Microbiology Course SIR1001 Quiz

Course Information

• Course Title: Fundamental Microbiology
• Course Code: SIR1001
• Instructors: Dr. Bong Chui Wei, Dr. Lee Choon Weng, Dr. Muhamad Afiq Bin Aziz

Course Synopsis

• Introduction to microbiology concepts & basic techniques
• Microbial evolution, structure, function, and dissemination
• Control and identification of microorganisms
• Exposure to aseptic laboratory techniques for transfer, isolation, and staining of microorganisms

Course Outcomes

• Distinguish various types of microorganisms
• Understand core concepts of microbiology (evolution, diversity, cell structure, function, growth, metabolism)
• Demonstrate basic practical microbiology skills

Lecture Schedule (Wednesday 10-11:50 am)

• Week 1: Foundation of Microbiology (microscope, smear preparation, simple staining)
• Week 2: Microbial evolution, characteristics of prokaryotes & eukaryotes, prokaryotic structure & function
• Week 3: Microbial transport systems & microbial systems biology
• Week 4: Microbial Growth & reproduction (nutrition & culture)
• Week 5: Control of microbial growth (basic techniques)
• Week 6: Techniques for Transfer, Isolation, Culture & Storage of Microorganisms
• Week 7: Differential Staining (endospore, capsule, flagella staining)
• Week 8: Enumeration of Microorganisms
• Week 9: Biochemical tests for bacterial identification
• Week 10: Overview of the Immune System I (innate & adaptive immunity)
• Week 11: History of Virology (basic characteristics of viruses/Comparison of virus & eukaryotes)
• Week 12: Diversity and classification of viruses (lytic cycle/lysogenic cycle)
• Week 13: Microbe-Human Interaction (presentation & discussion)
• Week 14: Practical (specific laboratory methods)

Practical Schedule (Wednesday 2-5 pm, M1 & M2)

• Week 1: Introduction to microscope, smear preparation, simple staining
• Week 2: Gram staining
• Week 3 - 4: Spread plate & Pour plate techniques, transfer techniques, dilution streaking
• Week 5: Membrane filtration technique, Most Probable Number (MPN)
• Week 6-7: Reviews of YouTube videos (CFU guidelines, MPN, MFT)
• Week 8-11: Endospore, Capsule & Flagella Staining
• Week 12: Bacterial and fungal isolation & microbial control
• Week 13: Bacterial chemical tests & bacterial identification
• Week 14: Antimicrobial Susceptibility Test
• Theoretical Test

Evaluation Structure

• 50% Final Examination
• 10% Test (calculation)
• 10% Test (theoretical)
• 5% Lab Report
• 25% Dr. Afiq's Part (details unspecified)
• Test dates unspecified
• Lab report submission date unspecified

Reference Materials

• Talaro, K.P. Foundations in Microbiology: Basic Principles, 10th ed, 2018, McGraw-Hill.
• Johnson, T.R. & Case, C.L. Laboratory Experiments in Microbiology, 12th ed, Pearson Education.
• Madigan M.T., Martinko J.M., Bender K.S., Buckley D.H., Stahl D.A. & Brock T. Brock Biology of Microorganisms, 15th ed, 2019, Benjamin Cummings.

Where to find lecture notes?

•  http://spectrum.um.edu.my/

Class Agreement

• Punctual attendance and QR code scanning for all classes/online classes.
• Mute oneself during online classes
• 80% minimum attendance to sit for final exam
• Provide medical certificate for illness-related absences

Contact Information (for Dr. Lee Choon Weng)

• Room 2.1.4, Block C, Bangunan Genetik dan Mikrobiologi
• Email : [email protected]
• Ext : 5841

Microbiology Overview

• Definition: The study of living organisms that are too small to be seen with the naked eye
• Importance & Functions: nutrient & energy flow, production of foods, drugs, vaccines, decomposition, bioremediation, infectious disease, and pathogens
• Key types of microorganisms: bacteria, archaea, viruses, fungi, protozoa, and algae

Microbiology Disciplines

• Diverse disciplines spanning various aspects of microbes, including genetics, physiology, characteristics, interactions, and uses for different applications like environmental microbiology, bacteriology, protozoology, mycology, virology, parasitology, immunology, & molecular biology

Main Themes in Microbiology Research

• Basic/Pure: Exploratory & conduct for better understanding of fundamental life processes & microbial ecology
• Applied: Apply existing knowledge of microorganisms to develop more practical applications (food, pharmaceutical, genetic engineering, etc.)

Origins of Microorganisms

• First bacteria-like cells existed for at least 3.5 billion years
• Characteristics of ancient cells: small, simple, lacking specialized internal structures for cell functions
• Prokaryotes (before the nucleus): simple cell, lacked a nucleus & other organelles
• Eukaryotes (true nucleus): complex cells, possess a nucleus & other organelles in more modern organisms

The Origin & Evolution of Microorganisms (Phylogeny)

• Relationships between all organisms on Earth and the evolutionary history of organisms from ancestral forms to more derived forms
• Phylogenetic knowledge about ancestor-and-descendant relationship, their similarities & differences

Evolutionary Model of Phylogeny

• Based on differences in nucleotide sequences of rRNA (ribosomal RNA), cell membrane lipid structure & their sensitivity to antibiotics

Common Characteristics of Cells (Prokaryotic & Eukaryotic)

• Cell shape (cubical, spherical, cylindrical)
• Ribosomes (protein synthesis)
• Cytoplasmic membrane (selective permeability)
• Cytoplasm (aqueous mixture of macromolecules)
• Cell wall (structural strength)
• Chromosomes (DNA)
• Cell division (binary fission, mitosis)
• Presence of organelles (only in eukaryotic cells)
• Cell size variation (prokaryotic: 0.2-2.0 µm;eukaryotic: 10-100 µm)

Cell Size & Volume

• Cells of Bacteria & Archaea vary in size (0.2 µm - >700 µm)
• Small cells have a larger ratio of surface area to volume
• Prokaryotic cells tend to grow faster & evolve more rapidly than eukaryotic cells

Cell Membranes

• Cytoplasmic membrane (lies inside cell wall)
• Structure: phospholipid bilayer
• Functions: Physical barrier, transport (passive & active), energy conservation

Passive Processes Across Membranes (Passive Transport)

• Simple Diffusion
• Facilitated Diffusion (with carrier proteins)
• Osmosis (movement of water)

Active Processes Across Membranes (Active Transport)

• Active Transport (protein pumps in plasma membrane required to move substances from low to high concentration
• Group Translocation (substance is chemically altered during process)

Cell Wall

• A semi-ridged structure outside the cell membrane in almost all bacteria
• Negative (thin, wavy outer membrane, LPS, peptidoglycan), positive (thick, smooth outer membrane/no outer membrane, peptidoglycan)

Gram Stain Mechanism

• Differential staining technique based on differences in cell wall structure (gram positive vs gram negative)
• Reaction to crystal violet, iodine & alcohol

Atypical Cell Walls

• Mycoplasmas (lack cell walls)
• Archaebacteria (lack peptidoglycan)

Cytoplasm

• Substance inside plasma membrane
• Contains water, enzymes, proteins, carbohydrates, etc
• Site of metabolic activities

Cytoplasmic Structures

• Ribosomes, Inclusions (storage granules), Chromosomes, Plasmids

Flagella

• Structures for motility in various bacteria (polar, lophotrichous, amphitrichous, peritrichous)
• Comprised of filament, hook, and basal body.

Fimbriae & Pili

• Short filamentous structures for attachment
• Similar in structure to flagella but shorter, typically used for attachment rather than movement
• Pili used in conjugation (genetic exchange)

Eukaryotic Flagella and Cilia

• Projections for cell movement & substances transportation
• Microtubules (9+2 array) structure
• Plasma membrane enclosure

Capsules & Slime Layers

• Polysaccharide or protein layers outside the cell wall
• Function in attachment and protection against phagocytosis

Bacterial Growth

• Growth is defined as an increase in the number of cells
• Various means of reproduction (binary fission, budding, etc.)
• Phases of bacterial growth curve (lag, log, stationary, death)

Generation Time

• Time required for a cell to double
• Exponential growth (population doubles at regular intervals)

Plate Counts

• Method for measuring viable bacterial cells
• Spread preparation
• Pour-plate preparation
• Measuring viable bacteria via colony-forming units (CFU)

Direct Microscopic Count

• Counting cells in a known volume using microscopy
• Used for viable, dead, or total microbes

Microbial Growth Requirements: Physical

• Temperature (psychrophiles, psychrotrophs, mesophiles, thermophiles, hyperthermophiles)
• pH (acidophiles, alkaliphiles)
• Osmotic pressure (halophiles, facultative halophiles)

Microbial Growth Requirements: Chemical

• Sources of carbon, nitrogen, sulfur, phosphorus, etc
• Trace elements, vitamins, and other essential nutrients

Methods for Measurement of Cell Mass

• Direct physical measurement (dry weight, wet weight)
• Direct chemical measurements (total protein, total DNA content, etc.)

Preservation/Maintenance Methods for Microbial Cultures

• Periodic transfer
• Refrigeration
• Lyophilization (freeze-drying)
• Cryopreservation

Sterilization & Disinfection

• Methods of killing/inactivating microbes (heat, radiation, chemical agents)
• Various types of sterilization & disinfection procedures (steam, boiling water, autoclaving, dry heat, filtration, gases, chemicals)

Mode of action of Antimicrobial Agents

• Disruption of cell walls, cell membranes, protein & nucleic acid
• Denaturing proteins, coagulating protein, or disruption of the cell membrane

Special Culture Techniques

• Sterilization procedures for various materials
• Anaerobic jars for cultivating anaerobic microbes
• Candle light jars for cultivating microaerophiles
• Filtration methods

Test your knowledge of the key concepts covered in the SIR1001 microbiology course. This quiz explores various topics, including microbial classification, growth techniques, and testing methods for coliforms. Assess your understanding of the course material and prepare for your evaluations.