Microbiology Exam 1 Study Guide: Classification, Cell Structure, Biochemistry, Genetics, and Metabolism

Classification and Evolution of Microorganisms

Major Groups of Organisms

Microorganisms are classified into several major groups based on their cellular structure and characteristics. These include bacteria, archaea, fungi, protozoa, algae, and viruses.

• Bacteria: Prokaryotic, unicellular, diverse metabolic capabilities.

• Archaea: Prokaryotic, often extremophiles, distinct genetic and biochemical traits.

• 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.

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, especially ribosomal RNA sequences.

• Binomial Nomenclature: Each organism is given a genus and species name (e.g., Escherichia coli).

• Modern Classification: Uses molecular data, such as DNA and RNA sequences, to determine evolutionary relationships.

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.

Biochemical Tests and Phylogenetic Trees

Biochemical tests are used to identify microorganisms based on their metabolic activities. Phylogenetic trees illustrate evolutionary relationships among organisms.

• Biochemical Tests: Detect enzymes, metabolic products, and substrate utilization.

• Phylogenetic Trees: Visual representations of evolutionary history.

Evolutionary Principles

Natural selection is a process where organisms with advantageous traits survive and reproduce, leading to evolution over time.

• Natural Selection: Drives adaptation and speciation.

• Evolution: Change in genetic composition of populations over generations.

Microbial Nomenclature and Classification

Binomial System and Biological Classification

The binomial system assigns each organism a two-part Latin name. Classification now emphasizes genetic characteristics rather than visual traits.

• Example: Alcanivorax borkumensis is a bacterium important for oil degradation.

Resident Microbiota

Non-pathogenic bacteria in the gut, known as resident microbiota, contribute to health by aiding digestion and protecting against pathogens.

Cell Structure and Function

Prokaryotic vs. Eukaryotic Cells

Prokaryotic cells lack a nucleus and membrane-bound organelles, while eukaryotic cells possess these structures.

• Prokaryotic: Bacteria, Archaea

• Eukaryotic: Fungi, Protozoa, Algae

• Acellular: Viruses

Cell Wall Composition

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

• Gram-positive: Thick peptidoglycan, teichoic acids.

• Gram-negative: Thin peptidoglycan, outer membrane.

• Mycolic Acid (Acid Fast): Waxy layer, e.g., Mycobacterium.

Teichoic acid: Associated with Gram-positive bacteria and MRSA resistance.

Cell Morphology and Arrangements

Bacteria exhibit various shapes (cocci, bacilli, spirilla) and arrangements (chains, clusters).

Osmosis and Osmotic Pressure

Osmosis is the movement of water across a membrane. Cells respond differently to hypertonic, isotonic, and hypotonic environments.

• Hypertonic: Cell shrinks (plasmolysis).

• Isotonic: No net water movement.

• Hypotonic: Cell swells (lysis possible).

Inclusions and Endospores

Inclusions store nutrients; endospores are resistant structures formed by certain bacteria (e.g., Bacillus, Clostridium).

• Vegetative Cell: Active, growing form.

• Endospore: Dormant, resistant form.

Membrane Transport

Cells transport substances via simple diffusion, facilitated diffusion, and active transport.

• Simple Diffusion: Movement down concentration gradient.

• Facilitated Diffusion: Uses carrier proteins.

• Active Transport: Requires energy (ATP).

Ribosomes

Prokaryotic ribosomes (70S) differ from eukaryotic ribosomes (80S), important for antibiotic targeting.

Endomembrane System

In eukaryotes, the endomembrane system includes the ER, Golgi, vesicles, and lysosomes, facilitating vesicular trafficking.

Historical Experiments and Theories

Spontaneous Generation and Pasteur's Experiment

Louis Pasteur's swan neck flask experiment disproved spontaneous generation, supporting biogenesis.

Cell Theory

All living things are composed of cells; cells arise from pre-existing cells.

Endosymbiotic Theory

Eukaryotic organelles (mitochondria, chloroplasts) originated from symbiotic prokaryotes.

Germ Theory of Disease

Microorganisms cause disease; supported by Koch's postulates.

Key Historical Figures

• Ignaz Semmelweis: Advocated handwashing to prevent puerperal fever.

• John Snow: Traced cholera outbreak to contaminated water.

• Joseph Lister: Demonstrated antiseptic surgery; Listerine named after him.

• Koch's Postulates: Criteria to establish causative relationship between microbe and disease.

Biochemistry and Macromolecules

Chemical Bonds and Functional Groups

Covalent, polar covalent, ionic, and hydrogen bonds are fundamental to molecular structure. Functional groups determine chemical properties.

• Hydrophilic: Water-loving.

• Hydrophobic: Water-repelling.

Macromolecules

Major macromolecules include carbohydrates, lipids, proteins, and nucleic acids.

• Glucose: Monosaccharide.

• Starch vs. Glycogen vs. Cellulose: Polysaccharides with different linkages and functions.

• Triglyceride: Glycerol + 3 fatty acids.

• Phospholipid: Forms bilayer in membranes.

• Amino Acids: Linked by peptide bonds.

• Steroids: Four-ring structure; cholesterol is a key example.

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

Protein Structure

Proteins have four levels of structure: primary, secondary, tertiary, and quaternary.

• Cystic Fibrosis: Caused by misfolded protein.

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

Dehydration vs. Hydrolysis

Dehydration reactions build macromolecules; hydrolysis breaks them down.

Deoxyribose vs. Ribose

Deoxyribose (DNA) lacks an oxygen atom compared to ribose (RNA).

Metabolism and Enzymes

Endergonic and Exergonic Reactions

Endergonic reactions absorb energy; exergonic reactions release energy.

• Reaction Pathway: Diagram showing energy changes during a reaction.

NAD+/NADH, FAD/FADH2, and ATP

These molecules are essential for energy transfer in cells.

• NAD+/NADH: Electron carrier.

• FAD/FADH2: Electron carrier.

• ATP: Energy currency; formed by substrate-level and oxidative phosphorylation.

Enzymes

Enzymes catalyze biochemical reactions by lowering activation energy.

• Holoenzyme: Complete enzyme with cofactor.

• Apoenzyme: Protein part of enzyme.

• Competitive Inhibition: Inhibitor binds active site.

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

Metabolic Pathways

Glycolysis, Krebs Cycle, Electron Transport Chain

These pathways generate ATP from glucose.

• Glycolysis: Occurs in cytoplasm.

• Krebs Cycle: Occurs in cytoplasm (prokaryotes) or mitochondria (eukaryotes).

• ETC: Plasma membrane (prokaryotes), mitochondrial membrane (eukaryotes).

Fermentation and Lactic Acid Formation

Fermentation allows ATP production without oxygen; lactic acid is a common product.

Microbial Growth and Communication

Biofilms and Quorum Sensing

Biofilms are communities of microorganisms; quorum sensing is cell-to-cell communication regulating gene expression.

Binary Fission

Bacteria reproduce by binary fission, doubling population each generation.

Genetics and Inheritance

Gregor Mendel and Chromosomal Theory

Mendel's experiments established inheritance laws; chromosomal theory links genes to chromosomes.

Hammerling Experiments

Demonstrated genetic information resides in the nucleus.

Nucleotide Structure and DNA/RNA

Nucleotides consist of a sugar, phosphate, and base. DNA and RNA differ in sugar and bases.

• Pyrimidine: Cytosine, thymine, uracil.

• Purine: Adenine, guanine.

• Chargaff's Rules: $\%A = \%T$, $\%C = \%G$

DNA Structure and Denaturation

DNA is a double helix held by hydrogen bonds; denaturation disrupts structure.

tRNA Structure

tRNA has a cloverleaf structure, carrying amino acids during translation.

Chromatin Structure

• Centromere: Region joining sister chromatids.

• Histone Proteins: Package DNA.

• Nucleosome: DNA wrapped around histones.

• Solenoid: Higher-order chromatin structure.

Plasmid DNA

Plasmids are small, circular DNA molecules in bacteria, often carrying antibiotic resistance genes.

Bacterial Growth Calculations

Bacterial growth is exponential; population can be calculated using:

• Formula: $N = N_0 \times 2^n$ Where: $N$ = final cell number, $N_0$ = initial cell number, $n$ = number of generations

Essay Topics Overview

• Cholesterol: Structure, function, and role in membranes.

• Competitive vs. Non-competitive Inhibition: Mechanisms and effects on enzyme activity.

• ETC in Eukaryotes vs. Prokaryotes: Location and differences.

• Glycolysis and Krebs Cycle: Steps, products, and significance.

Key Terms Table

Term	Definition
Prokaryotic	Cells lacking nucleus and organelles
Eukaryotic	Cells with nucleus and organelles
Acellular	Not composed of cells (e.g., viruses)
Natural Selection	Process favoring advantageous traits
Evolution	Change in genetic composition over time
Spontaneous Generation	Disproven idea that life arises from non-life

Additional info: For functions of macromolecules, refer to Table 7.1 in your textbook for detailed roles of carbohydrates, lipids, proteins, and nucleic acids.