Archaea vs. Bacteria: Characteristics

• The final exam is 3 hours long with two answer sheets.
• Answer sheet 1 includes ~8 practical observation questions at numbered stations and ~8-9 theoretical questions at a lab bench.
• Answer sheet 2 involves identifying unknown organisms at the windowsill bench using provided keys and requires ~40-60 minutes.
• Students will complete one answer sheet at a time and must leave at least 40 minutes for organism identification with a 1-hour maximum.
• Only pens or pencils are allowed; no lab coats, calculators, phones, books, or notes.

Archaea and Bacteria

• Both are prokaryotic and reproduce via binary fission and contain circular DNA

Archaea

• Many are extremophiles, thriving in extreme conditions like high temperature, acidic, or anaerobic environments.
• No archaea species are pathogenic.
• Have multiple types of RNA polymerase.
• Possess ether-linked lipids in their membranes.

Bacteria

• Small, diverse in shape, including cocci, rod-shaped bacilli, spirilla, or spirochetes.
• Primarily unicellular, but some form colonies.
• Can produce endospores in adverse conditions.
• Cell walls contain peptidoglycan.
• Have a single type of RNA polymerase.
• Possess ester-linked fatty acids in the membrane.

Transfer of Antibiotic Resistance

• Overuse of antibiotics, such as in animal feed, leads to the evolution of resistant bacteria, which can spread to crops and humans.
• Failure to complete full antibiotic courses contributes to resistance.
• Antibiotic use drives the evolution of resistant bacteria.

Antibiotic Sensitivity in Bacteria

• The zone of inhibition is the area where bacteria cannot grow due to an antibiotic's effect.
• A large zone indicates the antibiotic is effective at low concentrations, signifying bacterial sensitivity.
• A small zone or no zone indicates bacterial resistance to the antibiotic.

Carbon and Energy Sources in Bacteria

• Photoautotrophs use sunlight for energy and CO2 for carbon, e.g., cyanobacteria.
• Photoheterotrophs use sunlight for energy but get carbon from organic compounds, e.g., purple non-sulfur bacteria.
• Chemoautotrophs get carbon from CO2 and oxidize inorganic molecules for energy.
• Chemoheterotrophs obtain both energy and carbon from organic compounds.

Organization of Genetic Information in Bacteria

• A single, circular DNA molecule is located in the nucleoid.
• Plasmids are small, circular DNA molecules carrying genes.
• Bacteria lack a nucleus, so DNA floats in the cytoplasm.

Morphological Types of Bacteria

• Cocci are spherical or round-shaped bacteria.
• Bacilli are rod-shaped bacteria.
• Spirilla are spiral-shaped bacteria.
• Spirochetes are corkscrew-shaped bacteria.

Gram Types and Gram Staining Technique

Gram Types

• Gram-positive bacteria have a thick peptidoglycan layer in their cell walls, which stain purple.
• Gram-negative bacteria have a thin peptidoglycan layer and an outer membrane, staining pink.

Gram Staining Technique

• Bacteria are stained with crystal violet dye for 60 seconds and then rinsed.
• Slides are covered with Gram's iodine for 60 seconds.
• Samples are washed with ethanol for 10 seconds to dehydrate the cell wall and rinse out the dye-iodine complex.
• Safranin is used as a counterstain, staining Gram-negative bacteria pink while Gram-positive bacteria remain purple.

General Methods of Taxonomy Construction

• Taxonomy classifies organisms based on characteristics.
• Physical traits include shape, size, color, and symmetry.
• Molecular classification uses DNA or RNA similarities and differences.

Domains of Life

• The five-kingdom system includes Monera, Protista, Fungi, Plantae, and Animalia.
• The three-domain system divides prokaryotes from the Monera kingdom into Archaea, Bacteria, and Eukarya.

Key Distinctive Features of Three Domains

Bacteria

• Cell walls contain peptidoglycan.
• Membrane lipids have ester-linked fatty acids.
• One type of RNA polymerase.
• Can be pathogenic.
• Prokaryotic.

Archaea

• Ether-linked membrane lipids.
• Many are extremophiles, living in extreme environments.
• Unique metabolic pathways like methanogenesis.
• Prokaryotic.

Eukarya

• True nucleus and membrane-bound organelles.
• DNA is linear and packaged into multiple chromosomes.
• Reproduce via mitosis or meiosis, unlike binary fission in prokaryotes.
• Eukaryotic.

General Characteristics of Kingdoms and Major Groups in Domain Eukarya

Amoebozoa

• Unicellular, often with pseudopodia for movement and feeding.
• Lacks a cell wall.
• Includes amoebas and slime molds.

Excavata

• Unicellular with a groove for feeding.
• May have modified mitochondria.
• Includes euglenoids, kinetoplastids, and diplomonads (e.g., Trypanosoma).

Alveolata

• Have membrane-bound sacs called alveoli.
• Includes ciliates, dinoflagellates, and apicomplexans (e.g., Plasmodium).

Stramenopila

• Have two types of flagella.
• Often photosynthetic with chloroplasts.
• Multicellular.
• Includes diatoms, brown algae, and oomycetes (water molds), (kelp).

Rhizaria

• Mostly unicellular, with thread-like pseudopodia.
• Often have external shells made of calcium carbonate or silica.
• Includes foraminifera and radiolarians.

Plantae

• Multicellular and photosynthetic.
• Cell walls are made of cellulose.
• Includes mosses, ferns, gymnosperms, and angiosperms.

Fungi

• Can be multicellular or unicellular (yeasts).
• Heterotrophic.
• Cell walls are made of chitin.
• Includes mushrooms, molds, and yeasts.

Animalia

• Multicellular.
• Heterotrophic.
• Lack cell walls.
• Includes invertebrates and vertebrates.

General Characteristics of Protists

• Eukaryotic.
• Paraphyletic group.
• Mostly unicellular, some multicellular (certain algae).
• Diverse.
• Found in moist environments: freshwater, marine, or damp soil.
• Can be heterotrophic, autotrophic, or mixotrophic.
• Move using cilia, flagella, or pseudopodia.

Defining Features of Protists Studied in the Lab

Euglena

• Unicellular and spindle-shaped.
• Mixotrophic: photosynthetic and heterotrophic.
• Moves via flagella.

Trypanosoma

• Unicellular and elongated spindle shape.
• Heterotrophic (parasitic).
• Moves via flagella.

Micrasterias

• Star-shaped with two lobes.
• Autotrophic (photosynthetic).
• Moves via cilia

Amoebae

• Irregular shape, can change form.
• Heterotrophic (phagocytosis).
• Moves via pseudopodia.

Diatoms

• Glass-like silica-based shell.
• Autotrophic (photosynthetic).
• Movement relies on ocean currents.

Dinoflagellates

• Have two flagella.
• Autotrophic (photosynthetic) or heterotrophic.
• Moves via two flagella.

Spirogyra

• Filamentous with spiral-shaped chloroplasts.
• Autotrophic (photosynthetic).
• Movement involves bending and curving their long filaments.

Volvox

• Spherical colony of many cells.
• Autotrophic (photosynthetic).
• Moves via flagella.

Chlamydomonas

• Oval-shaped.
• Autotrophic (photosynthetic).
• Moves via two flagella.

Stentor

• Trumpet-shaped.
• Heterotrophic filter feeder.
• Moves via cilia.

General Characteristics of Cyanobacteria

• Photosynthetic, prokaryotic organisms containing chlorophyll.
• Perform oxygenic photosynthesis.
• Often form colonies and live in various environments.
• Some have heterocysts for nitrogen fixation and akinetes for survival.

General Characteristics of Plants

• Multicellular.
• Photoautotrophs.
• Chloroplasts contain chlorophyll a and b and β-carotene.
• Cell walls made of cellulose.
• Carbohydrates are stored as starch.
• Exhibit alternation of generations life cycle.

Adaptations to Land in Plants

• A waxy cuticle retains water to prevent drying out.
• Vascular tissue: xylem transports water and nutrients, and phloem transports food.
• Roots anchor the plant and absorb water and minerals from the soil.
• Stomata permit gas exchange and prevent desiccation.
• Lignin provides structural support, allowing plants to stand upright.

Alternation of Generations in Plants

• Bryophytes= gametophyte dominant
• Others= sporophyte dominant
• Bryophytes need water for fertilization, as sperm must swim to the egg.
• Angiosperms form seeds and do not require water for fertilization; they use pollen instead.

Differences in Reproductive Structures in Plants

Mosses

• Produce spores in sporangium and gametangia.
• Sperm swim to eggs in water.

Ferns

• Sporangium, which form sori.
• Flagellated sperm.

Pinophyta (Conifers, Gymnosperms)

• Reproductive structure: male and female cones.
• Have seeds. Wind pollination, pollen fertilizes ovules in female cones.

Angiosperms

• Structure: Stamens and carpels.
• Anthers produce pollen, ovary contains ovules.
• Have seeds that can be enclosed in fruit.

General Characteristics of Fungi

• Eukaryotic cells.
• Absorptive chemoheterotrophs.
• They secrete enzymes and absorb the products (extracellular digestion).
• Non-motile.
• Can be unicellular (yeasts) or multicellular, made of filaments called hyphae, which form a network known as a mycelium.
• Cell walls are made up of chitin
• Can reproduce asexually by budding or sexually
• Haploid dominant life cycles

Defining Characteristics of Phyla

Ascomycota

• Produce spores in an ascus.
• Includes yeasts, molds, and morels.
• Reproduce sexually via ascospores and asexually via conidia.
• Many form lichens with algae.

Basidiomycota

• Produce spores on basidia.
• Includes mushrooms, rusts, and puffballs.
• Sexual reproduction via basidiospores.

Zygomycota

• Form zygospores from zygosporangium during sexual reproduction.
• Usually asexual reproduction via sporangiospores from sporangium.

Sexual and Asexual Reproduction and Reproductive Structures

Ascomycota (Sac Fungi)

• Sexual Reproduction: Formation of ascospores inside ascus
• Sexual Reproductive Structures: Ascus (sac) containing 8 ascospores, found in ascocarps (fruiting bodies)
• Asexual Reproduction: Produces asexual spores, conidia
• Asexual Reproductive Structures: Conidiospores

Basidiomycota (Club Fungi)

• Sexual Reproduction: Formation of basidiospores
• Sexual Reproductive Structures: Basidium found in basidiocarps
• Asexual Reproduction: Rare some can through budding/fragmentation
• Asexual Reproductive Structures: Conidia (if present)

Zygomycota

• Sexual Reproduction: Formation of zygospores inside zygosporangium after fusion of hyphae
• Sexual Reproductive Structures: Zygosporangium
• Asexual Reproduction: Produces sporangiospores inside a sporangium
• Asexual Reproductive Structures: Sporangium

Differences in Cell Wall Structure

• Bacteria have peptidoglycan.
• Fungi have chitin.
• Animals don’t have cell walls but can have chitin in exoskeletons.
• Plants have cellulose.
• Archaea don't have peptidoglycan.

General Characteristics of Animals

• Multicellular.
• Chemoheterotrophic; obtain nutrition by ingestion (most species).
• Move under their own power at some point in their life cycle.
• Have eukaryotic cells.
• Lack cell walls but have extensive ECM.
• Have nerve cells and muscle cells.
• Can reproduce sexually or asexually.
• Diploid as adults, only haploid cells being gametes made during sexual reproduction (most species).

Evolution of Animal Body Plans in Different Animal Phyla

Porifera (Sponges)

• No true tissue layers (0 tissue layers).
• Asymmetrical.
• No cephalization.
• Digestive System: N/A
• Coelom: N/A

Cnidaria (Jellyfish, Sea Anemones, Corals)

• Two tissue layers.
• Radial symmetry.
• No cephalization.
• Digestive System: N/A
• Coelom: N/A

Platyhelminthes (Tapeworms, Flukes, Turbellaria)

• Three tissue layers.
• Bilateral symmetry.
• Yes cephalization.
• Protostomes development-mouth before anus formed
• Coelom: N/A

Nematoda (Roundworms)

• Three tissue layers.
• Bilateral symmetry.
• Yes cephalization.
• Protostomes development
• Pseudocoelom coelom

Annelida (Earthworms, Leeches)

• Three tissue layers.
• Bilateral symmetry.
• Yes cephalization.
• Protostomes development
• True coelom

Mollusca (Gastropods, Octopus, Cuttlefish, Squid)

• Three tissue layers.
• Bilateral symmetry.
• Yes cephalization.
• Protostomes development
• True coelom

Arthropoda (Spiders, Scorpions, Crustaceans)

• Three tissue layers.
• Bilateral symmetry.
• Yes cephalization.
• Protostomes development
• True coelom

Echinodermata (Starfish, Sea Urchins, Sea Cucumbers)

• Three tissue layers.
• Radial as adults, bilateral as larvae symmetry.
• No cephalization.
• Deuterostomes development
• Entrocoleic coelom

Chordata (Mammals, Vertebrates, Reptiles, Amphibians)

• Three tissue layers.
• Bilateral symmetry.
• Yes cephalization.
• Deuterostomes development
• Enterocoelem

General Characteristics of Major Invertebrate Phyla + Four Subphyla of Arthropods

Porifera

• Endoskeleton, sponges are porous with spicules for structure.
• Intracellular digestion
• Filter feeders
• NO CS, Water flows through pores facilitates gas exchange
• Sessile
• Pores and canals for water flow

Cnidaria

• No skeleton, soft body, some have hydrostatic skeleton
• Extracellular digestion.
• NO CS, diffusion for oxygen transport
• Mostly sessile or free swimming (jet propulsion) or muscle contraction
• Have stinging cells

Platyhelminthes (flat worms)

• No skeleton, soft body
• Incomplete digestive system only.
• Use mouth only. Have no anus
• No CS, diffusion for oxygen transport
• Slither or glide using cilia
• Bilaterally symmetric, some parasitic (tapeworms)

Nematoda (roundworms)

• Hydrostatic skeleton.
• Complete digestive system, mouth and anus.
• No CS, diffusion for oxygen transport
• Use muscles to move
• Parasitic species, flexible cuticle

Annelida (segmented worms)

• Hydrostatic skelton
• Complete digestive system, mouth and anus.
• Closed circulatory system
• Use setae or parapodia for movement
• Segmentation

Mollusca

• Exoskeleton in most, some have internal shell or none.
• Complete digestive system, mouth and anus.
• Open circulatory system
• Muscular foot for movement
• Have radula to scrape food

Echinodermata (star fishes etc)

• Endoskeleton, radial symmetry, spiny skins
• Complete digestive system, mouth and anus
• Water vascular system for oxygen transport
• Tube feet for movement, some slow moving others sessile
• Regeneration, spiny skin, unique water vascular system

Arthropoda

• Exoskeleton (chitin)
• Complete digestive system, mouth and anus
• Open circulatory system
• Jointed legs
• Can undergo molting, and exoskeleton for support

Chelicerata (spiders)

• Exoskeleton.
• Complete digestive system
• Open circulatory system
• Walking or crawling
• Fangs for feeding/defense

Myriapoda (centipedes)

• Exoskeleton.
• Complete digestive system
• Open circulatory system
• Walking
• Many body segments and legs, some venomous

Hexapoda (insects)

• Exoskeleton
• Complete digestive system
• Open circulatory system
• Walking, flying
• Three pairs of legs, wings in many species

Crustacea (aquatic crabs)

• Exoskeleton
• Complete digestive system
• Open circulatory system
• Walking, swimming
• Two pairs antennae, gills for respiration in many

Characteristics of Chordata

• Bilateral, triploblastic, coelomate with deuterostome development and exhbits the 4 below at some pt:
• Notochord: flexible rod that provides support along the animal's length, against which muscles can act for locomotion
• Dorsal, hollow nerve cord: a bundle of nerve cells that runs the body's length
• Pharyngeal slits: may fx in suspension or be modified as gill slits
• Muscular, post-anal tail: initially evolved for locomotion in water

Characteristics and Phyla of Invertebrate Chordates

Cephalochordate (Lancelets)

• Elongated, fish-like body, no distinct head.
• Notochord instead of backbone.
• Complete digestive system.
• Closed CS, no heart.
• Sexual reproduction, external fertilization.
• Swim using segmented muscles along body.
• Larvae free swimming, adults bury themselves in sand and Filter feeding.

Urochordata (Tunicates, "Sea Squirts")

• Bag-like sac body with tunic covering.
• Notochord only in larvae, not in adults.
• Complete digestive system.
• Open CS.
• Sexual reproduction, external fertilization.
• Larvae swim, adults sessile.
• Use pharyngeal slits for suspension feeding.
• Adult tunicates characterised by 2 siphons

General Characteristics of Major Vertebrate Phyla

Agnatha (Jawless Fish)

• Morphology: Elongated, eel-like body, no jaws, circular mouth
• Type of Skeleton: Cartilaginous skeleton
• Digestive System: Complete (mouth, intestine, anus)
• Circulatory System: Closed (2-chambered heart)
• Reproduction: External fertilization (some)
• Mode of Movement: Swim via undulating body, no paired fins
• Special Features: Lack jaws and paired fins, ancient lineage

Chondrichthyes (Cartilaginous Fish)

• Morphology: Streamlined body, cartilaginous skeleton, well-developed fins
• Type of Skeleton: Cartilage skeleton
• Digestive System: Complete (mouth, intestine, anus)
• Circulatory System: Closed (2-chambered heart)
• Reproduction: Internal fertilization
• Mode of Movement: Swim using fins
• Special Features: Placoid scales, electroreception, spiracles for breathing

Osteichthyes (Bony Fish)

• Morphology: Streamlined body, scales, paired fins, well-developed gills
• Type of Skeleton: Bony skeleton
• Digestive System: Complete (mouth, intestine, anus)
• Circulatory System: Closed (2-chambered heart)
• Reproduction: External fertilization (mostly)
• Mode of Movement: Swim with fins
• Special Features: Operculum covering gills, lateral line system, diverse group

Amphibia (Amphibians)

• Morphology: Moist, permeable skin, three distinct body regions
• Type of Skeleton: Bony skeleton
• Digestive System: Complete (mouth, intestine, anus)
• Circulatory System: Closed (3-chambered heart)
• Reproduction: External fertilization (mostly)
• Mode of Movement: Limbs for movement or by crawling, some aquatic larvae
• Special Features: Metamorphosis

Reptilia (Reptiles)

• Morphology: Dry, scaly skin, three distinct body regions
• Type of Skeleton: Bony skeleton
• Digestive System: Complete (mouth, intestine, anus)
• Circulatory System: Closed (3 or 4-chambered heart)
• Reproduction: Internal fertilization (mostly oviparous)
• Mode of Movement: Walk, crawl, some fly (e.g., birds)
• Special Features: Ectothermic

Aves (Birds)

• Morphology: Feathered body, beak, hollow bones
• Type of Skeleton: Bony skeleton
• Digestive System: Complete (mouth, intestine, anus)
• Circulatory System: Closed (4-chambered heart)
• Reproduction: Internal fertilization, oviparous
• Mode of Movement: Fly, walk, swim using wings and legs
• Special Features: Endothermic (warm-blooded)

Mammalia (Mammals)

• Morphology: Hair or fur, specialized teeth, mammary glands
• Type of Skeleton: Bony skeleton
• Digestive System: Complete (mouth, intestine, anus)
• Circulatory System: Closed (4-chambered heart)
• Reproduction: Internal, viviparous (most)
• Mode of Movement: Walk, run, swim, use limbs
• Special Features: Endothermic

Evolution of the Heart, Single and Double Circulation

• Single circulation (in fish): blood passes through the heart once per cycle, heart-> gills (oxygenated)-> body (delivers O2)-> heart.
  • Less efficient.
• Double circulation (amphibians, reptiles, birds, mammals): Blood passes through the heart 2x per cycle. More efficient
  • 2 loops:
  • 1. Pulmonary circulation- Heart-> lungs (oxygenated)-> heart
  • 2. Systemic circulation - Heart-> body (delivers O2)-> heart

Transfer of Oxygen to the Blood Using Gills

• Water flows in through the fish's mouth and over the gills.
• O2 from water moves into the blood in the gill capillaries.
• Co2 moves out from the blood into the water.
• Oxygen-rich blood travels to the fish's body.
• Water and blood flow in opposite directions, keeping oxygen transfer efficient

Defining Characteristics of Major Tetrapod Classes

Amphibia

• Morphology: Moist, permeable skin.
• Type of Skeleton: Bony skeleton.
• CS: Closed circulatory system (3-chambered heart)
• Reproduction: External fertilization (mostly), some internal fertilization
• Adaptations to Life Out of Water: Metamorphosis from aquatic larvae, gill or lung breathing

Reptiles

• Morphology: Dry, scaly skin.
• Type of Skeleton: Bony skeleton.
• CS: Closed circulatory system (3-chambered heart)
• Reproduction: Internal fertilization, mostly oviparous
• Adaptations to Life Out of Water: Amniotic egg, ectothermic

Mammals

• Morphology: Hair or fur covering.
• Type of Skeleton: Bony skeleton.
• CS: Closed circulatory system (3-chambered heart)
• Reproduction: Internal fertilization, viviparous (most)
• Adaptations to Life Out of Water: Endothermic, live birth, mammary glands, hair