BIO 101: Diversity of Living Things

BIO 101: Diversity of Living Things

• BIO 101 is a course on the diversity of living organisms, worth 3 credits.
• The course will cover the five kingdoms of taxonomic classification: Prokaryotae, Protoctista, Fungi, Plantae, and Animalia.
• Key features covered include morphological and evolutionary importance, habitats, adaptation mechanisms, locomotion, feeding, and reproduction.
• Ecological and economic importance of selected members within each taxonomic group will also be studied.

Lecturers and Contacts

• Dr. Isaac Okyere is the coordinator.
• Other lecturers include Dr. John Abraham, Dr. Levi Yafetto, Dr. Emmanuel E. Dzakah, and Dr. Justus Deikumah.

Course Delivery

• The theoretical content will be taught through lectures, class discussions, and the UCC E-learning platform.
• Practical aspects will involve laboratory rotation sessions in six School of Biological Sciences departments.
• Students will observe and examine specimens, taking notes on important features and characteristics.

Assessment

• Students are evaluated through quizzes, assignments, and practical work, constituting 40% of the assessment.
• The end-of-semester examination will account for the remaining 60%.

History of Taxonomy

• Taxonomy is the practice and study of classifying organisms according to their natural relationships.
• The term "taxonomy" comes from "taxis" (arrangement) and "nomos" (method).
• Aristotle (384-322 B.C.E.) is considered the first father of taxonomy.
• Aristotle introduced classification by type and binomial definition.
• Carolus Linnaeus (1707-1778) developed the modern taxonomic system using physical characteristics and genetics.

Classification of Living Things

• The Linnaean system uses a hierarchy of groups to differentiate levels of similarity among groups (taxon).
• Classification is dynamic.

Old Classification Systems

• The five-kingdom system includes Prokaryotae, Protista, Fungi, Plantae, and Animalia.
• The six-kingdom system includes Eubacteria/Monera, Archaebacteria, Protista, Fungi, Plantae, and Animalia.

Taxonomic Ranks

• Systems are composed of seven major taxonomic ranks: Kingdom, Phylum, Class, Order, Family, Genus, and Species.

Modern Classification

• It is also known as the Domain System of Classification.
• Domain system consists of eight taxonomic levels including the domain.
• There are 3 Domains: Archaea, Eubacteria, and Eukarya.

Why Three Domains?

• Evolutionary relationships of the domains were revealed by rRNA sequences.
• Prokaryotic Archaea and Bacteria differ more radically from each other than Archaea do from Eukarya.

The Three Domains of Life

• Domain Bacteria includes diverse and widespread prokaryotes.
• Domain Archaea includes prokaryotes living in extreme environments.
• Domain Eukarya includes kingdoms like Animalia, Plantae, and Fungi.

Comparison Between the 3 Domains

• Bacteria: Absent nuclear envelope, absent membrane-enclosed organelles, present Peptidoglycan in cell wall. Unbranched membrane lipids. One kind of RNA. Growth inhibited by Antibiotics.
• Archaea: Absent nuclear envelope, absent membrane-enclosed organelles and Peptidoglycan in cell wall. Branched membrane lipids. Multiple kinds of RNA. Doesnt respond to Antibiotics.
• Eukarya: Present nuclear envelopes and membrane-enclosed organelles. Absent Peptidoglycan in cell wall. Unbranched membrane lipids. Multiple kinds of RNA. Doesnt respond to Antibiotics.

Prokaryotes

• Prokaryotes have a simple interior organization compared to eukaryotes.
• Prokaryotic cells lack a membrane-enclosed nucleus and cytoplasmic organelles.

General Characteristics of Prokaryotes

• Prokaryotes lack a true nucleus and membrane-enclosed organelles.
• DNA is located in the cytoplasm.
• They move via flagella, gas vesicles, or gliding mechanisms.
• Reproduction is asexual through binary fission.
• They may be obligate anaerobes, facultative anaerobes, or obligate aerobes.
• Nutritional types include photoautotrophs, photoheterotrophs, chemoautotrophs, and chemoheterotrophs.
• They include bacteria and archaea with similar cell structures.

Prokaryotic Cell Structure

• External components: Appendages (flagella, pili, fimbriae) and Glycocalyx (capsule, slime layer).
• Cell envelope: Outer membrane (in some), cell wall, and cell membrane.
• Internal components: Cytoplasm, ribosomes, inclusions, nucleoid/chromosome, actin cytoskeleton, and endospore.

Prokaryotic Cell Structure Components

• Glycocalyx: A coating outside the cell wall for protection, adhesion, and receptor functions.
• Bacterial chromosome or nucleoid: Condensed DNA directing genetics and heredity.
• Plasmid: Double-stranded DNA circle with extra genes.
• Fimbriae: Hairlike bristles aiding adhesion.
• Inclusion/Granule: Stored nutrients.
• Cell wall: Semirigid casing providing structural support.
• Pilus: Elongate appendage for DNA transfer.
• Ribosomes: Sites of protein and RNA synthesis.
• Actin cytoskeleton: Fibers maintaining cell shape.
• Cell membrane: Controls material flow in and out of the cell.
• Outer membrane: Extra membrane with lipopolysaccharide.
• Endospore: Dormant body for survival in harsh conditions.
• Flagellum: Rotating filament for movement.
• Cytoplasm: Water-based solution filling the cell.

Classification of Prokaryotes

• Prokaryotes are grouped into two domains: Archaea and Bacteria.

Domain Archaea

• Domain Archaea is dominated by extremophiles that live in extreme environments.
• Archaea include methanogens, halophiles, thermophiles, and acidophiles.

Characteristics of Archaea

• Share traits with bacteria and eukaryotes.
• Tolerate harsher environments.
• Cell walls lack peptidoglycan, and membranes contain different lipids.
• Under a microscope archaea look very similar to bacteria, but the biochemicals of cell walls, proteins associated with DNA, and some metabolic pathways are different from Bacteria.
• DNA is more like that of eukaryotes.
• Archaea and eukaryotes are closely related.

Classification of Archaea

• Classification is usually on the basis of habitat.
• Methanogens: harvest energy by converting H2 and CO2 into methane gas, and live in anaerobic environments.
• Halophiles: Thrive in salty environments.
• Thermophiles: Thrive in very hot environments.
• Acidophiles: Live in acidic environments.

Domain Bacteria

• Includes cyanobacteria (blue-green algae) and purple sulfur bacteria.

Characteristics of Bacteria

• They are unicellular, absorptive-heterotrophic, photoautotrophic, or chemoautotrophic prokaryotes.
• Typically have only one set of genes in a single-stranded loop.
• Their cell walls contain peptidoglycan.
• Bacteria have several chemical types of cell walls.
• They lack organelles, such as centrioles, mitochondria, and chloroplasts.
• Photoautotrophic species have chlorophyll but no chloroplasts.

Bacterial Phyla

• Major bacterial phyla are Proteobacteria, Chlamydias, Spirochaetes, Cyanobacteria, and Gram-positive bacteria.

The Proteobacteria

• Proteobacteria is one of up to 52 bacteria phyla.
• It is further subdivided into five classes: Alpha, Beta, Gamma, Delta, and Epsilon.

Bacterial Shapes

• Three common shapes of prokaryotes are Bacilli, Spirilla, and Cocci

Prokaryotes Colony Shapes

• Diplo-: occur in pair
• Strepto-: occur in chains
• Staphylo-: occur in clumps

Movement/ Motility of Prokaryotes

• Prokaryotes use flagella as a structure for motility.
• Some also have gas vessicles or gliding mechanisms

The Prokaryotic Flagellum

• A prokaryotic flagellum has 3 parts :
  • Filament - comprised of proteins
  • Hook
  • Basal Body - stack of rings, anchored in the cell wall

Flagellar Arrangements

• Monotrichous: Single flagellum at one end.
• Lophotrichous: Small bunches of flagella at one end.
• Amphitrichous: Flagella at both ends.
• Peritrichous: Flagella dispersed over the surface.

Prokaryote Nutrition and Metabolism

• Prokaryotes obtain energy and nutrients to live and reproduce.
• Nutritional needs determine their ecological niche and role in biogeochemical cycles.

Classification of Prokaryotes Based on Metabolism

• The major nutritional groups are carbon metabolism and energy metabolism

Carbon Metabolism

• Heterotrophic organisms use organic compounds from other organisms.
• Autotrophic organisms use carbon dioxide (CO2) as a carbon source.

Energy Metabolism

• Phototrophic organisms use light energy from the sun.
• Chemotrophic organisms use organic or inorganic molecules.
• Photoheterotrophs use light energy and organic carbon sources.
• Chemoheterotrophs use organic sources for energy and carbon.
• Photoautotrophs capture light energy and use carbon dioxide.
• Chemoautotrophs break down inorganic molecules and use carbon dioxide.

Metabolism

• Prokaryotes release energy by two main processes : Respiration (occurs in the presence of oxygen) and Fermentation (occurs in the absence of oxygen).
• On the basis of the mode of metabolism (energy released), prokaryotes are classified as : obligate aerobes, obligate anaerobes, facultative anaerobes.

Sulfur and Nitrogen Metabolism

• Some bacteria and archaea metabolize nitrogen and sulfur.
• Some use nitrogen- or sulfur-containing molecules to obtain energy.
• They expend energy to convert these molecules.
• Certain prokaryotes oxidize hydrogen sulfide (H2S) for chemosynthesis.

Nitrogen Fixation Types

• Nitrogen-fixing prokaryotes convert atmospheric nitrogen (N2) into ammonia (NH3).
• Nitrifying prokaryotes convert ammonia into nitrates and nitrites.
• Denitrifying prokaryotes reverse the process, turning nitrates into N2 gas.

Forms of Nitrogen Fixation

• There are three forms of nitrogen fixation in the biosphere.
• Atmospheric nitrogen fixation
• Industrial nitrogen fixation
• Biological nitrogen fixation

Biological Nitrogen Fixation

• Certain bacteria carry out biological nitrogen fixation.
• The bacterial process requires a complex set of enzymes and ATP.
• Nitrogen fixing bacteria exist in a symbiotic relationship with leguminous plants.
• They also establish symbiotic relationships with non-leguminous plants.
• Cyanobacteria are the primary nitrogen fixing bacteria in aquatic environments and maintain nitrogen balance..

Biological Nitrogen Fixation Process

• In the biological nitrogen fixation process, 16 moles of ATP, 8 moles of electrons and 8 moles of hydrogen ions (protons) are used toconvert one mole of nitrogen gas (N₂) to two moles of ammonia.
• The reaction is exclusively executed by prokaryotes (bacteria and some archaea) by using an enzyme complex referred to as Nitrogenase complex consisting of two proteins that Convert N₂ to NH3.

Example of Nitrogen Fixing Bacteria

• Free living aerobic bacteria: Azotobacter, Beijerinckia, Klebsiella, Cyanobacteria.
• Free living anaerobic bacteria: Desulfovibrio, purple Sulphur and non Sulphur bacteria and Green sulphur bacteria.
• Free associative nitrogen bacteria: Azospirillum.
• Symbionts: Rhizobium (legumes), Frankia (alden trees).

Cyanobacteria (Blue-Green Algae/Cyanophyta)

• They are photoautotrophic bacteria seen as "green slime" in water.
• Cyanobacteria are described as Oxygenic Photosynthetic Bacteria because They produce oxygen gas (O2) as a by-product using the same pathways as plants.
• They contain Chlorophyll, and can fix N₂ into NH3.
• Most produce toxins

Nitrogen Fixing in Cyanobacteria.

• Some Cyanobacteria (nitrogen starved) form heterocysts, which carries out nitrogen fixation.
• When photosynthesis is haltered in the heterosyst, O2 is stopped, therefore there would be no destruction of the nitrogenase complex: An enzyme
• A heterocyst is an enlarged cell with a thick wall to allow N2, while blocking O2.

Role of Heterocyst

• Functions of the Heterocyst
  • Heterocyst generates the anaerobic environment required by the nitrogenase complex by:
• Forming a thick cell wall with three layers.
• Degrading of photosystem II which is involved in the production of O2.
• Producing oxygen scavenging species.

Reproduction and Adaptation

• Prokaryotes grow to a fixed size and reproduce asexually via binary fission.
• They successfully inhabit all habitats due to rapid reproduction in favorable conditions
• .Some bacteria can divide every 1-3 hrs and reproduce in every 20 minutes.
• Reproduction is limited by lack of nutrients, metabolic wastes, competition, or consumption.

Adaptation

• Prokaryotes can adapt to harsh environmental conditions by Dormancy and endosporulation, Antibiotic synthesis and mutation (random changes in DNA) .

Endosporulation

• Prokaryotic cells form Endospore during unfavourable growth conditions which contains the DNA.
• Endospores multilayered coat protect it to survive in soil for long period.

Gram-Positive and Gram-Negative Bacteria

• Gram stain distinguishes two large groups of bacteria.

Gram-Positive Bacteria

• Gram +ve cell walls have an inner plasma membrane, a thick peptidoglycan layer, acidic polysaccharides (teichoic acid), and an outer capsule.
• During Gram +ve bacterial cell wall retains crystal violet which stains purple/violet/blue

Gram-Negative Bacteria

• Gram -ve cell walls have an inner plasma membrane, a thin peptidoglycan layer, an outer membrane with lipopolysaccharides (LPS), and an outer capsule.
• During Gram -ve bacterial cell walls looses crystal violet which stains pink/red.

Gram Staining Procedure

1. Fixation of sample
2. Application of crystal violet (primary stain) - stain cells purple/violet/blue.
3. Application of iodine (I) solution (Mordant)
4. Decolourization- differentiates gram-positive from gram-negative cells.
5. Application of safranin (counter stain)- stains the decolourized gram -ve cells pink/red,.

Clinical Relevance of Gram Stain

• Many antibiotics target peptidoglycan and damage bacterial cell walls.
• Gram -ve bacteria are more likely to be resistant to antibiotics because they possess an outer plasma membrane .