adapting to either condition