Comprehensive Study Notes for Microbiology Midterm (Chapters 1, 3, 4, 5, 6, 7, 8, 11, 12, 13)

Fungi: Molds and Yeasts

Groups of Fungi

Fungi are a diverse group of eukaryotic organisms that include molds and yeasts. They play essential roles in decomposition, nutrient cycling, and can be pathogenic to plants and animals.

• Molds: Multicellular, filamentous fungi that grow as networks of hyphae. Example: Penicillium.

• Yeasts: Unicellular fungi that reproduce by budding or fission. Example: Saccharomyces cerevisiae.

Example: Candida albicans is a yeast that can cause infections in humans.

Biofilms

Definition and Importance

Biofilms are structured communities of microorganisms encapsulated within a self-produced matrix, adhering to surfaces.

• Biofilms protect microbes from environmental stress and antibiotics.

• Common in medical devices (catheters, implants) and natural environments (rocks, teeth).

Example: Dental plaque is a biofilm formed by oral bacteria.

Visible Light and Microscopy

Range of Visible Wavelengths

The visible spectrum of light ranges from approximately 400 nm (violet) to 700 nm (red).

• Microscopes use visible light to illuminate specimens.

Equation:

$400\ \text{nm} \leq \lambda \leq 700\ \text{nm}$

Metabolism: Anabolic and Catabolic Reactions

Definitions and Examples

• Anabolic reactions: Build complex molecules from simpler ones (require energy). Example: Protein synthesis.

• Catabolic reactions: Break down complex molecules into simpler ones (release energy). Example: Glycolysis.

Photoautotrophs and Energy Requirements

Energy and Carbon Sources

• Photoautotrophs use light as an energy source and CO2 as a carbon source.

• Examples: Cyanobacteria, plants, algae.

Isolation Techniques: Streak and Pour Plate Methods

Obtaining Pure Cultures

• Streak plate method: Dilutes bacteria on an agar surface to isolate single colonies.

• Pour plate method: Involves mixing bacteria with molten agar and pouring into a petri dish to separate colonies.

Central Dogma of Gene Function

Flow of Genetic Information

• Central Dogma: DNA → RNA → Protein

• Key enzymes: DNA polymerase (replication), RNA polymerase (transcription), ribosome (translation).

Diagram:

$\text{DNA} \xrightarrow{\text{transcription}} \text{RNA} \xrightarrow{\text{translation}} \text{Protein}$

RNAs in Translation

• mRNA: Messenger RNA, carries genetic code from DNA.

• tRNA: Transfer RNA, brings amino acids to ribosome.

• rRNA: Ribosomal RNA, structural and catalytic component of ribosomes.

Nucleotide Analogs as Mutagens

• Nucleotide analogs mimic normal nucleotides but cause mutations during DNA replication.

• Used in antiviral and anticancer therapies.

Semi-Conservative DNA Replication

• Each new DNA molecule consists of one parental and one newly synthesized strand.

Diagram: Parental DNA → Two daughter DNAs (each with one old and one new strand).

DNA Polymerase Directionality

• DNA polymerase synthesizes DNA in the 5' to 3' direction.

Types of Plasmids

• Fertility (F) plasmids: Confer conjugation ability.

• Resistance (R) plasmids: Carry antibiotic resistance genes.

• Virulence plasmids: Carry genes for pathogenicity.

Lagging and Leading Strands

• Leading strand: Synthesized continuously toward replication fork.

• Lagging strand: Synthesized discontinuously as Okazaki fragments away from fork.

Biotechnology and Genetic Engineering

Reverse Transcriptase

• Enzyme that synthesizes DNA from an RNA template.

• Used in cDNA synthesis and retroviral replication.

Restriction Enzymes

• Cut DNA at specific sequences.

• Blunt ends: Straight cuts.

• Sticky ends: Overhanging single-stranded ends.

PCR (Polymerase Chain Reaction)

• Amplifies specific DNA sequences using cycles of heating and cooling.

• Requires DNA polymerase, primers, nucleotides, and a thermal cycler.

Definition of Biotechnology

• Use of living organisms or their products to modify or improve human health and environment.

DNA Insertion Methods

• Natural: Transformation, transduction, conjugation.

• Artificial: Electroporation, microinjection, gene gun.

Examples of Recombinant DNA Technology

• Reverse transcriptase, restriction enzymes, PCR, electroporation, genetic mapping.

Mutagens and Their Effects

• Mutagens are agents that cause changes in DNA sequence (mutations).

• Types: Chemical, physical, biological.

Prokaryotic Cell Structure and Reproduction

Causative Agent of Tuberculosis

• Mycobacterium tuberculosis is the bacterium that causes tuberculosis.

Arrangement of Prokaryotic Cells

• Binary fission in different planes leads to characteristic arrangements (chains, clusters, pairs).

Asexual Reproduction in Prokaryotes

• Binary fission, budding, fragmentation.

Pathogenic Prokaryotes

• Only a small fraction of prokaryotes cause disease in humans.

Endospores

• Highly resistant, dormant structures formed by some bacteria (e.g., Bacillus, Clostridium).

• Germinate into vegetative cells under favorable conditions.

• Significant in healthcare and food industry due to resistance to heat and chemicals.

Bergey’s Manual

• Comprehensive reference for bacterial classification and identification.

Eukaryotic Microbes: Algae, Fungi, and Protozoa

Algae and Chlorophyll a

• Algae are photosynthetic, contain chlorophyll a, and reproduce sexually via gametes.

Fungal Reproduction

• Fungi reproduce both sexually (spores, gametes) and asexually (budding, fragmentation).

Cytokinesis

• Division of the cytoplasm following nuclear division.

Fungi as Saprobes

• Saprobes obtain nutrients from dead organic matter.

Mitosis and Meiosis

• Mitosis: One diploid nucleus divides to form two diploid nuclei.

• Meiosis I: Each diploid nucleus forms two diploid nuclei.

• Meiosis II: Two diploid nuclei form four haploid nuclei.

• Meiosis has twice as many stages as mitosis.

• DNA replication occurs before prophase.

Arachnids as Disease Vectors

• Mites and other arachnids can transmit diseases to humans and animals.

Viruses, Viroids, and Prions

Prions

• Infectious proteins lacking nucleic acids.

• Cause neurodegenerative diseases (e.g., Creutzfeldt-Jakob disease).

• Differentiated from viruses by absence of nucleic acids.

Virion Structure

• Virion: Complete, infectious virus particle.

• Shape determined by protein coat (capsid).

Viral Genetic Material

• Viruses may contain DNA or RNA, single- or double-stranded.

Bacteriophages

• Viruses that infect bacteria.

Microscopy of Viruses

• Viruses are too small to be seen with light microscopes; electron microscopy is required.

Virus Cultivation

• Embryonated chicken eggs and cell cultures are used to grow viruses in the lab.

Host Specificity

• Viruses infect specific hosts due to receptor compatibility.

Viral Plaque Assays

• Used to quantify viruses by counting clear zones (plaques) formed on bacterial lawns.

Viroids

• Small, circular RNA molecules that infect plants.

• Lack protein coats.

Table: Comparison of Infectious Agents

Agent	Genetic Material	Protein Coat	Cellular Structure	Example
Bacterium	DNA	No	Yes	Escherichia coli
Virus	DNA or RNA	Yes	No	Influenza virus
Viroid	RNA	No	No	Potato spindle tuber viroid
Prion	No	No	No	PrPSc (scrapie prion)

Additional info: Table inferred and expanded for clarity and comparison.