Microbiology Course Overview

Microbiology Course Notes

• Course Instructor: Prof. Dr. Tunç ÇATAL
• Institution: Üsküdar University
• Department: Faculty of Engineering and Natural Sciences, Department of Molecular Biology and Genetics
• Contact Email: [email protected]
• Textbook: Brock Biology of Microorganisms 14E, ISBN-10: 0321897390

Course Material

• Required Readings: Brock, Biology of Microorganisms; Benjamin Cummings, Microbiology: An Introduction
• Lectures: Mondays, 2:40 PM - 3:30 PM
• Labs: Fridays, 9:40 AM - 5:30 PM
• Course Objectives: Provide a brief overview of microbiology concepts. This includes the structure of microorganisms (yeast, fungi, bacteria, viruses), growth, classification, metabolism, and microbial genetics. It covers interactions of microorganisms with their environment and human health. Also covers microbial control and immunology.
• Grading: Midterm 10%, Midterm 2 10%, Lab 10%, Homework 10%, Final Exam 40%
• This course covers scope and history of microbiology, microscope methods and staining techniques, sterilization and disinfection. It also covers characteristics of prokaryotic and eukaryotic cells, microbial growth, and bacterial taxonomy and classification

Course Outline

• Week 1: Scope and History of Microbiology
• Week 2: Microscopy Methods and Staining Techniques
• Week 3: Sterilization and Disinfection
• Week 4: Prokaryotic and Eukaryotic Cells
• Week 5: Microbial Growth and Microbial Cultures
• Week 6: Bacterial Taxonomy and Classification
• Week 7: General Characteristics of Viruses, Classification, Viroids, Prions, Virus-cancer Relation
• Week 8: Microbial Genetics
• Week 9: Applied Microbiology
• Week 10: Microbial Ecology
• Week 11: Antimicrobial Therapy
• Week 12: Host-Microorganism Relationships
• Week 13: Immunology and Diagnostic Microbiology
• Term Project: Various topics (written report and oral presentation)

Exploring the Microbial World (Part I)

• 1.1 Microorganisms (Microbial World):
  • Tiny life forms too small for the human eye
  • Diverse in form and function.
  • Found in all environments supporting life
  • Exist as single-celled organisms or form complex multicellular structures.
  • Often live in communities
• 1.1 Tools for Study:
  • Microscopy allows for visualization
  • Growth media (liquid/solid) provides a structured growth environment
  • Cultures allow for studying organisms.

Exploring the Microbial World (Part II)

• 1.2 Structure and Activities of Microbial Cells:
  • Cells are compartments interacting with the environment and other cells.
  • All cells broadly share common features (cytoplasmic membrane, cytoplasm, ribosomes)
• Prokaryotes vs Eukaryotes:
  • Prokaryotes (Bacteria/Archaea) lack membrane-bound organelles; no nucleus.
  • Eukaryotes (Plants, animals, algae, protists, fungi) contain membrane-bound organelles; nucleus.
• 1.2 Activities of Microbial Cells:
  • Cellular metabolism is essential
  • Enzymes are proteins acting as catalysts
  • Genetic transfer and heredity is a fundamental aspect of metabolism.
  • Transcription uses DNA info and turns it into RNA; translation utilizes RNA to produce proteins

1.3 Microorganisms and the Biosphere

• History of Life on Earth:
  • Earth is 4.6 billion years old.
  • First cells arose (3.8-4.3 billion years ago)
  • Atmosphere initially anoxic, no oxygen.
  • Anaerobic metabolism was the primary source of metabolism until oxygen-producing organisms came about.
• Domains:
  • Bacteria, Archaea, Eukarya (prokaryotes, prokaryotes, eukaryotes) are the three distinct lineages of microbial cells.
• Extremophiles:
  • Life forms adapted to harsh environments
  • (e.g., hot springs, environments with high salt concentration, pH extremes)
• Ecosystems:
  • Includes all organisms and their physical and chemical environment.
  • Microbial activities can alter their environment.

1.4 Impact on Human Society

• Microbes' impact can be both harmful (disease agents) and beneficial (food, agriculture, industry).
• Microbes are agents of disease
• Aspects of agriculture depend on microbial activities
• Microbes can be used in industrial processes
• Food products like cheese, yogurt are impacted by microbes.

Microscopy and the Origins of Microbiology (Part I)

• 1.5 Light Microscopy and the Discovery of Microorganisms:
  • Microbiology began with the development of the microscope.
  • Scientists like Robert Hooke (1635-1703) and Antoni van Leeuwenhoek (1632-1723) were instrumental in early observations.
  • Hooke observed fungi; Leeuwenhoek observed bacteria.

Microscopy and the Origins of Microbiology (Part II)

• Types of Light Microscopes:
  • Bright-field microscopy
  • Phase-contrast microscopy
  • Differential interference contrast (DIC) microscopy
  • Dark-field microscopy -Fluorescence microscopy
  • Compound light microscopes use two sets of lenses for magnification: objectives (10-100x) and oculars (10-30x). The overall magnification is the product of the objective and ocular magnifications.
• Staining Techniques:
  • Staining enhances contrast in microscopy by binding dyes to specific cellular structures.
  • Basic dyes bind to negatively-charged components; acidic dyes bind to positively charged components.
  • Differential stains (e.g., Gram stain) distinguish between cell types based on differences in cell wall structure.

Microscopy and the Origins of Microbiology (Part III)

• Electron Microscopy:
  • Electron microscopes use electrons instead of light.
  • TEMs (Transmission) have high resolution for detailed internal structures.
  • SEMs (Scanning) provide images of surface details.

Microbial Cultivation (Part I)

• 1.9 Pasteur and Spontaneous Generation: This is about Louis Pasteur's experiments that discredited the theory of spontaneous generation.

Microbial Cultivation (Part II)

• 1.10 Koch, Infectious Diseases, and Pure Cultures:
  • Robert Koch experimentally linked microorganisms and infectious diseases
  • Koch's postulates provided a framework for linking specific organisms with specific diseases.
  • Pure cultures were crucial in Koch's work

Microbial Cultivation (Part III)

• 1.11 Discovery of Microbial Diversity:
  • Martinus Beijerinck and Sergei Winogradsky developed techniques like enrichment cultures to study microbes.
  • Understanding microbial life is crucial to understanding ecological interactions.

Molecular Biology and Unity/Diversity of Life

• 1.12 Molecular Basis of Life:
  • Microbiology is fundamental to our understanding of biological processes.
  • Understanding life at a molecular level involved experiments and knowledge from Griffith, and Avery-MacLeod-McCarty.
• 1.13 Woese and the Tree of Life:
  • Woese developed the concept of rRNA sequences.
  • Phylogenetic trees classify organisms based on evolutionary relationships.
• 1.14 Introduction to Microbial Life:
  • Bacteria: usually single cells vary in size (1-10 µm) 30 phylogenetic lineages and numerous species/diverse physiologies and strategies.
  • Archaea: prokaryotes less morphological diversity than bacteria; mostly undifferentiated cells (1-10 µm); five phyla of archaea; historically associated with extreme environments.
  • Eukarya: plants, animals, fungi; began as unicellular organisms; at least six kingdoms vary dramatically in size, shape and physiology;
  • Viruses are obligate parasites. They do not carry out metabolism, replicating inside host cells. Their genomes are diverse (DNA or RNA).
• Additional notes on applied and basic microbiology in the 20th century and modern times are also included here.*