- Bacteria & Archaea: Prokaryotic cells without nucleus, smaller and simpler structures. Archaea have unique membrane lipids and often inhabit extreme environments.

### Evolutionary Time of Microbes:

- Microbes are ancient, appearing around 3.5 billion years ago.

- Fundamental to the development of the biosphere and life.

### Theory of Evolution:

- Explains the diversity of life through natural selection and genetic variation.

- Microbes evolve rapidly due to high reproduction rates and mutation rates.

### Importance of Decomposition by Fungi & Bacteria:

- Recycling nutrients back into the ecosystem.

- Breaking down organic matter into simpler substances.

### Uses of Microorganisms:

- Production of antibiotics, enzymes, and hormones.

- Fermentation in food and beverage production.

- Waste treatment and bioremediation.

### Bioremediation:

- Use of microorganisms to clean up contaminated environments (e.g., oil spills, heavy metals).

### Genetic Engineering:

- Manipulating genes to create genetically modified organisms (GMOs) for beneficial purposes.

- Examples: GM yeast for ethanol production, bacteria producing TPA (tissue plasminogen activator), monoclonal antibodies.

### Compounds from GMO:

- Yeast for fermentation

- TPA (thrombolytic agent)

- Monoclonal antibodies for treatments

- Bacterial strains for bioremediation

### Recombinant DNA:

- DNA molecules formed by laboratory methods to bring together genetic material from multiple sources.

### Examples of Diseases from Microorganisms:

- Bacteria: Tuberculosis, cholera

- Viruses: Influenza, HIV

- Fungi: Candidiasis, athlete's foot

- Protozoa: Malaria, amoebiasis

### Communicable vs. Noncommunicable Diseases:

- Communicable: Infectious diseases that can be transmitted (e.g., influenza).

- Noncommunicable: Diseases that cannot be transmitted (e.g., diabetes).

### Examples of Infectious Diseases:

- Influenza, tuberculosis, HIV/AIDS, malaria

### Differentiate among Bacteria, Archaea, and Eukaryotic:

- Bacteria: Prokaryotic, peptidoglycan cell wall.

- Archaea: Prokaryotic, no peptidoglycan, often extremophiles.

- Eukaryotic: Eukaryotic, with nucleus and organelles.

### What do Fungi Produce?

- Enzymes, antibiotics (penicillin), alcohol (yeast fermentation)

Moldy Bread and

Lecture 2: Chapter 3

How to Culture Microorganisms

- Using appropriate media and conditions to grow microorganisms in the lab.

Five I’s

1. Inoculation: Introducing microbes into culture media.

2. Incubation: Providing appropriate conditions for growth.

3. Isolation: Separating individual microbes.

4. Inspection: Observing cultures.

5. Identification: Determining the type of microbe.

#### Physical States of Media

1. Liquid Media: For growth and biochemical testing.

2. Solid Media: For isolation and colony morphology.

3. Semi-solid Media: For motility and fermentation tests.

#### Selective vs. Differential Media

- Selective Media: Inhibit some microbes, allow others (e.g., MacConkey agar for Gram-negative bacteria).

- Differential Media: Distinguish microbes by their biological characteristics (e.g., blood agar for hemolysis).

#### Defined vs. Complex Media

- Defined Media: Exact chemical composition known.

- Complex Media: Contains extracts and digests, composition not precisely known.

#### Incubation Temperature: 37°C

- Optimal temperature for human pathogens.

#### CO2 in Incubation

- Some microbes require CO2 for growth.

#### Different Media Uses

- Various media used for isolation, differentiation, and growth of specific microbes.

#### Hemolysins

- Enzymes that lyse red blood cells, releasing hemoglobin.

#### Clear Zone

- Area where hemolysis has occurred on blood agar.

#### Mycobacterium on Lowenstein-Jensen Medium

- Used for culturing Mycobacterium species.

#### Staphylococcus on Mannitol Salt Agar

- Selective for Staphylococcus due to high salt concentration.

#### Sabouraud’s Agar

- Used for fungal isolation, inhibits bacterial growth.

#### MacConkey Agar

- Isolates Gram-negative enterics, differentiates lactose fermenters.

#### pH Indicator

- Used to detect changes in pH (e.g., phenol red turning yellow in acidic conditions).

#### Isolation Techniques

- Methods to obtain pure cultures (streak, pour, spread plating).

#### Light Microscopes

- Various types used for different applications (e.g., fluorescence microscope for specific antibodies).

#### Stains

- Gram Stain: Differentiates Gram-positive (purple) and Gram-negative (pink) bacteria.

- Endospore Stain: Stains endospores red.

### Lecture 3: Chapter 4

#### Structures All Bacteria Possess

- Cytoplasmic membrane, cytoplasm, ribosomes, genetic material.

#### Structures Some Bacteria Possess

- Flagella, pili, fimbriae, capsules.

#### Major Shapes of Bacteria

- Cocci (spherical), Bacilli (rod-shaped), Spirilla (spiral-shaped).

#### Unusual Shapes of Bacteria

- Star-shaped, rectangular.

#### Bacterial Arrangements

- Diplo (pairs), Strepto (chains), Staphylo (clusters), Tetrads (groups of four).

#### LPS (Lipopolysaccharide)

- Component of Gram-negative bacterial outer membrane, can cause septic shock.

#### Bacterial Movement

- Flagella allow bacteria to move towards or away from stimuli (chemotaxis).

#### Transmission of Bacteria

- Contact, airborne, vector-borne, waterborne.

#### Pleomorphism

- Variability in shape and size among cells of a single species.

#### Biofilm

- Complex community of microbes adhered to surfaces.

#### Quorum Sensing

- Communication between bacterial cells to coordinate activity.

#### Chemotaxis

- Movement towards or away from chemical stimuli.

#### Common Bacterial Structures

1. Cytoplasmic membrane

2. Cytoplasm

3. Ribosomes

#### Additional Bacterial Structures

1. Flagella

2. Pili

3. Fimbriae

4. Capsules

#### Three General Shapes of BacteriaZZ a

- Cocci, Bacilli, Spirilla.

#### Bacterial Arrangements

- Chains, clusters, pairs.

#### Bacterial Flagellum

- Composed of filament, hook, basal body. Moves by rotation, powered by proton motive force.

#### "Run" and "Tumble"

- Run: Smooth movement.

- Tumble: Abrupt, random change in direction.

#### Capsules vs. Biofilms

- Capsules: Protective outer layer.

- Biofilms: Aggregates of microorganisms in a self-produced matrix.

#### B

acterial Chromosome

- Single, circular DNA molecule.

#### Plasmids

- Small, circular DNA molecules independent of the chromosome.

#### Ribosome Structure and Function

- Site of protein synthesis, composed of rRNA and proteins.

#### Bacterial Endospores

- Dormant, resistant structures formed under adverse conditions.

#### Endospores Formed By

- Bacillus and Clostridium species.

#### Why Endospores are Difficult to Destroy

- Resistant to heat, desiccation, chemicals.

#### Characteristics to Identify Unknown Bacteria

- Morphology, staining properties, biochemical tests.

#### Importance of Lipopolysaccharide (LPS)

- Endotoxin triggers immune responses.

#### Koch's Postulates

1. Microorganisms must be found in all diseased organisms.

2. Must be isolated and grown in pure culture.

3. Must cause the disease when introduced to a healthy organism.

4. Must be re-isolated from the experimentally infected host.

### Endosymbiont Theory and Antibiotics

Relevance to Antibiotics:

The endosymbiont theory, which posits that mitochondria and chloroplasts originated from free-living bacteria that were engulfed by ancestral eukaryotic cells, has important implications for antibiotic use. Many antibiotics target bacterial structures or functions that are similar in these organelles, potentially leading to side effects. For instance, antibiotics that inhibit bacterial protein synthesis or DNA replication might also affect mitochondrial function, as these organelles have their own bacterial-like ribosomes and DNA.

- Prokaryotic Cells: Genome is typically a single, circular chromosome located in the nucleoid region.

- Eukaryotic Cells: Genome is organized into linear chromosomes within the nucleus. Mitochondria and chloroplasts also contain their own small, circular genomes.

#### The Central Dogma

The central dogma of molecular biology describes the flow of genetic information within a biological system:

1. DNA → RNA → Protein

- Transcription: DNA is transcribed into RNA.

- Translation: RNA is translated into protein.

#### Micro-RNA Bind to Messenger RNA

Micro-RNAs (miRNAs) are small, non-coding RNA molecules that bind to complementary sequences on messenger RNA (mRNA) molecules, leading to the repression of translation or degradation of the mRNA.

#### Summary of the Flow of Genetic Information in Microbes

1. Replication: DNA is copied to produce two identical DNA molecules.

2. Transcription: A segment of DNA is transcribed into mRNA.

3. Translation: mRNA is translated by ribosomes into a specific sequence of amino acids, forming a protein.

#### Transfer of Amino Acids to Ribosomes

- tRNA (Transfer RNA): Transfers specific amino acids to the ribosome, matching its anticodon with the mRNA's codon during protein synthesis.

#### Sequencing Our Genome and Proteomics

- Genomic Sequencing: Determines the complete DNA sequence of an organism's genome.

- Proteomics: The large-scale study of proteins, particularly their structures and functions, to understand the proteome (the entire set of proteins expressed by a genome).

#### Understanding DNA Replication

- DNA Replication: The process by which a DNA molecule makes a copy of itself. It involves unwinding the double helix, complementary base pairing, and synthesis of the new strands by DNA polymerase.

#### Understanding Types of RNA

1. mRNA (Messenger RNA): Carries genetic information from DNA to ribosomes for protein synthesis.

2. tRNA (Transfer RNA): Brings amino acids to the ribosomes during translation.

3. rRNA (Ribosomal RNA): Forms the core of the ribosome's structure and catalyzes protein synthesis.

4. miRNA (Micro RNA): Regulates gene expression by binding to mRNA molecules.

#### Genes and Genetics

- Genes: Segments of DNA that encode functional products, usually proteins.

- Genetics: The study of genes, genetic variation, and heredity in living organisms.

#### Genotype vs. Phenotype

- Genotype: The genetic makeup of an organism; the specific set of genes it carries.

- Phenotype: The observable physical or biochemical characteristics of an organism, determined by both genotype and environmental factors.

#### Size of Genomes

- Genome sizes vary widely among organisms. For example, bacterial genomes are typically smaller than eukaryotic genomes.

#### Structure of DNA

- DNA is a double helix composed of two strands of nucleotides. Each nucleotide consists of a sugar, a phosphate group, and a nitrogenous base (adenine, thymine, cytosine, or guanine).

#### Differences Between Prokaryotic and Eukaryotic Transcription and Translation

- Prokaryotes: Transcription and translation occur simultaneously in the cytoplasm.

- Eukaryotes: Transcription occurs in the nucleus, and translation occurs in the cytoplasm. mRNA processing (capping, polyadenylation, splicing) is also involved.

#### Steps in Translation

1. Initiation: The ribosome assembles around the target mRNA. The first tRNA is attached at the start codon.

2. Elongation: tRNAs bring amino acids to the ribosome, which are added to the growing polypeptide chain.

3. Termination: The process ends when a stop codon is reached, and the newly formed protein is released.

### Antibiotic Drugs and Their Targets

- Rifampicin: Inhibits RNA polymerase, blocking transcription.

- Tetracycline: Binds to the 30S subunit of the ribosome, preventing the attachment of aminoacyl-tRNA.

- Chloramphenicol: Binds to the 50S subunit of the ribosome, inhibiting peptide bond formation.

- Erythromycin: Binds to the 50S subunit of the ribosome, preventing translocation during protein synthesis.

- Streptomycin: Binds to the 30S subunit, causing misreading of mRNA.

### Mutation and Its Impact

- Mutation: A change in the DNA sequence that can have various effects on an organism.

- Positive Example: Antibiotic resistance in bacteria, which allows them to survive in the presence of antibiotics.

- Negative Example: Mutations in essential genes can be lethal or cause diseases.

### Types of Mutations

- Frameshift Mutation: Insertion or deletion of nucleotides that changes the reading frame of the gene.

- Nonsense Mutation: A change that converts a codon into a stop codon, resulting in premature termination of translation.

- Silent Mutation: A change in the DNA sequence that does not alter the amino acid sequence of the protein.

- Missense Mutation: A change that results in the substitution of one amino acid for another in the protein.

These concepts provide a comprehensive overview of the nature of genetic material, its functions, and its implications for cellular processes and biotechnology.

Attenuation-The process of reducing the virulence of a virus, as done by Pasteur through desiccation of infected rabbit spinal cords to create the rabies vaccine.

Filterable-Refers to the ability of viruses to pass through filters that trap bacteria, indicating their smaller size compared to bacteria.

Viral envelope-A lipid bilayer surrounding the capsid in some viruses, derived from the host cell membrane during viral budding.

Papovaviridae- Family including Human Papillomavirus and Polyomavirus, causing warts, cervical cancer, and diseases in immunocompromised individuals.

Herpesviridae- Family including Herpes Simplex Virus 1, Herpes Simplex Virus 2, Varicella-Zoster Virus, and Epstein-Barr Virus, causing various diseases.

Orthohepadnavirus-Genus including Hepatitis B Virus, causing hepatitis B.

Broad Host Range- Coronaviruses can infect various animal species, including humans, indicating a broad host range.

Lytic Cycle- Results in immediate production of new virions and destruction of the host cell.

Lysogenic Cycle-Involves integration of the viral genome into the host genome, allowing the virus to remain dormant and replicate along with the host cell.

Oncogenic Viruses-Viruses that can transform cells through various mechanisms like oncogene insertion and tumor suppressor gene disruption.

Note