Comprehensive Study Guide for Microbiology Exam #1

Introduction to Microbiology

Major Groups of Organisms

Microbiology studies a variety of organisms, including bacteria, archaea, fungi, protozoa, algae, and viruses. Each group has distinct characteristics that define their classification and biological roles.

• Bacteria: Prokaryotic, unicellular, diverse metabolic capabilities.

• Archaea: Prokaryotic, often extremophiles, unique membrane lipids.

• Fungi: Eukaryotic, includes yeasts and molds, decomposers.

• Protozoa: Eukaryotic, unicellular, often motile.

• Algae: Eukaryotic, photosynthetic, aquatic.

• Viruses: Acellular, require host for replication.

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

Classification Systems

Classification of organisms has evolved from visual characteristics to genetic similarities.

• Carolus Linnaeus: Developed binomial nomenclature and grouped organisms by physical traits.

• Modern Classification: Uses genetic characteristics (e.g., DNA sequencing) for grouping.

• Binomial System: Each organism is named with a genus and species (e.g., Escherichia coli).

Archaea: Prokaryotic or Eukaryotic?

Archaea are prokaryotic but share some features with eukaryotes, such as certain genetic and metabolic pathways.

• Prokaryotic: Lack a nucleus and membrane-bound organelles.

• Relatedness: Molecular evidence (e.g., ribosomal RNA) shows Archaea are more closely related to Eukaryotes than to Bacteria.

Biochemical Tests

Biochemical tests are essential for identifying microorganisms based on their metabolic activities.

• Importance: Different species metabolize substrates differently, allowing for identification.

• Example: Catalase test distinguishes between Staphylococcus and Streptococcus.

Phylogenetic Trees and Evolution

Phylogenetic trees illustrate evolutionary relationships among organisms.

• Evolutionary Principles: Natural selection drives evolution by favoring traits that enhance survival.

• Natural Selection: Process where organisms with advantageous traits reproduce more successfully.

Resident Microbiota

Non-pathogenic bacteria in the gut, known as resident microbiota, play beneficial roles.

• Functions: Aid digestion, synthesize vitamins, protect against pathogens.

Prokaryotes and Eukaryotes

Definitions

• Prokaryotic: Cells without a nucleus or membrane-bound organelles.

• Eukaryotic: Cells with a nucleus and membrane-bound organelles.

• Acellular: Lacking cellular structure (e.g., viruses).

Cell Theory

Cell theory states that all living things are composed of cells, and cells are the basic unit of life.

Endosymbiotic Theory

This theory proposes that eukaryotic organelles (mitochondria, chloroplasts) originated from prokaryotic cells engulfed by ancestral eukaryotes.

Germ Theory of Disease

States that microorganisms are the cause of many diseases.

Historical Experiments

• Louis Pasteur: Swan neck flask experiment disproved spontaneous generation.

• Ignaz Semmelweis: Observed 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 to establish a causative relationship between microbe and disease.

Cell Structure and Function

Prokaryotic Cell Components

• Cell Wall: Peptidoglycan in bacteria; Gram-positive (thick), Gram-negative (thin + outer membrane), Mycolic acid (acid-fast).

• Teichoic Acid: Found in Gram-positive cell walls; important in MRSA resistance.

• Capsule: Protection and adherence.

• Flagella: Motility.

• Pili: Attachment and conjugation.

• Ribosomes: 70S in prokaryotes.

• Inclusions: Storage of nutrients.

• Endospores: Survival structures; produced by Bacillus and Clostridium.

Eukaryotic Cell Components and Organelles

• Nucleus: Contains DNA.

• Mitochondria: ATP production.

• Endoplasmic Reticulum: Protein and lipid synthesis.

• Golgi Apparatus: Protein modification and sorting.

• Lysosomes: Digestion.

• Ribosomes: 80S in eukaryotes.

• Endomembrane System: Vesicular trafficking between organelles.

Cell Morphology and Arrangements

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

• Arrangements: Chains, clusters, pairs.

Osmosis and Osmotic Pressure

Osmosis is the movement of water across a semipermeable membrane.

• Hypertonic: Cell loses water, shrinks.

• Isotonic: No net water movement.

• Hypotonic: Cell gains water, may burst.

Prokaryotic cell walls help resist osmotic pressure; eukaryotic cells may use contractile vacuoles.

Membrane Transport

• Simple Diffusion: Movement of molecules from high to low concentration.

• Facilitated Diffusion: Uses transport proteins.

• Active Transport: Requires energy (ATP).

Ribosomes: Clinical Importance

Differences in ribosome structure allow antibiotics to target bacterial ribosomes without affecting eukaryotic cells.

Biomolecules

Chemical Bonds and Functional Groups

• Covalent Bonds: Shared electrons.

• Polar Covalent Bonds: Unequal sharing, leads to partial charges.

• Ionic Bonds: Transfer of electrons.

• Hydrogen Bonding: Weak attraction between polar molecules.

• Functional Groups: Specific groups of atoms (e.g., hydroxyl, carboxyl).

• Hydrophilic: Water-loving.

• Hydrophobic: Water-fearing.

Carbohydrates

• Glucose: Monosaccharide, energy source.

• Starch: Storage in plants.

• Glycogen: Storage in animals.

• Cellulose: Structural in plants.

Lipids

• Triglyceride: Glycerol + 3 fatty acids.

• Fatty Acid: Long hydrocarbon chain.

• Phospholipid: Glycerol, 2 fatty acids, phosphate group; forms bilayer.

• Steroids: Four fused rings; cholesterol is a key example.

• HDL vs. LDL: High-density vs. low-density lipoproteins; statins lower LDL.

Proteins

• Amino Acids: Building blocks; peptide bonds formed by dehydration reaction.

• 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 (CFTR).

• Conjugated Proteins: Proteins with non-protein components (e.g., glycoproteins).

Macromolecule Functions

Macromolecule	Function
Carbohydrates	Energy, structure
Lipids	Energy storage, membranes
Proteins	Enzymes, structure, transport
Nucleic Acids	Genetic information

Additional info: Table 7.1 summarizes these functions.

Dehydration vs. Hydrolysis

• Dehydration Reaction: Forms bonds by removing water.

• Hydrolysis: Breaks bonds by adding water.

Deoxyribose vs. Ribose

• Deoxyribose: Sugar in DNA, lacks an oxygen atom.

• Ribose: Sugar in RNA.

Microbial Metabolism

Energy and Reactions

• Endergonic Reaction: Requires energy input.

• Exergonic Reaction: Releases energy.

• Reaction Pathway: Sequence of steps in a reaction; often shown as a diagram.

NAD+/NADH and FAD/FADH2

• NAD+: Electron carrier; reduced to NADH.

• FAD: Electron carrier; reduced to FADH2.

ATP

• Structure: Adenosine triphosphate.

• Formation: Substrate-level and oxidative phosphorylation.

• Function: Powers cellular reactions by transferring phosphate.

$\text{ATP} \rightarrow \text{ADP} + \text{P}_i$

Enzymes

• Function: Catalyze reactions by lowering activation energy.

• Holoenzyme: Complete enzyme with cofactors.

• Apoenzyme: Protein part only.

• Competitive Inhibition: Inhibitor binds active site.

• Non-competitive Inhibition: Inhibitor binds elsewhere, changes enzyme shape.

Metabolic Pathways

• Glycolysis: Breakdown of glucose to pyruvate.

• Krebs Cycle: Oxidizes acetyl-CoA to CO2, produces NADH and FADH2.

• Electron Transport Chain (ETC): Uses NADH/FADH2 to generate ATP.

• Fermentation: Anaerobic process; produces lactic acid.

Location: In prokaryotes, all occur in cytoplasm or plasma membrane; in eukaryotes, glycolysis in cytoplasm, Krebs and ETC in mitochondria.

Microbial Growth

Biofilms and Quorum Sensing

• Biofilms: Communities of microorganisms attached to surfaces.

• Quorum Sensing: Cell-to-cell communication to coordinate behavior.

Binary Fission

Bacteria reproduce by binary fission, doubling their population each generation.

$\text{N}_t = \text{N}_0 \times 2^n$

Where $\text{N}_t$ is the final number of cells, $\text{N}_0$ is the initial number, and $n$ is the number of generations.

DNA and Genes

Chromosomal Theory of Inheritance

Genes are located on chromosomes, which are inherited as units.

Hammerling Experiments

Demonstrated that hereditary information is in the nucleus.

Nucleotide Structure

• Pyrimidines: Cytosine, Thymine, Uracil (single ring).

• Purines: Adenine, Guanine (double ring).

• Linkage: Nucleotides linked by phosphodiester bonds.

DNA Structure

• Double Helix: Two strands held by hydrogen bonds.

• Chargaff’s Rules: %A = %T, %C = %G.

• Denaturing: Breaks hydrogen bonds, separates strands.

DNA vs. RNA

• DNA: Deoxyribose, thymine, double-stranded.

• RNA: Ribose, uracil, single-stranded.

tRNA Structure

tRNA has a cloverleaf structure, carries amino acids to ribosome.

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; often carries antibiotic resistance genes.

Essay Topics Overview

• Cholesterol: Essential for membrane fluidity; precursor for steroid hormones.

• Competitive vs. Non-competitive Inhibition: Mechanisms of enzyme regulation.

• ETC in Eukaryotes vs. Prokaryotes: Eukaryotic ETC in mitochondria; prokaryotic ETC in plasma membrane.

• Glycolysis and Krebs Cycle: Central metabolic pathways for energy production.