Riya Kodukula Chapter 2: Microbiology

What is spontaneous generation?

Belief that lifeless substances can give rise to living organisms.

What was John Needham’s experiment?

supported the theory of spontaneous generation by boiling broth, sealing it, and then observing the growth of microorganisms

What was Needham’s hypothesis?

Microorganisms come into existence “spontaneously” from clear air

How did Pasteur disprove Needham using the heated air experiment?

demonstrated that microorganisms in the air caused broth to spoil, not a "vital force" in the air

What was Pasteur’s Swan-Neck flask experiment?

demonstrated that microbial life does not arise spontaneously but is carried by airborne dust and particles, disproving the theory of spontaneous generation

What is the Germ Theory of Disease?

microorganisms are capable of living in the body and can cause illness

What was Pasteur’s Yeast experiment?

why does wine go bad

What are the steps to the yeast experiment?

1. poured grape juice into flask

What was Pasteur’s conclusion from the yeast experiment?

life forms, including yeast, evolve from pre-existing living things and that microorganisms are responsible for processes like fermentation and spoilage

What was the thought behind the bacteria experiment?

What are the steps to Pasteur’s bacteria experiment?

filling a swan-neck flask with nutrient broth, boiling the broth to sterilize it, and allowing it to cool

What was Pasteur’s conclusion from the bacteria experiment?

life does not arise from non-living matter through spontaneous generation; instead, microorganisms from the air cause contamination, spoilage, and disease

What are Koch’s postulates?

1. Constant Association:

   The microorganism must be present in all cases of the disease and absent in healthy individuals. 

2. Isolation and Culture:

   The microorganism must be isolated from the diseased host and grown in pure culture. 

3. Re-infection:

   The pure culture of the microorganism must cause the same disease when inoculated into a healthy, susceptible host. 

4. Re-isolation:

   The microorganism must be re-isolated from the experimentally infected host and confirmed to be the same as the original isolate. 

What disease was killing the cows that Koch observed?

anthrax

What was the first step in Koch’s experiment?

observe that the microorganism is present in all diseased individuals and absent from healthy ones, establishing a correlation between the microorganism and the disease

What was the second step in Koch’s experiment?

the suspected pathogen must be isolated from the diseased host and grown in pure culture in the laboratory

What was the fourth step in Koch’s experiment?

the microorganism must be re-isolated from the inoculated, diseased host and confirmed to be identical to the original microorganism that was isolated from the first diseased host

How did Koch confirm his observations?

fulfilling a set of criteria known as Koch's postulates

What is the metric system?

a global standard for measurement based on powers of 10, using base units like the meter for length, the gram for mass, and the liter for volume, along with prefixes (like kilo- for 1,000 and centi- for 1/100) to create larger or smaller units

Why is measurement important in biology?

it quantifies observations, enabling scientists to validate hypotheses, achieve reproducibility, and develop reliable models of biological processes

How long is a centimeter?

0.393701 in

How long is a millimeter?

0.0393701 in

How long is a micrometer?

3.93701e-5 in

How long is a nanometer?

3.93701e-8 in

How are measurements used in biotechnology?

provide essential quantitative data for accurate, reproducible, and comparable experimental results

What are eukaryotic cells used for in biotechnology?

Eukaryotic cells are used in biotechnology to produce complex proteins (like antibodies, hormones, and vaccines) because they can perform proper folding and modifications that bacteria can’t. They’re also used in drug testing, cell therapies (like stem cells and CAR-T), and industrial fermentation.

What is a nucleus?

Control center of a eukaryotic cell that stores DNA and directs activities

What is the mitochondria?

The “powerhouse of the cell,” since they convert food into usable energy

What are ribosomes?

Small cellular structures made of RNA and proteins that build proteins by linking amino acids together according to genetic instructions

What is the endoplasmic reticulum?

Endoplasmic Reticulum (ER): A network of membranes in eukaryotic cells; the rough ER makes proteins (with ribosomes) and the smooth ER makes lipids and helps detoxify.

What is the golgi apparatus?

A stack of flattened membranes in eukaryotic cells that modifies, sorts, and packages proteins and lipids for transport or secretion.

What are lysosomes?

Membrane-bound organelles containing digestive enzymes that break down waste, damaged cell parts, and foreign substances.

What are the key features of prokaryotic cells?

• No nucleus – DNA is free-floating in the cytoplasm (nucleoid region).

• No membrane-bound organelles – lack mitochondria, ER, Golgi, etc.

• Small and simple – usually 0.1–5 µm in size.

• Cell wall present – in most, for shape and protection.

• Ribosomes – present but smaller (70S) than in eukaryotes.

• Reproduction – mostly by binary fission (asexual).

• Examples – bacteria and archaea.

How are prokaryotic cells used in biotechnology?

• Genetic engineering: E. coli is commonly used to produce insulin, growth hormones, and vaccines.

• Bioremediation: Certain bacteria break down pollutants, oil spills, and toxic waste.

• Fermentation: Bacteria are used in making yogurt, cheese, vinegar, and other foods.

• Industrial production: Produce enzymes, antibiotics, biofuels, and bioplastics.

• Research tools: Model organisms for studying gene function and molecular biology.

What are viruses?

Non-living infectious particles made of genetic material (DNA or RNA) enclosed in a protein coat; they replicate only inside a host cell.

How are viruses used in biotechnology?

• Gene therapy: Modified viruses deliver healthy genes to replace defective ones.

• Viral vectors: Used to insert foreign DNA into host cells for research and medicine.

• Vaccines: Weakened or modified viruses help trigger immunity (e.g., adenovirus-based COVID-19 vaccines).

• Phage therapy: Bacteriophages target and kill harmful bacteria.

• Protein production: Engineered viruses make therapeutic proteins or antibodies.

What are algae?

Simple, mostly aquatic, photosynthetic organisms (can be unicellular or multicellular) that produce oxygen and form the base of many food chains.

How are algae used in biotechnology?

Used for biofuel production (algal biodiesel), carbon capture, wastewater treatment, producing food additives (agar, carrageenan, alginate), pharmaceuticals, nutraceuticals (omega-3 fatty acids), and as a sustainable protein source.

What are protozoa?

Single-celled, eukaryotic organisms that live in water or as parasites; they move using cilia, flagella, or pseudopodia and feed on organic matter.

How are protozoa used in biotechnology?

Used in biotechnology as model organisms for studying cell biology, genetics, and disease; in wastewater treatment to consume bacteria; in bioremediation to degrade pollutants; and in drug testing for understanding parasitic diseases like malaria.

What are cyanobacteria?

Photosynthetic prokaryotes (also called blue-green algae) that produce oxygen, fix nitrogen, and are important for ecosystems and biotechnology applications.

How are cyanobacteria used in biotechnology?

Used in biotechnology for producing biofuels (hydrogen, ethanol, biodiesel), natural pigments, and biofertilizers (nitrogen fixation); in wastewater treatment; as a source of pharmaceuticals and nutraceuticals; and in carbon capture for reducing greenhouse gases.

What are fungi?

Eukaryotic organisms that can be unicellular (yeasts) or multicellular (molds, mushrooms); they absorb nutrients from organic matter and play key roles as decomposers, symbionts, or pathogens.

How are fungi used in biotechnology?

Used in biotechnology to produce antibiotics (penicillin), enzymes, alcohol (yeast fermentation), organic acids, biofuels, and food products (bread, cheese, beer); also applied in bioremediation and as model organisms in genetics research.

What is bacillus?

A genus of rod-shaped, Gram-positive bacteria, some of which form resistant endospores; species are found in soil, water, and as part of the normal microbiota, with some used in industry and others causing disease.

What is coccus?

A spherical or oval-shaped bacterium, which may occur singly or in characteristic arrangements such as pairs (diplococci), chains (streptococci), clusters (staphylococci), or groups of four (tetrads).

What is staphylococcus?

A genus of Gram-positive, round-shaped bacteria that typically form grape-like clusters; some species are harmless skin microbiota, while others cause infections such as boils, pneumonia, and food poisoning.

What spiral?

A type of bacterial shape characterized by curves, coils, or twists; includes spirilla (rigid spirals), spirochetes (flexible spirals), and vibrios (comma-shaped).

How do spirochetes move?

Move by using internal flagella called axial filaments, which run between the cell wall and outer membrane, allowing a corkscrew-like motion through viscous environments.

Why does bacterial shape matter?

Matters because it influences nutrient uptake, motility, surface attachment, ability to evade the immune system, and adaptation to environments; it also helps in bacterial identification and classification.

Why does biotechnology care about the shape of bacteria?

Because it affects how bacteria grow, move, form biofilms, and interact with hosts or environments. Shape can influence efficiency in fermentation, drug delivery, genetic engineering, and bioremediation, making it important for selecting and optimizing bacterial strains.

What is the flagella?

Long, whip-like appendages made of protein that enable movement in many bacteria and some eukaryotic cells by rotating or undulating to propel the cell.

What is the cell wall?

A rigid outer layer surrounding the cell membrane that provides shape, strength, and protection; in bacteria, it is made of peptidoglycan, while in plants it is mainly cellulose, and in fungi chitin.

What is cytoplasm?

The gel-like substance inside a cell that surrounds organelles, composed mostly of water, salts, and proteins; it is the site of many metabolic reactions and provides structural support.

What is the plasma membrane?

A selectively permeable phospholipid bilayer that surrounds the cell, controlling the movement of substances in and out while maintaining homeostasis and enabling cell communication.

What are plasmids?

Small, circular DNA molecules found in many bacteria (and some eukaryotes) that replicate independently of chromosomal DNA and often carry beneficial genes, such as those for antibiotic resistance.

What is the nucleiod?

The irregularly shaped region in a prokaryotic cell where the single, circular chromosome (DNA) is located, not enclosed by a membrane.

What are pilli?

Hair-like surface structures on bacteria that help in attachment to surfaces, exchange of genetic material (conjugation), and sometimes movement.

How are bacterial structures targeted in biotechnology?

• Cell wall – Targeted by antibiotics (e.g., penicillin) and engineered enzymes for breaking down pathogens or in food processing.

• Plasma membrane – Used for drug delivery studies and to test antimicrobial peptides.

• Ribosomes – Targeted in protein production systems or by antibiotics to stop bacterial growth.

• Plasmids – Engineered as vectors to insert and express foreign genes.

• Pili/flagella – Explored for developing vaccines, antimicrobial agents, and controlling biofilm formation.

• Nucleoid/DNA – Manipulated in genetic engineering to create strains for insulin, enzymes, and biofuels.

What is a cell envelope?

The protective outer layer of a bacterial cell, consisting of the plasma membrane, cell wall, and (in some species) an outer membrane; it provides structure, protection, and selective transport.

What is the capsule?

A thick, sticky outer layer made of polysaccharides (or proteins) found in some bacteria; it protects against drying, helps evade the immune system, and aids in attachment to surfaces.

What are the functions of the cell capsule?

• Protects bacteria from drying (desiccation).

• Shields against host immune defenses like phagocytosis.

• Helps bacteria attach to surfaces and form biofilms.

• Stores nutrients and helps resist toxic substances.

What is the cell wall made up of?

• Bacteria: Mainly peptidoglycan (sugar + amino acid polymer).

• Plants: Primarily cellulose (polysaccharide).

• Fungi: Chitin (polysaccharide).

• Algae: Cellulose, glycoproteins, or sometimes silica.

What is peptidoglycan?

A mesh-like polymer of sugars (N-acetylglucosamine and N-acetylmuramic acid) cross-linked by short peptide chains; it forms the rigid structure of bacterial cell walls, providing strength and shape.

Describe the peptidoglycan layer on gram-negative bacteria?

Thin and located between the inner plasma membrane and the outer membrane; only 1–2 layers thick, making it much weaker than in Gram-positive bacteria. Surrounded by the periplasmic space and protected by the outer membrane containing lipopolysaccharides (LPS).

Describe the peptidoglycan layer on gram-positive bacteria?

Thick and multilayered (up to 40 layers), making up most of the cell wall. Contains teichoic acids for stability and rigidity, and is directly exposed to the environment since there is no outer membrane.

What is the cell membrane made up of?

Made up of a phospholipid bilayer with embedded proteins, cholesterol (in eukaryotes), and carbohydrates; this structure gives it fluidity, selective permeability, and allows communication and transport.

What do proteins on the cell membrane do?

Perform key functions such as transporting molecules across the membrane, acting as receptors for signaling, providing structural support, catalyzing reactions (enzymes), and helping cells recognize and interact with each other.

Why does bacteria need to be stained?

Because they are mostly transparent under a light microscope; staining increases contrast, allows visualization of shape and arrangement, and helps differentiate types (e.g., Gram-positive vs Gram-negative) for identification and diagnosis.

Describe the Simple Stain Technique

A method where a single basic dye (e.g., methylene blue, crystal violet, safranin) is applied to a bacterial sample to add contrast. It makes cells visible under a microscope, showing their shape, size, and arrangement, but not distinguishing between types.

Describe the Negative Stain Technique

A method where an acidic dye (e.g., India ink, nigrosin) stains the background instead of the bacteria. Cells remain clear and unstained, outlined against a dark background, which helps observe shape, size, and capsules without heat-fixing or distortion.

What are the steps for gram-staining?

• Crystal violet – Primary stain that colors all cells purple.

• Iodine – Mordant that binds with crystal violet to form a complex inside cells.

• Alcohol/acetone – Decolorizer; removes dye from Gram-negative cells but not Gram-positive.

• Safranin – Counterstain; colors Gram-negative cells pink/red, while Gram-positive remain purple.

How is gram-staining used in biotechnology?

Used to quickly identify and classify bacteria as Gram-positive or Gram-negative, guiding antibiotic selection, monitoring contamination in fermentation/industrial processes, ensuring quality control in pharmaceuticals and food production, and supporting microbial research and genetic engineering.

What are two ways life propagates itself?

• Asexual reproduction – Single organism reproduces without gametes (e.g., binary fission, budding, mitosis).

• Sexual reproduction – Involves gametes (sperm and egg), genetic recombination, and produces genetically diverse offspring.

What is binary fission?

A form of asexual reproduction in prokaryotes where one cell duplicates its DNA and divides into two identical daughter cells.

What happens during the growth phase?

The period in a cell cycle when a cell increases in size, produces proteins and organelles, and duplicates its DNA in preparation for cell division.

What happens during DNA replication?

The process where the double-stranded DNA molecule unwinds, and each strand serves as a template for building a new complementary strand, resulting in two identical DNA molecules.

What happens during organelle reproduction and cytoplasmic division?

Organelle reproduction – Cell organelles like mitochondria and ribosomes duplicate to ensure each daughter cell has enough machinery to function.

Cytoplasmic division (cytokinesis) – The cytoplasm splits after nuclear division, forming two separate daughter cells, each with its own nucleus and organelles.

What happens during membrane pinching?

During the final step of cell division, the plasma membrane constricts inward (cleavage furrow in eukaryotes or septum in bacteria) until the cell splits into two daughter cells, each enclosed by its own membrane.

What happens during cell division?

The process where one parent cell splits into two daughter cells. It includes DNA replication, organelle duplication, and cytoplasmic division, ensuring each daughter cell receives genetic material and the cellular components needed to function.

What does generation time mean?

The time it takes for a microbial population (or a single cell) to double in number through cell division under given conditions.

Why do bacteria form spores?

To survive harsh conditions such as heat, radiation, chemicals, and lack of nutrients. Spores are highly resistant, dormant structures that allow bacteria to persist until conditions become favorable again.

What triggers spore formation?

When bacteria face stressful or unfavorable conditions such as nutrient depletion, extreme temperatures, desiccation, radiation, or exposure to toxic chemicals.

What happens during the DNA preparation stage of spore formation?

The bacterial DNA is replicated and positioned into a specific region of the cell, ensuring that the developing spore receives a complete copy of the genetic material before protective layers form.

What happens when spore septum is formed?

A partition of plasma membrane forms around one copy of the bacterial DNA, separating it from the rest of the cell and creating the initial compartment that will develop into the endospore.

What happens when the core wall forms?

A protective layer develops around the forespore’s DNA, enclosing it and helping create the spore’s structure; this layer later contributes to the spore’s resistance and stability.

What happens when the cortex develops?

A thick layer of specialized peptidoglycan forms between the core wall and spore coat, helping the spore dehydrate and providing heat and chemical resistance.

What is the exosporium?

The outermost, thin, protein-rich covering of some bacterial spores that provides an additional protective barrier and helps the spore interact with its environment.

Why are bacterial spores important in biotechnology?

• Sterilization testing – Spores test whether sterilization methods (autoclaving, radiation, chemicals) are effective.

• Probiotics & agriculture – Spore-forming bacteria (e.g., Bacillus) survive processing and improve soil fertility or gut health.

• Drug delivery – Engineered spores can carry vaccines or therapeutic molecules.

• Bioremediation – Spores persist in harsh environments while breaking down pollutants.

• Industrial production – Provide robust strains for enzyme, antibiotic, and biofuel manufacturing.

What are the two ways bacteria get nutrients?

• Autotrophy – Make their own food (e.g., photosynthetic or chemosynthetic bacteria).

• Heterotrophy – Obtain food by consuming organic matter from the environment or host.

What are the two ways bacteria get nutrients?

• Autotrophy – Make their own food (e.g., photosynthetic or chemosynthetic bacteria).

• Heterotrophy – Obtain food by consuming organic matter from the environment or host.

What is autotrophy?

A mode of nutrition where organisms produce their own food from inorganic sources (like CO₂, water, and minerals) using energy from sunlight (photosynthesis) or chemical reactions (chemosynthesis).

What is heterotrophy?

A mode of nutrition where organisms obtain energy and carbon by consuming organic compounds from other organisms, rather than making their own food.

How are autotrophic bacteria used in biotechnology?

• Carbon capture: Used to fix CO₂ and reduce greenhouse gases.

• Biofuel production: Cyanobacteria engineered to produce ethanol, hydrogen, or biodiesel.

• Bioplastics: Produce biodegradable polymers from CO₂.

• Bioremediation: Remove pollutants by metabolizing inorganic compounds.

• Food & feed supplements: Source of proteins, vitamins, and pigments (e.g., spirulina).

How do autotrophs create their own food?

• Photosynthesis: Use sunlight, CO₂, and water to produce glucose and oxygen.

• Chemosynthesis: Use energy from chemical reactions (e.g., oxidizing sulfur, nitrogen, or iron compounds) to make organic molecules from CO₂.

What are saprobes?

Organisms (often bacteria or fungi) that feed on dead or decaying organic matter by secreting enzymes to break it down and then absorbing the nutrients.

What are parasites?

Organisms that live on or inside a host, obtaining nutrients at the host’s expense and often causing harm or disease.

What do heterotrophs eat?

Organic compounds such as carbohydrates, proteins, and lipids, which they obtain from other organisms (living or dead) for energy and growth.

How are heterotrophs used in biotechnology?

• Fermentation: Yeasts and bacteria produce alcohol, bread, yogurt, cheese, and vinegar.

• Antibiotics & drugs: Fungi and bacteria synthesize antibiotics (e.g., penicillin) and pharmaceuticals.

• Enzyme production: Microbes make industrial enzymes for detergents, food, and biofuels.

• Bioremediation: Break down organic pollutants and waste.

• Biomass & protein: Used to create single-cell protein for animal feed and human nutrition.

What are obligate anaerobes?

Bacteria that cannot survive in the presence of oxygen; they obtain energy through anaerobic respiration or fermentation.