Comprehensive Study Guide for Microbiology Exam #1

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Microbial Classification and Evolution

Major Groups of Organisms

Microbiology studies a diverse range of organisms, including bacteria, archaea, fungi, protozoa, algae, and viruses. Each group possesses unique characteristics that distinguish them from one another.

Bacteria: Prokaryotic, unicellular, possess peptidoglycan cell walls.
Archaea: Prokaryotic, lack peptidoglycan, often inhabit extreme environments.
Fungi: Eukaryotic, can be unicellular (yeasts) or multicellular (molds), have chitin cell walls.
Protozoa: Eukaryotic, unicellular, often motile.
Algae: Eukaryotic, photosynthetic, can be unicellular or multicellular.
Viruses: Acellular, require host cells for replication, not included in phylogenetic trees.

Additional info: Viruses are excluded from phylogenetic trees because they lack cellular structure and do not share common ancestry with cellular life forms.

Carolus Linnaeus and Modern Classification

Carolus Linnaeus developed the binomial system of nomenclature and grouped organisms based on visible characteristics. Today, classification relies on genetic similarities, reflecting evolutionary relationships.

Binomial Nomenclature: Each organism is given a two-part scientific name (Genus species).
Modern Classification: Uses molecular data (e.g., DNA sequencing) to group organisms by shared genetic traits.

Archaea: Prokaryotic or Eukaryotic?

Archaea are prokaryotic, lacking a nucleus and membrane-bound organelles. However, their genetic and biochemical features are more similar to eukaryotes than to bacteria.

Evidence: Ribosomal RNA sequences and certain metabolic pathways are shared with eukaryotes.

Biochemical Tests and Phylogenetic Trees

Biochemical tests identify microbial species based on metabolic capabilities. Phylogenetic trees illustrate evolutionary relationships among organisms.

Biochemical Tests: Used to differentiate species by their enzymatic activities.
Phylogenetic Trees: Visual representations of evolutionary history, constructed using genetic data.

Evolutionary Principles

Natural selection drives evolution by favoring traits that enhance survival and reproduction.

Natural Selection: Process where organisms with advantageous traits are more likely to survive and reproduce.
Evolution: Change in the genetic composition of populations over time.

Alcanivorax borkumensis and Resident Microbiota

Alcanivorax borkumensis is a bacterium important for biodegradation of oil spills. Resident microbiota in the gut contribute to health by aiding digestion and preventing pathogen colonization.

Example: Alcanivorax borkumensis is used in bioremediation.
Resident Microbiota: Non-pathogenic bacteria that maintain gut health.

Cell Structure and Function

Prokaryotic vs. Eukaryotic Cells

Cells are classified as prokaryotic or eukaryotic based on structural features.

Prokaryotic: No nucleus, no membrane-bound organelles, includes bacteria and archaea.
Eukaryotic: Nucleus present, membrane-bound organelles, includes fungi, protozoa, algae, plants, and animals.
Acellular: Lacking cellular structure (e.g., viruses).

Cell Wall Composition

Bacterial cell walls vary in composition, affecting staining and pathogenicity.

Gram-positive: Thick peptidoglycan layer, contains teichoic acids.
Gram-negative: Thin peptidoglycan layer, outer membrane with lipopolysaccharides.
Mycolic Acid (Acid Fast): Waxy cell wall, characteristic of Mycobacterium.

Teichoic Acid: Contributes to cell wall stability and is associated with MRSA resistance.

Cell Theory and Key Experiments

Cell Theory: All living things are composed of cells; cells are the basic unit of life.
Endosymbiotic Theory: Eukaryotic organelles originated from symbiotic prokaryotes.
Germ Theory of Disease: Microorganisms cause disease.
Louis Pasteur's Swan Neck Flask Experiment: Disproved spontaneous generation by showing that sterilized broth remained free of microbes unless exposed to air.
Ignaz Semmelweis: Observed that handwashing reduced puerperal fever.
John Snow: Traced cholera outbreak to contaminated water.
Joseph Lister: Demonstrated antiseptic techniques; Listerine named after him.
Koch's Postulates: Criteria for establishing a causal relationship between a microbe and a disease.

Cell Morphology and Arrangements

Shapes: Cocci (spherical), bacilli (rod-shaped), spirilla (spiral).
Arrangements: Chains (strepto-), clusters (staphylo-), pairs (diplo-).

Osmosis and Osmotic Pressure

Osmosis is the movement of water across a semipermeable membrane. Cells respond to osmotic pressure differently depending on their environment.

Hypertonic: Water leaves the cell; cell shrinks.
Isotonic: No net water movement; cell remains unchanged.
Hypotonic: Water enters the cell; cell may swell or burst.

Inclusions and Endospores

Inclusions: Storage granules for nutrients (e.g., glycogen, polyphosphate).
Endospores: Dormant, resistant structures formed by Bacillus and Clostridium species.
Vegetative Cell: Active, growing form.
Importance: Endospores survive harsh conditions.

Membrane Transport

Simple Diffusion: Movement of molecules from high to low concentration.
Facilitated Diffusion: Uses transport proteins.
Active Transport: Requires energy (ATP).

Ribosomes

Prokaryotic Ribosomes: 70S (30S + 50S subunits).
Eukaryotic Ribosomes: 80S (40S + 60S subunits).
Clinical Importance: Antibiotics target prokaryotic ribosomes without affecting eukaryotic ones.

Endomembrane System

Includes the endoplasmic reticulum, Golgi apparatus, vesicles, and lysosomes. Responsible for protein and lipid trafficking in eukaryotic cells.

Biomolecules and Chemical Bonds

Covalent, Ionic, and Hydrogen Bonds

Covalent Bonds: Atoms share electrons.
Polar Covalent Bonds: Unequal sharing of electrons.
Ionic Bonds: Transfer of electrons; forms charged ions.
Hydrogen Bonding: Weak attraction between hydrogen and electronegative atoms.

Functional Groups, Hydrophilic, and Hydrophobic

Functional Groups: Specific groups of atoms (e.g., hydroxyl, carboxyl) that determine chemical properties.
Hydrophilic: Water-loving, polar.
Hydrophobic: Water-fearing, nonpolar.

Macromolecules

Glucose: Monosaccharide, energy source.
Starch vs. Glycogen vs. Cellulose: Starch (plant storage), glycogen (animal storage), cellulose (plant structure).
Triglyceride: Glycerol + 3 fatty acids.
Phospholipid: Glycerol, 2 fatty acids, phosphate group; forms bilayer.
Amino Acids: Building blocks of proteins; peptide bonds formed by dehydration reaction.
Steroids: Four fused rings; cholesterol is a key example.
HDL vs. LDL: HDL (good cholesterol), LDL (bad cholesterol); statins lower LDL.

Protein Structure

Primary: Sequence of amino acids.
Secondary: Alpha helices and beta sheets.
Tertiary: 3D folding.
Quaternary: Multiple polypeptides.
Cystic Fibrosis: Caused by misfolded protein.

Dehydration Reaction vs. Hydrolysis

Dehydration: Forms bonds by removing water.
Hydrolysis: Breaks bonds by adding water.

Table: Functions of Macromolecules (from Table 7.1)

Macromolecule	Function
Carbohydrates	Energy storage, structural support
Lipids	Energy storage, membrane structure
Proteins	Enzymes, structural, transport
Nucleic Acids	Genetic information storage and transfer

Additional info: Functions inferred from standard textbook content.

Metabolism and Enzymes

Deoxyribose vs. Ribose

Deoxyribose: Sugar in DNA, lacks an oxygen atom at the 2' position.
Ribose: Sugar in RNA, has an OH group at the 2' position.

Endergonic vs. Exergonic Reactions

Endergonic: Requires energy input.
Exergonic: Releases energy.

Reaction Pathway (Diagram)

Shows energy changes during a reaction, including activation energy and overall energy change.

NAD+/NADH and FAD/FADH2

NAD+ / NADH: Electron carriers in metabolism.
FAD / FADH2: Electron carriers in metabolism.

ATP: Structure and Function

ATP: Adenosine triphosphate, main energy currency.
Formation: Substrate-level and oxidative phosphorylation.
Function: Powers cellular reactions by transferring phosphate groups.

Equation:

Enzymes

Function: Catalyze biochemical reactions by lowering activation energy.
Holoenzyme: Complete enzyme with cofactor.
Apoenzyme: Protein part of enzyme without cofactor.
Competitive Inhibition: Inhibitor binds active site.
Non-competitive Inhibition: Inhibitor binds elsewhere, changing enzyme shape.

Microbial Metabolism

Glycolysis, Krebs Cycle, Electron Transport Chain

Glycolysis: Occurs in cytoplasm; breaks down glucose to pyruvate.
Krebs Cycle: Occurs in cytoplasm (prokaryotes) or mitochondria (eukaryotes).
Electron Transport Chain: Located in plasma membrane (prokaryotes) or mitochondrial inner membrane (eukaryotes).

Fermentation and Lactic Acid Formation

Fermentation: Anaerobic process; regenerates NAD+.
Lactic Acid Formation: Occurs in muscle cells and some bacteria.

Microbial Growth and Genetics

Biofilms and Quorum Sensing

Biofilms: Communities of microbes attached to surfaces.
Quorum Sensing: Cell-to-cell communication regulating gene expression.

Binary Fission

Binary Fission: Asexual reproduction in prokaryotes.

Genetics and Inheritance

Gregor Mendel: Father of genetics; studied inheritance in pea plants.
Chromosomal Theory of Inheritance: Genes are located on chromosomes.
Hammerling Experiments: Demonstrated genetic material in nucleus.

Nucleotide Structure and DNA

Pyrimidine vs. Purine: Pyrimidines (C, T, U) are single-ring; purines (A, G) are double-ring.
Nucleotide Linkage: Phosphodiester bonds connect nucleotides.
DNA Structure: Double helix; bases held by hydrogen bonds.
Chargaff's Rules: %A = %T, %C = %G.
Denaturing DNA: Disrupts hydrogen bonds, separates strands.
DNA vs. RNA: DNA has deoxyribose, thymine; RNA has ribose, uracil.
tRNA Structure: Cloverleaf shape; carries amino acids.

Chromatin Structure

Centromere: Region joining sister chromatids.
Histone Proteins: Package DNA.
Nucleosome: DNA wrapped around histones.
Solenoid: Higher-order chromatin structure.
Plasmid DNA: Small, circular DNA in bacteria.

Bacterial Growth Calculation

Bacterial growth is exponential. The number of cells after n generations is:

Where is the initial number of cells and is the number of generations.

Essay Topics Overview

Cholesterol: Structure, function, and clinical relevance.
Competitive vs. Non-competitive Inhibition: Mechanisms and effects on enzyme activity.
ETC in Eukaryotes vs. Prokaryotes: Location and differences.
Glycolysis and Krebs Cycle: Pathways and significance.