More lectures chapter 1 micro

What is a microbe?

Answer

• A microbe is usually something so small that you need a microscope to see it clearly.

• Examples: bacteria, yeast, and many protists.

What does taxonomy mean?

• Taxonomy = classification and naming. Scientists group organisms and give them names.

• Memory trick: Taxonomy = labels.

What does phylogeny mean?

• Phylogeny = evolutionary relationships. Scientists study how organisms are related through evolution.

• Memory trick: Phylogeny = family tree.

What are the three domains of life?

Answer

• 1. Bacteria 2. Archaea 3. Eukarya Remember:

• Viruses are NOT a fourth domain.

What does LUCA stand for?

• Last Universal common ancestor

• shared feature included DNA , Ribosomes , and genetic code

Which rRNA markers should you know?

• 16S rRNA = Bacteria and Archaea.

• 18S rRNA = Eukarya.

What does PCR do?

• PCR makes many copies of a selected DNA region.

• Memory trick: PCR = copy DNA.

• Sequencing: Determines the order of DNA bases.

• Genetic trees: Help show evolutionary relationships and microbial diversity.

What colors do the two main bacterial groups become?

• Gram-positive = PURPLE.

→ Thick peptidoglycan wall;

• Gram-negative = PINK/RED.

→Thin peptidoglycan wall + outer membrane; PINK/RED.

• Remember: Positive is purple.

What are the main bacterial shapes?

Cocci = round.

Bacilli = rods.

Vibrios = curved rods.

Cccobacillus:

Spirilla = rigid spirals.

Spirochetes = flexible corkscrews.

Major Groups of Microbes

• Prokaryotes: Cells without a nucleus; include Bacteria and Archaea.

• Gram-positive bacteria:

  • Thick cell wall.

  • Stain purple.

• Gram-negative bacteria:

  • Thin cell wall and an outer membrane.

  • Stain pink/red.

• Bacterial shapes:

  • Cocci = round.

  • Rods (bacilli) = rod-shaped.

  • Vibrio = curved rods.

  • Spirilla = rigid spirals.

  • Spirochetes = flexible corkscrews.

• Archaea:

  • Prokaryotes that differ from Bacteria.

  • Have no nucleus and have unique cell membrane chemistry.

  • Some are extremophiles (live in extreme environments).

  • No well-established archaeal pathogens of humans are known.

Eukaryotes

• Eukaryotes: Cells that have a nucleus.

• Protists: Mostly single-celled organisms; some are parasites.

  • Protozoa: Single-celled organisms that may cause disease.

• Fungi: Include microscopic yeasts and molds.

  • Yeast: Single-celled fungi.

  • Mushrooms are fungi too, but they are not microscopic.

• Helminths: Parasitic worms that can live inside a host.

Viruses

• Not alive: Viruses cannot reproduce on their own.

• Acellular: Viruses are not made of cells.

• Main parts:

  • Nucleic acid: Contains genetic material (DNA or RNA).

  • Capsid: Protein coat that protects the genetic material.

  • Envelope: Outer lipid covering found in some viruses.

---

--

Lecture 2 Bacterial growth

1. Review from Lecture 1

Type	Easy definition
Bacteria	Prokaryotes; no nucleus
Archaea	Prokaryotes; no nucleus; different from bacteria
Eukaryotes	Cells with a nucleus
Viruses	Not cells; need a host cell to reproduce

Remember: viruses can contain DNA or RNA. Some have an envelope, but not all.

How bacteria grow Bacteria usually reproduce through binary fission.

2. Bacterial Growth

• Bacterial growth: One cell divides to make two cells.

• Binary fission: The most common way bacteria reproduce.

Four steps of binary fission:

1. DNA replication: The cell copies its DNA.

2. Cell elongation: The cell grows longer.

3. Septum formation: A dividing wall forms in the middle. FtsZ helps.

4. Separation: Two daughter cells form.

Measuring Bacterial Growth

3. Measuring Bacterial Growth

• Spectrophotometer (OD): Measures how cloudy a liquid is. More cloudiness usually means more cells. Fast, but cannot distinguish live cells from dead cells.

• CFU (colony-forming units): Estimates viable, culturable bacteria by counting colonies on agar plates. Takes time, and one colony may come from multiple cells.

• Live/dead staining: Uses fluorescent dyes to help distinguish living and dead cells.

• Hemocytometer: Counts cells in a measured volume but usually cannot tell if cells are alive.

Bacterial Growth Curve

Bacterial Growth Curve

1. Lag phase: Bacteria adjust to their environment.

2. Log phase: Bacteria grow and divide rapidly.

3. Stationary phase: Growth levels off because nutrients become limited and waste builds up.

4. Death phase: The number of viable cells decreases.

Oxygen Requirements

• Obligate aerobe: Must have oxygen.

• Obligate anaerobe: Oxygen harms or inhibits it.

• Facultative anaerobe: Can grow with or without oxygen; often grows better with oxygen.

• Aerotolerant anaerobe: Does not use oxygen but can tolerate it.

• Microaerophile: Needs a low oxygen concentration.

Detox enzymes:

• Superoxide dismutase (SOD): Helps remove harmful superoxide.

• Catalase: Breaks hydrogen peroxide into water and oxygen.

pH Preferences

pH Preferences

• Acidophile: Prefers acidic conditions.

• Neutrophile: Prefers near-neutral pH.

• Alkaliphile: Prefers basic conditions.

• Helicobacter pylori: Can survive in the stomach by producing urease, which helps reduce acidity around the bacterium.

• Microbes adapt to their environments through changes in proteins, membranes, and other cell components.

Temperature Preferences

• Psychrophile: Prefers cold temperatures.

• Mesophile: Prefers moderate temperatures.

• Thermophile: Prefers hot temperatures.

• Hyperthermophile: Prefers extremely hot temperatures.

• Proteins and membranes must remain functional at the organism’s preferred temperature.

• GC content: The percentage of DNA bases that are guanine (G) and cytosine (C). It may be associated with adaptation, but does not alone determine heat stability.

Pressure and Salt

• Barophile (piezophile): A microbe that grows best under high pressure. Pressure can affect membranes, proteins, and DNA-related processes.

• Halophile: A microbe adapted to high-salt environments.

---

Water movement:

• Hypotonic: Water moves into the cell, making it swell (get bigger).

• Isotonic: Water moves in and out equally, so the cell stays the same size.

• Hypertonic: Water moves out of the cell, making it shrink (get smaller).

Lecture 3

Lecture 1: Microbes, classification, and domains of life

• Microbes: Tiny organisms or biological agents, such as bacteria, archaea, fungi, and viruses.

• Classification: Classification means putting organisms into groups based on their characteristics.

• Three domains of life:

  1. Bacteria — prokaryotes without a nucleus.

  2. Archaea — prokaryotes without a nucleus.

  3. Eukarya — organisms with cells that have a nucleus.

• Prokaryotes: Cells without a nucleus.

• Eukaryotes: Cells with a nucleus.

Lecture 2: Bacterial growth, binary fission, environmental

adaptations

1. Bacterial Growth

• Bacterial growth means the number of bacterial cells increases.

2. Binary Fission

• Binary fission is how bacteria reproduce.

• One bacterial cell divides into two new cells.

Four Growth Phases

1. Lag phase: Bacteria adjust to their environment.

2. Log phase: Bacteria grow and divide quickly.

3. Stationary phase: The number of new cells is about equal to the number of cells dying.

4. Death phase: The number of living cells decreases.

4. Environmental Adaptations

• Bacteria respond to their surroundings to survive.

• Temperature: How hot or cold it is.

• pH: How acidic or basic it is.

• Salt: How much salt is present.

• Oxygen: Whether oxygen is available.

• Pressure: The force around the bacteria.

Clinical Case Study: Meningitis

• Meningitis: Inflammation of the membranes around the brain and spinal cord.

• Symptoms: Fever, headache, and stiff neck.

• Cocci: Round-shaped bacteria.

• Diplococcus: Two round bacteria together.

• Rapid diagnosis: Helps doctors choose the correct antibiotics quickly.

Cell Membranes of Prokaryotes

The cell membrane controls what enters and leaves a bacterial cell.

• Phospholipid bilayer: Two layers that make up the membrane.

• Hydrophilic heads: Like water.

• Hydrophobic tails: Avoid water.

• Hopanoids: Help control membrane fluidity.

Four functions:

1. Barrier — controls movement in and out.

2. Energy — contains the electron transport chain in many bacteria.

3. Transport — moves substances.

4. Sensing — detects environmental changes.

Cell Wall

The cell wall gives bacteria shape and helps prevent bursting.

• Peptidoglycan (PG): Made of NAG and NAM sugars connected by peptide cross-links.

• Lysis: When a cell bursts or breaks open.

Important enzymes:

• Lysozyme: Breaks bonds between NAG and NAM.

• Transglycosylase: Builds bonds between sugars.

• Transpeptidase: Builds peptide cross-links.

Gram Stain

Steps:

1. Crystal violet — purple stain.

2. Iodine — helps hold the purple stain.

3. Alcohol — removes purple stain from Gram-negative cells.

4. Safranin — stains Gram-negative cells pink/red.

Antibiotics

• Lysozyme: Breaks cell-wall sugar bonds.

• Penicillin: Blocks transpeptidase activity.

• Vancomycin: Interferes with cell-wall construction.

Antibiotic Resistance

• Efflux: Pumps certain antibiotics out.

• β-lactamase: Breaks down certain antibiotics.

• Mutation/modification: Changes bacterial structures or antibiotic targets.

Mycolic Acid Layer (Acid-Fast Bacteria)

• A waxy layer found in some bacteria.

• Makes it harder for substances to enter.

• Can make nutrient uptake difficult and growth slow.

• Found in Mycobacterium.

• M. tuberculosis causes TB.

• M. leprae causes leprosy.

• Acid-fast stain: Helps identify these bacteria.

Remember: Mycolic acid = waxy layer.

Gram-Negative Outer Membrane

Gram-negative bacteria have an extra outer membrane containing LPS (lipopolysaccharide).

LPS has three parts:

• Lipid A: Causes toxic effects.

• Core polysaccharide: Connects the parts of LPS.

• O antigen: Outer sugar chain.

Periplasmic space: The space between the inner and outer membranes. It contains:

• Peptidoglycan (cell wall)

• Enzymes

• Transport proteins

Transport Across Membranes

• Porins: Channels that allow certain small molecules to pass by passive diffusion.

• Active transporters: Use energy to move substances.

• Capsule: Gooey outer coating that helps retain water and protect bacteria.

Remember:

• Porins = channels.

• Active transport = energy.

• Capsule = protection.

---

Lecture 4 — Prokaryotic Cell Interior

. Lecture 3 Review

• Cell membrane: Controls what enters and leaves the cell.

• Cell wall: Gives shape and prevents bursting.

• NAG + NAM: Build the bacterial cell wall.

• Lysozyme: Breaks down the cell wall.

• Mycolic acids: Waxy layer in some bacteria.

• Gram-negative bacteria: Have an outer membrane with LPS.

• Capsule: Protects bacteria and helps them attach to surfaces.

Case Study: E. coli Lysis Experiment

Lysis = cell breaks open.

• Lysozyme: Breaks the cell wall.

• Detergent: Breaks the cell membrane.

• Chelator: Binds metal ions like Mg²⁺.

• Released contents: DNA, RNA, proteins, ribosomes, and small molecules.

Nucleoid and Genome Organization

• Prokaryotes: Do not have a membrane-bound nucleus.

• Nucleoid: Region where DNA is found.

• Genome: All the DNA in an organism.

• Chromosome: DNA molecule containing genes.

• Mbp: Million base pairs.

• Bacterial genome sizes vary wide which helps bacteria adapt to different environments.

DNA Compaction in the Nucleoid

• DNA has a negative charge.

• Cations: Positive ions, such as Mg²⁺, help reduce repulsion between DNA sections.

• Supercoiling: Twists DNA to make it compact.

• Nucleoid-associated proteins: Help organize and compact DNA.

Central Dogma in Prokaryotes

DNA → RNA → Protein

• Transcription: DNA → RNA.

• Translation: RNA → protein.

• RNA polymerase: Makes RNA from DNA.

• Ribosomes: Make proteins.

• Transcription and translation can happen at the same time in prokaryotes because they have no nucleus separating DNA from ribosomes.

Cytoplasmic Contents

Cytoplasm and Plasmids

• Cytoplasm: Contains proteins, ribosomes, and small molecules.

• Ribosomes: Make proteins.

• Metabolites: Small molecules used in cell reactions.

• Plasmids: Small DNA molecules separate from the main chromosome.

• Plasmids can carry extra genes, such as antibiotic-resistance genes, and can sometimes transfer between bacteria.

Specialized Intracellular Structures – examples

• PHB granules: Store carbon and energy.

• Lipid inclusions: Store fats (lipids).

• Gas vesicles: Help some bacteria float in water.

• Magnetosomes: Contain magnetic iron minerals that help some bacteria orient along magnetic fields.

Key Takeaways

• Prokaryotes have no membrane-bound nucleus or typical membrane-bound organelles.

• DNA is stored in the nucleoid.

• Plasmids carry extra genes.

• Ribosomes make proteins.

• Specialized structures give certain bacteria extra advantages but are not found in all bacteria.

---

Lecture 5 — Metabolism and Energetics

Review of Previous Lectures

Key Metabolic Activities of Microbes

• Metabolism: All chemical reactions in a cell.

• Enzymes: Speed up chemical reactions.

• Redox reactions: Transfer electrons to release or store energy.

• Coupling: Uses energy from one reaction to power another.

• Proton motive force (PMF): Energy stored in a difference in proton concentration across a membrane.

Sources of Energy and Carbon

Energy source = where energy comes from.

• Phototroph: Gets energy from light.

• Chemotroph: Gets energy from chemicals.

• Lithotroph: Gets electrons from inorganic chemicals.

• Organotroph: Gets electrons from organic chemicals

Carbon source = where carbon comes from.

• Autotroph: Gets carbon from CO₂.

• Heterotroph: Gets carbon from organic compounds.

Examples:

• Photoautotroph: Uses light for energy and CO₂ for carbon.

• Chemoorganoheterotroph: Gets energy and electrons from organic chemicals and carbon from organic compounds.

ATP as Energy Currency

• ATP: Main energy-carrying molecule in cells.

• ATP has adenosine and 3 phosphate groups.

• ATP → ADP + Pi: Releases usable energy through hydrolysis.

• Cells use this energy to perform work.

• Energy coupling: Uses energy from ATP breakdown to power reactions that need energy.

Electron Carriers

• NAD⁺: Accepts electrons and becomes NADH.

• NADH: Carries high-energy electrons.

• NADP⁺/NADPH: Another electron carrier pair, often used in biosynthesis.

• Electron carriers help transfer energy during metabolism.

Central Metabolism Pathways

5. Glycolysis

• Breaks 1 glucose (6 carbons) into 2 pyruvate (3 carbons each).

• Happens in the cytoplasm.

• Net gain per glucose: 2 ATP + 2 NADH.

• Does not directly require oxygen.

6. TCA Cycle

• Further breaks down carbon compounds derived from pyruvate.

• Releases CO₂.

• Produces NADH and other energy-carrying molecules.

• NADH can deliver electrons to the electron transport chain.

Electron Transport Chain (ETC) & Oxidative Phosphorylation

• Located in the cytoplasmic membrane of prokaryotes.

• NADH donates electrons to the chain.

• Energy from electron transfer pumps protons across the membrane.

• This creates a proton motive force (PMF).

• ATP synthase uses the PMF to make ATP.

• Oxygen is a common final electron acceptor in aerobic respiration.

Fermentation

• Makes ATP mainly through glycolysis.

• Does not use an electron transport chain.

• Transfers electrons from NADH to an organic molecule, such as pyruvate or a derivative.

• Regenerates NAD⁺ so glycolysis can continue.

• Produces a small amount of ATP.

Examples of products: Lactate, ethanol, acetate, and propionate.

Respiration

• Uses an electron transport chain to help make ATP.

• Aerobic respiration: Uses oxygen as the final electron acceptor.

• Anaerobic respiration: Uses another final electron acceptor, such as nitrate or sulfate.

• Respiration usually produces more ATP than fermentation.

Oxygen Requirements of Microbes

ype	Meaning

Obligate aerobe

Must have oxygen.

Obligate anaerobe

Oxygen harms or kills it.

Facultative anaerobe

Can grow with or without oxygen.

Aerotolerant anaerobe

Does not use oxygen but tolerates it.

Microaerophile

Needs low levels of oxygen.

Catalase and SOD: Enzymes that protect cells from harmful oxygen-related compounds.

Key Takeaway

• ATP: Provides energy for cell activities.

• NADH: Carries high-energy electrons.

• Glycolysis + fermentation: Produces a small amount of ATP.

• Respiration: Uses the electron transport chain (ETC) to produce more ATP.

• Oxygen: The most common, high-energy-yielding final electron acceptor.

• Anaerobic respiration: Uses other electron acceptors, such as nitrate or sulfate, instead of oxygen.