Domains of Life: Bacteria, Archaea, and Eukarya

Domains of Life

• Life splits into Bacteria, Archaea, and Eukarya (Eukaryotes).

Prokaryotic Characteristics

• They lack membrane-bound nuclei and organelles.
• Most are unicellular but may form colonies.
• The makeup of their plasma membranes and cell walls vary.

Eukaryotic Characteristics

• They have nuclei and membrane-bound organelles.

Microbiology & Extremophiles

• Microbiology is the study of microbes.
• Extremophiles are organisms thriving in extreme habitats like hydrothermal vents (pH < 1.0), under Antarctic ice (0°C), or in water 5-10 times saltier than seawater.
• Studying extremophiles can help with understanding the origin of life.

Morphological Diversity in Prokaryotes

• Size ranges from small to large.
• Shapes and arrangements include filaments, spheres, rods, and chains to spirals.
• Motility can be achieved using flagella for swimming.

Genetic Variation & Lateral Gene Transfer

• Lateral Gene Transfer allows DNA to move between cells.

Three Ways of Lateral Gene Transfer

• Transformation: Bacteria take DNA from their environment after its released by cell lysis or secretion.
• Transduction: Viruses transfer DNA from one prokaryotic cell to another.
• Conjugation: Genetic information transfers through direct cell-to-cell contact via a sex pilus, moving a small, circular DNA piece (plasmid).

Obtaining Organic Compounds

• Organisms must make or obtain organic compounds.
• These compounds are essential as building blocks for synthesizing molecules and cellular components.
• Organic compounds contain carbon.
• Autotrophs make their own organic compounds using various methods such as plants that use CO2 as their carbon source.
• Heterotrophs consume building-block compounds from their environment, including other organisms.
• Mixotrophs are capable of both autotrophic and heterotrophic modes.

Metabolic Diversity

• All organisms need chemical energy to make ATP.

ATP Production Methods

• Phototrophs use light to excite electrons for energy.
• Chemoorganotrophs obtain energy from organic molecules.
• Chemolithotrophs get energy from inorganic molecules.
• Electrons transfer down the electron transport chain (ETC) from electron donors to acceptors with ATP being produced.
• Eukaryotes use glucose as an electron donor and oxygen (O2) as the final electron acceptor.
• Prokaryotes utilize a variety of electron donors and acceptors.
• Fermentation makes ATP without using the electron transport chain.
• Fermentation is less efficient than respiration and doesn't use an outside electron acceptor.
• Prokaryotic and archaea use light to turn ADP into ATP through photophosphorylation.

Types of Photophosphorylation

• Bacteriorhodopsin uses energy from light to create a proton gradient that drives ATP synthesis.
• Geothermal Radiation: Some bacteria use geothermal radiation.
• Pigments move electrons through electron transport chains to generate ATP.
• Different Electron Donors & Acceptors that can be used.

Oxygenic vs. Anoxygenic Photosynthesis

• Oxygenic Photosynthesis produces O2 such as in cyanobacteria.
• Anoxygenic Photosynthesis does not produce O2.
• Methanogens produce methane (CH4) as a byproduct of cellular respiration.

The Oxygen Revolution

• There was no O2 for the first 2.3 billion years of Earth's history.
• Cyanobacteria are a monophyletic group of photosynthetic bacteria and were the first organisms to perform oxygenic photosynthesis.
• Before this, only anaerobic respiration was possible.
• It changed Earth’s atmosphere to one with a high concentration of oxygen.
• It likely led to a mass extinction called the "Oxygen Revolution" or "The Great Oxygen Catastrophe".
• This allowed for aerobic respiration.
• Oxygen is electronegative and as such is an efficient electron acceptor.

The Nitrogen Cycle

• Nitrogen Fixation: Some prokaryotes turn atmospheric N₂ into Ammonia (NH3) to make nitrogen usable for other organisms.

Examples of Nitrogen-Fixing Organisms

• Azolla: An aquatic fern has a mutualistic relationship with nitrogen-fixing cyanobacteria (Anabaena).
• Other nitrogen-fixing plants are legumes, alders (Alnus), and cycads.
• Denitrification is where prokaryotes convert nitrogen compounds into atmospheric N2 and occurs in anaerobic conditions.
• Nitrogen compounds act as electron acceptors in respiration.

The Haber Process

• Industrial nitrogen fixation converts N2 into NH3 for synthetic fertilizers.
• Revolutionized agriculture, feeding billions.
• About 50% of the nitrogen in the body comes from this process.

Nitrate Pollution & Eutrophication

• Excess fertilizers containing nitrogen enter water bodies, causing disruption of ecosystems.
• Eutrophication is the excessive nutrient buildup leads to algal blooms (rapid algae growth).
• Algal Blooms can produce toxins and can be harmful to other organisms.
• Dead Zones occur where oxygen levels are too low to support most life, caused by decomposing algal blooms consuming oxygen.

Major Bacterial Lineages

• Actinobacteria are filamentous bacteria found in soil and are key decomposers.
• Streptomyces produces over 3,000 antimicrobial compounds, including antibiotics.
• Frankia some species fix nitrogen.
• Mycobacterium tuberculosis causes tuberculosis.
• Chlamydiae is the least diverse bacterial group, with only 13 known species.
• They are endosymbionts that live inside host cells.
• Chlamydia causes the sexually transmitted infection.
• Cyanobacteria are a diverse group of photosynthetic bacteria.
• The first group to produce oxygen through oxygenic photosynthesis.
• Some species fix nitrogen using heterocysts – specialized cells that create an anaerobic environment.
• Spirochaetes are corkscrew-shaped bacteria that move with endoflagella.
• Endoflagella are internal flagella located inside a sheath around the cell.
• Borrelia causes Lyme disease.
• Firmicutes are commonly found in animal intestines.
• They are often involved in mutualistic digestion.
• Some species are vital in food processing, and others cause diseases.
• Proteobacteria is one of the largest and most diverse bacterial groups including E. coli which is widely used in research.
• Nitrogen-fixing bacteria in root nodules are essential for plant growth.
• Wolbachia is a parasitic bacterium that manipulates the reproductive systems of insects and arthropods.
• Mitochondria's ancestor: The endosymbiotic origin of mitochondria traces back to a proteobacterium.

Eukaryotic Features & Evolution

• Fundamental Features of Eukaryotes are that they are mostly large, have more organelles, a nuclear envelope.
• They evolved multicellularity multiple times and can reproduce both asexually and sexually.
• Protists are a paraphyletic group of eukaryotes (excluding fungi, animals, and land plants).
• They have diversity in size and habitat.
• Protists are medically and ecologically important.

Endosymbiosis Theory & the Origin of Mitochondria

• This theory states some organelles originated from engulfed bacterial cells.
• The engulfed bacteria lived inside the host in a mutualistic relationship, eventually evolving into organelles.
• Evidence That Mitochondria Originated from Endosymbiosis: they share similar size to bacteria, have their machinery (ribosomes), and two sets of membranes.
• Chloroplasts Came from Cyanobacteria:
• Cyanobacterium was engulfed by a eukaryotic cell.
• This allowed the host cell to gain the ability to perform photosynthesis. -The chloroplast have bacterial-like characteristics, have cell walls containing peptidoglycan, and contain circular DNA.
• Secondary Endosymbiosis occurs when a eukaryotic cell engulfs another eukaryotic cell that has already undergone primary endosymbiosis.
• The Evolution of the Nuclear Envelope came when it was formed from the infolding of the plasma membrane.
• Early infolding likely gave rise to the endoplasmic reticulum (ER).
• It evolved to separate DNA transcription from translation.
• Synapomorphy of the Nucleus: a distinctive structure that defines a monophyletic group.

Structures for Support and Protection in Eukaryotes

• Cell Walls:
• Diatoms are surrounded by a glass-like cell wall of silicon dioxide.
• Cellulose Plates are found in some protists.
• Also hard external shells occur and rigid internal structures inside the plasma membrane

Multicellularity

• Multicellular organisms have more than one cell.
• Mutation led to multicellularity.
• It first caused cells to stick together (mutation prevented complete mitosis).
• Not all cells express the same genes in multicellular organisms.

How Do Protists Obtain Food?

• Ingesting packets of food
• Absorbing organic molecules directly from the environment
• Performing photosynthesis

Autotrophic Protists

• Autotrophic protists produce organic compounds via photosynthesis.
• CO2 is used as their primary source of carbon.

Ingestive Feeding

• Ingestive feeding done by taking in chunks of food (organic debris).
• Phagocytosis is a process where a protist surrounds and ingest prokaryotes, other protists, or even animals
• This process happens due to the lack of a cell wall.
• Absorptive Feeding occurs when nutrients are taken up across the plasma membrane, directly from the environment.
• Decomposers feed on dead organic matter (detritus).
• Parasites absorb nutrients from the host's environment.
• Amoeboid Motion happens when they move using pseudopodia (long, finger-like projections)
• It requires ATP and is similar to muscle movement in animals
• Immune system cells in humans use amoeboid motion.
• Swimming via Flagella or Cilia
• Flagella are long and found alone or in pairs.
• Cilia are short and numerous.

Reproduction in Protists

• Asexual Reproduction is when one cell splits into two identical cells.
• Prokaryotic asexual reproduction is called binary fission.
• Unicellular eukaryotic asexual reproduction occurs via mitosis (cell division).
• Multicellular eukaryotes can also reproduce asexually through various methods.
• Sexual Reproduction in Eukaryotes is when Eukarya is the only domain capable of sexual reproduction, based on meiosis (cell division that produces gametes) and fusion of gametes.
• The benefits of sexual reproduction is that it helps genetically variable offspring to fight diseases in the populations, and allows natural selection and gene shuffling which leads to genetic purging and new trait combinations.

Life Cycles in Eukaryotes

• Haploid vs. Diploid Dominated: the evolution of meiosis introduced haploid and diploid phases in life cycles.
• Bacteria and archaea are always haploid.
• Some eukaryotes have life cycles that are dominated by haploid cells and others dominated by diploid cells.
• Alternation of Generations is when some multicellular protists and all land plants exhibit alternation of generations where it always involves the same sequence of events

1. Sporophyte (diploid) produces haploid spores by meiosis.
2. Spores germinate and divide by mitosis to develop into multicellular haploid gametophytes.
3. Gametophytes produce unicellular haploid gametes by mitosis.
4. Two gametes fuse during fertilization, forming a diploid zygote.
5. Zygote divides by mitosis, developing itno a multicellular diploid sporophyte.

• Gametophytes produce gametes through mitosis.
• Sporophytes produce spores through meiosis.
• Eukaryotes are classified based on cell structure and distinctive organelles.

Seven Major Eukaryotic Lineages

• Amoebozoa which lacks cell walls, engages with engulfing food (phagocytosis), moves by ameboid motion, and is found in freshwater habitats, wet soil, and as parasites of animals and humans.
• Opisthokonta includes fungi, animals, and some protists and have a single flagellum at the base of reproductive cells.
• "Opisthen" = means behind and “Kontos" = "pole" and refers to the flagellum.
• Excavata have an excavated feeding groove, some lack mitochondria, move with flagella and reproduce mostly asexually.
• Plantae are a monophyletic group where all subgroups have chloroplasts from a cyanobacterial ancestor, a wall containing cellulose and are important producers.
• Rhizaria are single-celled, lack cell walls, and move by amoeboid motion with slender pseudopodia.
• Alveolata have alveoli (flattened vesicles under the memebrane) and some exihibit bioluminescence, are unicellular and can emit light.
• Stramenopila have "hairy" flagella, include diatoms, brown algae, and water molds and a mix of unicellular and multicellular organisms.
• Green Algae & Land Plants (Viridiplantae)
• Green Algae is unicellular, the oldest group and primary producers in freshwater habitats.
• Lichens have a mutualistic association between fungi and green algae/cyanobacteria.

Adaptations for Life on Land

• Preventing Water Loss via cuticle and Stomata.
• Cuticle: Waxy covering that prevents water loss
• Stomata: Pores for gas exchange, controlled by guard cells
• Protection from UV Radiation happens by UV-absorbing compounds that act as a sunscreen to prevent DNA damage

Reproduction Adaptations in Land Plants

• Spores are Single-celled, haploid encased in sporopollenin (a tough, chemically-inert polymer) and are resistant to drying
• Gametangia are Structures that protect gametes from drying where antheridium produce sperm and archegonium produces eggs
• Retention of the Fertilized Egg happens when land plants retain eggs or zygotes instad of sheddding them instead retain them.

The development of Plants

• The zygote begins development on the parent plant.
• Multicellular embryos remain attached and nourished by the parent plant.
• Land plants belong to Embryophyta – "the embryo plants".
• Nonvascular Plants appeared was the first plants on land at ~475 MYA and it lacks vascular tissue and cannot transport water due to being small.
• They are low-growing and require water.
• They reproduce with spores (not seeds) and have a gametophyte-dominant life cycle.
• Flagellated sperm require water to swim to the egg.
• Examples of this are mosses, liverworts and hornworts.
• Nonvascular Plant Life Cycle:
• They go though a Gametophyte-dominant life cycle, where sporophyte is small, short-lived, and dependent on gametophyte for nutrition.

Challenges of Upright Growth for adapting to Life on Land

• Nonvascular plants must be small or hug the ground for water.
• Growing upright provides better sunlight access but creates challenges:

1. Transporting water from soil to air-exposed tissues
2. Providing structural support to prevent falling over

• Solution: Evolution of Vascular Tissue
• It allowed plants to transport water along with nutrients and provided support.
• Origins of Vascular Tissue
• Earliest land plants had elongated water-conducting cells that are similar to modern mosses.
• Water-conducting cells evolved over time and the first that arose was true walls when lignin rings reinfoced the cell walls.
• Lignin is a strong polymer that offers support.

Tracheids and Vessel Elements

• Tracheids are long, thin, tapering water-conducting cells.
• Tracheids have a thick lignin and pits to allow water to pass between cells and is present in vascular plants at -380 MYA. -Vessels elements came later at ~250–270 MYA and are shorter, wide than tracheidswith performations and are in angiosperms.
• Vascular Plants that are Monophyletic and evolves vascular tissue one with two groups.

1. Seedless vascular plants that are not seeeded plants reprouces spores
2. Seed plants (embryo + food + protective coat) Seedless Vascular Plants that spoe and seedess.
3. Spores are despersed withind.

• Has tracheids with vessels.

Seed Plants

• Seeds protect the embryo & provide nutrients.
• Pollen allows without.
• 2 groups gymnosperms Angiosperms - Flowers and have encased seeds.
• Help water regulation
• Allows reproduc
• Symbiosis with fungi enhance and nutrient obsorptio.

adaptations:

• Seed protection
• Seed structure.
• Heterosory is the productions by diffent types of structures.
• microsporangia
• megosparagia
• Gametophyte are the seed that is either female or male never both.
• Plant are homoporyus.
• Pollin is the male.
• Micropores develops into

Seeds

• Seed protected in ovaries
• Seed product
• Flower is a synapomorphy
• Pollinator effect pollen transfer
• Pollinators

Structure:

Sepals protection with color and attraction

• Stamen pollen
• Carples ovaries egg
• Poly lands
• Polinates stimia to egg
• Sperm endosperm
• Plants cornn on same plant

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• Clima flowers
• Triggers to embryos and derived to ovary that are on the plnts wind or transport and Help aid to sperseal

Clina is ripwened till attached

• Angisperm
• Angio so good at the tree main things
• Vessel water transfer
• Flowers effectivity
• Fruits the deiversal
• One monocots.

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• Need Light water
• Macromolecule synthesis.
• Shoot is harvest and

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