Comprehensive Biology Cheat Sheet: From Microbes to Mammals

Posted on Jun 14, 2024 in Biology

Microbiology

Lecture 2: Biodiversity

Definition of Biodiversity

Biodiversity: Variety of plant, animal, and microbial life in a habitat or globally.

  • Scales: Specific habitats to entire landscapes.
  • Aspects: Native vs. introduced species, ecosystem diversity.

Components of Biodiversity

  • Genetic Diversity: Genetic variation within and between populations. Allows adaptation and resistance to environmental stressors.
  • Species Diversity: Number of different species in an area. Measured by species richness and species abundance. Indices: Shannon-Wiener Index, Simpson Index.
  • Ecosystem Diversity: Diversity of ecosystems in an area. More diverse ecosystems support more species.

Measuring Biodiversity

  • Alpha (α) Diversity: Species diversity within a specific habitat.
  • Gamma (γ) Diversity: Total species diversity across a larger region.
  • Beta (β) Diversity: Difference in species composition between habitats.

Benefits of Biodiversity

  • Ecosystem Health and Stability: Higher biodiversity = greater productivity and stability.
  • Agricultural Benefits: Diverse pollinators improve crop yields.
  • Psychological and Human Health: Biodiverse green spaces enhance mental health.

Lecture 3: Importance of Microorganisms

Global Importance

  • Significant biomass and abundance.
  • Essential in nutrient cycling, climate regulation, and human health.
  • Adaptable to extreme environments.

Microbial Diversity

  • Most branches on the Tree of Life are microbial.
  • Prokaryotic domains: Bacteria and Archaea.
  • Cyanobacteria: First oxygen producers.

History of Microbiology

  • Antony van Leeuwenhoek: First to observe microorganisms.
  • Louis Pasteur: Disproved spontaneous generation.
  • Robert Koch: Developed Koch’s postulates.
  • Carl Woese: Distinguished Bacteria and Archaea using rRNA.
  • Modern Techniques: PCR, DNA sequencing, next-generation sequencing.

Lecture 4: Microbial Species

Species Concept Differences

  • Animals: Defined by interbreeding.
  • Microbes: Asexual reproduction, horizontal gene transfer (HGT).

Horizontal Gene Transfer (HGT)

  • Transformation: Uptake of free DNA.
  • Transduction: Gene transfer via viruses.
  • Conjugation: Direct cell-to-cell DNA transfer.

Species Definitions

  • 16S rRNA Similarity: >97% similarity criterion.
  • Whole Genome Data: More comprehensive analysis.
  • ASVs: Sequence-based variants.

Diversity Measurement

  • Alpha: Local diversity.
  • Beta: Between habitats.
  • Gamma: Regional diversity.

Lecture 5: Prokaryotes – Bacteria and Archaea

Defining Features

  • Bacteria: Peptidoglycan cell wall, ester-linked phospholipids.
  • Archaea: No peptidoglycan, ether-linked phospholipids, some thrive >100°C.

Metabolism & Ecology

  • Chemoautotrophs: Use inorganic compounds.
  • Photoautotrophs: Use sunlight.
  • Heterotrophs: Use organic compounds.

Lifestyles

  • Planktonic: Free-swimming.
  • Biofilms: Surface-associated communities.

Quorum Sensing

Cell density-based signaling affecting bioluminescence, motility, biofilm formation.

Lecture 6: Fungi

Defining Features of Eukaryotes

Membrane-enclosed nucleus, organelles, complex cells.

Types of Fungi

  • Chytridiomycota: Zoospores with flagella.
  • Zygomycota: Bread molds.
  • Glomeromycota: Symbiotic with plant roots.
  • Ascomycota: Yeasts, molds, truffles.
  • Basidiomycota: Mushrooms, rusts, smuts.
  • Microsporidia: Parasitic.

Ecological Roles

  • Decomposers: Nutrient recycling.
  • Symbiotic: Mycorrhizae, lichens.

Industrial Uses

  • Fermentation: Bread, wine, beer.
  • Drugs: Penicillin, insulin.
  • Organic Acids: Citric, gallic acid.

Lecture 7: Algae

Protists Overview

  • Diverse Eukaryotes: Unicellular/multicellular.
  • Metabolic Types: Photoautotrophs, heterotrophs, mixotrophs.

Types of Algae

  • Macroalgae: Seaweeds (brown, red, green).
  • Microalgae: Dinoflagellates, diatoms, chlorophytes.

Phytoplankton

  • Primary Producers: Photosynthesis.
  • Carbon Fixation: Measured by chlorophyll absorbance.

Iron Hypothesis

  • HNLC Regions: Iron limitation affects chlorophyll levels.
  • Experiments: SOIREE, SERIES show limited long-term carbon sequestration from iron addition.

Lecture 8: Viruses

Key Terms

  • Virion: Complete virus particle.
  • Capsid: Protein coat around nucleic acid.
  • Bacteriophage: Virus infecting bacteria.
  • Human Virome: All viruses in/on the human body.

Medically Relevant Viruses

  • HIV: Causes AIDS, targets T-helper cells.
  • Influenza: Respiratory illness, high mutation rate.
  • SARS-CoV-2: Causes COVID-19.

Virus Classification

  • Host-Based: Bacteria, Archaea, Eukaryotes.
  • Genome-Based: DNA/RNA, single/double-stranded.
  • Structure-Based: Naked or enveloped.

Ecosystem Roles

  • Gene Transfer: Among microbes.
  • Population Control: Regulates microorganisms.
  • Nutrient Cycling: Releases nutrients through host lysis.

HIV Lifecycle

Attachment / Entry / Replication / Assembly

Diagnosis and Treatment of HIV

  • Diagnosis: ELISA, PCR.
  • Treatment: Antiretroviral therapy.

Zoonotic Diseases

  • Examples: Ebola, Rabies, Zika.
  • Transmission: Contact with infected animals/products.

Human Virome

Impact on immune system and health.

Lecture 9: Gut Microbiota

Key Terms

  • Microbiota: Microbial community.
  • Microbiome: Collective genomic content.
  • Dysbiosis: Disturbed microbial community.

Contributions to Health

  • Nutrition: Digestion of dietary compounds.
  • Immune System: Education and stimulation.
  • Pathogen Resistance: Occupying niches.

Conditions Linked to Gut Microbiota

Autism, malnutrition, autoimmune disorders, diabetes, etc.

Manipulation Methods

  • Modifying Nutrient Input: Dietary changes, prebiotics.
  • Introducing Beneficial Bacteria: Probiotics, FMT.
  • Eliminating Undesired Bacteria: Phage therapy, antibiotics.

Lecture 10: Microbial Function

Key Terms

  • Functional Redundancy: Multiple species with similar roles.
  • Shotgun Metagenomics: Sequencing all genes.
  • Metatranscriptomics: Sequencing RNA.
  • Metaproteomics: Identifying proteins.
  • Metametabolomics: Studying metabolites.

Importance of Studying Function

  • Crucial for understanding biogeochemical cycles.
  • Reveals microbial activities and ecosystem roles.

Functional Redundancy Examples

Human Gut Microbiome: Consistent functional roles despite taxonomic variability.

Methods to Study Function

  • Cultivation: Pure/co-culture experiments.
  • Shotgun Metagenomics: DNA sequencing.
  • Metatranscriptomics: RNA sequencing.
  • Metaproteomics: Protein identification.
  • Metametabolomics: Metabolite analysis.

Lecture 11: Microbial Biogeography

Key Terms

  • Biogeography: Study of biodiversity distribution.
  • Functional Redundancy: Similar ecological roles by multiple species.
  • Shotgun Metagenomics: Sequencing all genes.
  • Beta Diversity: Diversity comparison between ecosystems.

Importance of Studying Microbial Distribution

Understands microbial presence, abundance, environmental influence.

Examples of NZ Research

  • 1000 Springs Project: Microbial diversity influenced by pH and temperature.
  • CRS Microbiome Study: Disease severity linked to microbial profiles.
  • Stream Bacteria Biogeography: Geographic and environmental impacts on communities.

Plant Science

Lecture 12: Plant Fundamentals

Plant Importance

  • Vital for oxygen production, food supply, and habitat creation.
  • Foundation of ecosystems and biodiversity.

Plant Taxonomy

  • Major groups: Bryophytes, Pteridophytes, Gymnosperms, Angiosperms.
  • Classified by reproductive structures and life cycles.

Alternation of Generations

  • Life cycle alternates between haploid (gametophyte) and diploid (sporophyte) phases.
  • Meiosis ensures genetic diversity.

NZ Flora Features

  • High endemism and unique adaptations.
  • Conservation is crucial for biodiversity.

Lecture 13: Algae and Transition to Land

Algae Characteristics

  • Photosynthetic, chlorophyll-containing, unicellular/multicellular organisms with cell walls.
  • Diverse habitats, originated from endosymbiotic events with cyanobacteria.

Kelp Forest Threats

Urchin overgrazing and trophic cascade disruption affect biodiversity and ecosystem stability.

Algae in Food Products

  • Alginates (brown algae) as thickeners.
  • Red algae (Porphyra) for nori.
  • Green algae compounds (β-carotene) for food and medicine.

Transition to Land

  • Benefits: Abundant sunlight, CO2, initial lack of herbivores.
  • Challenges: Desiccation, structural support, UV radiation, reproduction, dispersal.
  • Adaptations: Cuticles, lignin-reinforced walls, UV-protective pigments, reproductive and dispersal mechanisms.

Lecture 14: Bryophytes and Ferns

Bryophytes: Non-Vascular Land Plants

  • Includes mosses, liverworts, and hornworts.
  • Adaptations: Cuticle, stomata, protective reproductive structures, sporopollenin for spore protection.

Bryophyte Life Cycle

  • Dominant gametophyte generation.
  • Sporophyte partially dependent on gametophyte.
  • Spore dispersal through elongation of seta.

Bryophytes in NZ

  • Over 500 moss species, ~100 endemic.
  • Important for water retention, soil acidification, and carbon storage.

Ferns: Vascular Cryptogams

  • True vascular tissue (xylem and phloem).
  • Diverse group with ~11,916 species.
  • Dominant sporophyte generation, free-living gametophyte.

Lecture 15: Seed Plants – Gymnosperms and Angiosperms

Gymnosperms

  • ‘Naked seed’ plants, cone-bearing.
  • Innovations: Dominant sporophyte stage, reduced gametophyte, seeds, pollen, and ovules.

Gymnosperm Lifecycle

  • Gametophyte dependent on sporophyte.
  • Wind pollination, seed dispersal.

Angiosperms

  • ‘Encased seed’ plants, bear flowers and fruit.
  • Lifecycle: Dominant sporophyte stage, dependent gametophyte.
  • Double fertilization: One sperm fertilizes egg, another fuses with polar nuclei to form endosperm.

Lecture 16: Angiosperms

Angiosperm Diversity

  • Over 300,000 species.
  • Divisions: Basal angiosperms, monocots, eudicots.

Lifecycle

  • Dominant sporophyte stage.
  • Pollination strategies: Wind, animals, insects.
  • Seed dispersal mechanisms.

Flower Structure

  • Flowers can be hermaphrodite or unisexual.
  • Male gametophyte: Pollen with tube and generative cells.
  • Female gametophyte: Megaspore undergoes mitosis to form 8 cells.

Lecture 18: Plant Domestication

Challenges of Feeding a Growing Population

Limited arable land, soil degradation, climate change, water scarcity, food waste.

Origins of Agriculture

  • Major crops domesticated 13,000-7,000 years ago.
  • Steps: Gathering wild plants, cultivation, artificial selection.

Examples of Crop Domestication

Wheat, maize, tomato, kiwifruit, Brassica.

Staple Crops and Diet Diversification

  • Most calories from maize, rice, wheat.
  • Diversification with underutilized crops and new farming methods.

Lecture 19: Plant Nutrition

Nutrient Acquisition

  • Stomata for gas exchange.
  • Root hairs for water/mineral absorption.
  • Vascular system (xylem, phloem) for transport.

Nitrogen Fixation

  • Symbiotic relationship between legumes and Rhizobium bacteria.
  • Mycorrhizal fungi provide nutrients in exchange for carbohydrates.

Mycorrhizal Associations

  • Ectomycorrhizae and arbuscular mycorrhizae.
  • Transport nutrients and create shared resource systems in ecosystems.

Lecture 20: Plant Movement and Signal Transduction

Plant Movement

  • Phototropism (towards light).
  • Thigmotropism (towards touch for support).
  • Gravitropism (shoots away from gravity, roots towards gravity).

Signal Transduction

  • Plant hormones regulate growth, development, and responses to stimuli.
  • Photoreceptors control development and flowering.

Lecture 21: Abiotic Stressors

General

  • Stressors: Drought, flooding, heat, cold, salinity, heavy metals, UV radiation.
  • Phytohormones: Crucial in stress response regulation.
  • Sessile Plants: Evolved complex mechanisms to cope.

Drought Response

  • Phytohormone: Abscisic Acid (ABA).
  • Mechanism: ABA causes ion and water loss from cells, leading to stomata closure to reduce water loss.

Flooding Response

  • Oxygen Deprivation: Roots cut off from essential gases.
  • Mechanism: Ethylene induces cortex cell death, creating aerenchyma (air channels) for gas exchange.

Mechanical Stressors

  • Examples: Wind, rain, touch, soil compaction.
  • Response: Thigmomorphogenesis (growth pattern changes), increased stem strength, altered leaf morphology.

Lecture 22: Biotic Stressors

General

  • Stressors: Bacteria, fungi, viruses, nematodes, insects, weeds.
  • Physical Defenses: Spikes, thorns, spines, hairs (trichomes).
  • Chemical Defenses: Toxic compounds (e.g., nicotine), VOCs attracting predators/parasites.

Pathogen Defense

  • Physical Barriers: Cell wall, waxes, bark.
  • Recognition: PRRs detect PAMPs, triggering defense.
  • Immunity:
    • PAMP-triggered: Produces phytoalexins.
    • Effector-triggered: Recognizes effectors, triggers hypersensitive response and systemic acquired resistance.

Herbivore Defense

  • Physical: Spikes, thorns, spines, trichomes.
  • Chemical:
    • Direct: Toxic compounds.
    • Indirect: VOCs.
  • Trichomes: Some release deterrent compounds.
  • Jasmonic Acid (JA): Triggers chemical defenses (terpenoids, phytoalexins, proteinase inhibitors, VOCs).

Animal Kingdom

Lecture 24: Introduction to Animalia

Key Features for Classifying Animals

  • Multicellularity
  • Heterotrophic feeding
  • Reproduction via a blastula stage
  • Distinct cell types
  • Cytological and biochemical features (connective proteins, extracellular matrix)

Animal Phylogenetic Tree

  • Interprets evolutionary relationships among animal groups.
  • Key steps in animal evolution: Origins of life (prokaryotes), Eukaryotes, Multicellularity.

Structure and Function

Relationship between form and function in animals (SA ratio critical for nutrition and gas exchange).

Lecture 25: Worms

Bilateria

  • Radial vs. Bilateral symmetry.
  • Diploblastic (2 layers) vs. Triploblastic (3 layers).

Body Cavities

  • Acoelomate: No body cavity (Platyhelminthes)
  • Pseudocoelomate: Body cavity between endoderm and mesoderm (Nematoda)
  • Coelomate: Body cavity completely lined by mesoderm (Annelida)

Key Phyla

  • Platyhelminthes (Flatworms): Acoelomate, diverse habitats.
  • Nematoda (Roundworms): Pseudocoelomate, cylindrical bodies.
  • Annelida (Segmented Worms): Coelomate, segmented bodies.

Lecture 26: Morphogenesis

Morphogenesis

  • Development stages: Cleavage, Blastula formation, Gastrulation, Morphogenesis.
  • Homeotic Hox genes control body segmentation.

Phylum Mollusca

  • Coelomate, protostomes.
  • Body regions: Head, foot, visceral mass.
  • Mantle, radula, open/closed circulatory system.

Phylum Echinodermata

  • Deuterostomes.
  • Radial symmetry (adults), bilateral (larvae).
  • Water vascular system, tube feet, endoskeleton, regeneration.

Lecture 27: Arthropods

Arthropoda

  • Most diverse animal phylum.
  • Subphyla: Hexapoda, Trilobita, Chelicerata, Myriapoda, Crustacea.
  • Modular body plan: segmented, jointed limbs, exoskeleton.

Transition to Land

  • Adaptations: Jointed legs, exoskeleton, varied respiratory structures.
  • Sensory adaptations: Enhanced sight, sound, touch.
  • Reproductive adaptations: Ecdysis, metamorphosis, social behaviors.

Lecture 28: Chordates and Early Vertebrates

Phylum Chordata

  • Bilateral symmetry, segmented body, three germ layers.
  • Notochord, dorsal nerve cord, pharyngeal slits, post-anal tail.

Agnathans (Jawless Fish)

Median fins, 2-chambered heart, external fertilization.

Vertebrates

  • Innovations: Vertebral column, jaws, mineralized skeleton.
  • Class Chondrichthyes: Cartilaginous fish (sharks, rays).
  • Class Osteichthyes: Bony fish (ray-finned, lobe-finned).

Lecture 30: Transition to Land

Phylogeny of Chordates

  • Chordates share a common ancestor with deuterostomes.
  • Key characteristics: notochord, vertebral column, jaws, mineralized skeleton, limbs with digits.
  • Major groups: Echinodermata, Cephalochordata, Urochordata, Myxini, Petromyzontida, Chondrichthyes, Actinopterygii, Actinistia, Dipnoi, Amphibia, Reptilia, Mammalia.
  • Tetrapods include Amphibia and Reptilia; amniotes include Reptilia, Aves, Mammalia.

Tiktaalik: The “Fishbian”

Transitional form between fish and tetrapods from the Devonian period (~375 mya).

Amphibian Characteristics

  • Reproduction, egg development, and respiration are water-dependent.
  • Undergo metamorphosis from aquatic larval stage to terrestrial adult.
  • Moist skin for gas exchange, lack of amniotic egg.
  • Examples: New Zealand’s endangered native frogs (Leiopelma spp.).

Amphibian Threats

  • Indicators of pollution.
  • Chytrid fungus is a major concern.

Reptilian Characteristics

  • Amniotic egg for terrestrial reproduction.
  • Keratinized scales, rib breathing, diverse orders (Crocodilia, Testudines, Squamata, Sphenodonta).

Reptilian Sense Organs and Breathing

  • Pit organs detect infrared.
  • Kinetic skull for large prey consumption.
  • Breathing advantages: simple sac-like (salamanders) to highly compartmentalized lungs (lizards) and thoracic pump in crocodilians.

Circulatory Systems

  • Amphibians: single circuit.
  • Reptiles: more efficient double circuit.
  • Compared to birds and mammals.

Nitrogenous Waste

Amphibians excrete ammonia.

Lecture 31/32: Birds

Key Features of Chordates

  • Closed circulation, pharyngeal gill slits, dorsal hollow nerve cord, muscular post-anal tail.

Circulatory System of Chondrichthyes and Actinopterygii

Two circulatory circuits.

Constraints for Animals to Survive on Land

  • Key constraint: water loss.
  • Other constraints: obtaining oxygen, eating protein.

Key Characteristics of Living Birds

  • Endothermy, maintain heat via metabolism.
  • Brown adipose tissue, key molecules: Adenosine Nucleotide Translocase, Uncoupling Protein 1.

Evolution of Avian Lineages

  • Furcula (wishbone) analogous to hyoid bone.
  • Furcula allows the supracoracoideus muscle to create the upstroke.

Avian Diversity

  • Aotearoa (New Zealand) has the highest diversity of flightless birds.
  • Flightlessness due to lack of predators on islands, ecological release.

Flight

  • Independently evolved in insects, pterosaurs, birds, bats.
  • Avian form limited by flight, more uniform than mammals.

Traits for Flight in Birds

  • Feather, scale, hair development regulated by FGF, Shh, CBP, K, and KAP.
  • Bird bones: lightweight but dense and strong.
  • Four key structural characters: rigidity, reduction, wing-forelimb, wing shape.

Wing Shape

Determined by FGF8 expression and SHH signaling.

Flying Diving Birds

Use GPS, dive loggers, accelerometers to study behavior.

Air Sacs and Metabolic Demand

Unidirectional airflow in bird lungs.

Extreme Flight – Frigatebird

Remarkable soaring and gliding abilities.

Migrating Birds

Use fat for energy due to high energy density.

Pigmentation in Birds

Diverse coloration due to various pigments.

Lecture 33: Mammals

Key Characteristics of Mammals

Large brain, endothermy, high metabolic rate, high parental care, four-chambered heart.

Soft Tissues

  • Milk/Lactation, hair (keratin, waterproofed by sebum), thermoregulation (radiation, conduction, convection, evaporation).

Hard Tissues

Dentary bone (lower jaw), auditory ossicles (three small bones in the middle ear), heterodonty and tooth replacement.

Reproductive Strategies

  • Monotremes (egg-laying), marsupials (pouch), eutherians (placental mammals).

Parental Investment

  • Eutherians: heavy gestation investment.
  • Marsupials and monotremes: heavy lactation investment.

New Zealand Marine Mammals

Home to 56 species including Baleen whales, Toothed whales, Beaked whales, Pinnipeds.

Whale Adaptations

Blue whales: significant weight gain during feeding, calves gain weight rapidly from high milk production.