Structural Biochemistry/Three Domains of Life/Eukarya

History
Thought to be more than 1.7 billion years ago, the Domain Eukarya was the last to evolve. The Domain includes all organisms with a eukaryotic cell which contain membranous organelles such as mitochondria and chloroplasts. Through comparison of ribosomal RNAs and nucleotide sequences, the Eukarya domain finds itself more closely related to the Archaea rather than Bacteria domain. Eukaryotic organisms are characterized by a membrane-enclosed nucleus containing the organism's genetic material, or DNA, and corresponding proteins. All animals, plants, fungi, and protists fall under this taxonomic group.

Eukaryotes are classified according to how they obtain energy from the surrounding environment. Phototrophs obtain energy from light, whereas chemotrophs obtain energy via oxidation of chemical fuels. All phototrophic eukaryotes derive carbon from CO2. All non-phototrophic eukaryotes depend on organics for their carbon source, and are therefore termed organotrophs.

Animals
Animals belong to the kingdom Animalia. They are heterotrophs and therefore require the ingestion of organic compounds for energy. Animals are usually multi-cellular. About 95% are invertebrates. Unlike other classes of eukaryotes, animals contain cells that lack cell walls.

Kingdom Animalia is divided into two subkingdoms:

a. Parazoa: lack tissues and organs.

- Porifera (Sponges) : mostly live in marine, though some live in freshwater. They are asymmetrical. Their shape and size depends on the environment or substrate to which they are attached. Sponges are sessile and contain stationary life. They are made up of two layers: the epidermis and an inner layer of flagellated choanocytes. They capture food suspended in the water. Individual sponges are capable of producing both eggs and sperm.

b. Eumetazoa: remains as the rest of animal phyla. They are true multicellular animals with differentiated tissues.

- Cnidaria : Some examples of this phylum are coral, sea anemores, and jelly fish. They have radial symmetry. The body is divided into 2 layers of tissues: outer epidermis and inner gastrodermis. Furthermore, there is also mesoglea, which is a gelatinous layer between these top layers.

- Ctenophora : Comb jellies. They are radially symmetrical and have two layers with a very thick mesoglea between them. The mouth is located downward. They move by using 8 vertical rows of cilia or combs. They also posses two long tentacles.

- Protostomes : tripoblastic eumetazoans, possess mesoderm but lack a body cavity. Platyhelminthes (flatworms) falls into this phyla. They are bilaterally symmetrical and flattened animals with distinctive heads. Platyhelminthes are divided into three classes: class Tuberllaria (free-living flatworms), class Trematoda (flukes), class cestoda (tapeworms).

- Pseudocoelomate Protosomes : have mesoderm lines outside of the body cavity and possess pseudocoelom.

+ Rotifera (Wheel Animals) : some live in fresh water ponds and streams, while others are marine and live in soil. They are multicellular animals. They posses a corona, which is used for feeding and locomotion. They have complete digestive tracts consisting of a mouth and anus.

+ Nematoda (Roundworms): are cylindrical worms that taper at both ends. Although some live in soil and water, most are parasitic.

- Annelida (Segmented Worms) : Segmented. They have complete digestive system with specialized compartments: segmented excretory system, closed circulatory systems, and well-developed nervous system. The Annelida are divided into 3 classes:

+ Class Obligochaeta (Earthworms): they have pairs of setae on each segment for locomotion

+ Class Polychaeta (Marine Worms): they have numerous setae (spines). Parapodia, well-developed head but lacks sedentary forms.

+ Class Hirudinea (Leeches): are ectoparasites which feed on blood and tissue fluid of their hosts. The external segmentation is expansion of wrinkles for feeding. They are found in terrestrial, fresh water, and marine environments.

- Mollusca (Clams, Snail, Squid) : Most live in marine while some in fresh water and terrestrial environments. They lack segmentation but have well-developed circulatory system (with a heart), well-developed nervous system, possess radula (rasp-like plate in mouth used for scraping food), mantle ( a layer of cell that secrete a shell CaCO3 and create mantle cavity), feet (muscular organs for locomotion) and visceral mass.

+ Class Polyplacophora (Chitons): marine mollusks that have shells made up of eight plates.

+ Class Gastropoda (Snails): have single, spiraled shell and a distinct head with well-developed eyes and sensory tentacles. This class exhibit torsion which is the coiling shell and internal organs.

+ Class Cephalopoda (Octopus, Squid and Nautilus): The foot is modified into grasping tentacles with suckers. The shell is reduced and internal. All have well-developed eyes and complex nervous systems.

- Arthropoda (Insects, Arachnids, Crustaceans) : They have distinguishing features due to the presence of chitinous, a joined exoskeleton. Also, they have circulatory system, external segmentation, complex sensory organs, and nervous system even though they are invertebrate. Furthermore, they have complex musculat system and exoskeleton that cannot grow but be shed and replaced.

- Trilobitomorpha (Trilobites) : they were once the most numerous arthropods. They have three-lobed shield dorsally. The second segment had a pair of antennae and all following segments have a pair of biramous appendages used as walking legs. Unfortunately, they went extinct.

- Cheliceriformes (Arachnids) : lack antennae but have chelicerae as feeding apparatus. Their body is composed of a cephalothorax and abdomen. The appendages consists of chelicerae, pedipalps, and four pairs of walking legs.

+ Class Arachnida (Scorpions, Spiders, and Ticks): Most of them are terrestrial.

+ Class Merostomata (include Horseshoe Crabs): they all live in marine. The cephalothorax is covered by a single carapace while the abdomen is covered by a shield. Moreover, they have a stout, which is a spike-like telson.

- Myriapoda : Terrestrial. They have single pair of antennae. This phylum is divided into 3 classes:

+Centipedes: the body is segmented with one pair of walking legs per segment.

+ Millipedes: the body is made up of fused double segments and each segment hold two pairs of walking legs. The first four segments that are not fused make up the thorax (which don't have any legs).

- Hexapoda (insects) : are considered as the most successful group. The body consists of three parts : head, thorax, and abdomen. They have three pairs of walking legs on the thorax. Generally, they have wings on the thorax.

+ Class Coleoptera (Beetles)

+ Class Diptera (Flies)

+ Class Hymenoptera (Ants, Bees, Wasps)

+ Class Lepidoptera (Butterflies, Moths)

+ Class Orthoptera (Grasshoppers, Crickets, Katydids)

- Phylum Crustacea : live in aquatic environments, or marine. The head and thorax form a cephalothorax. They have two pairs of antennae, mouth bearing mandibles.

+ Class Cirripedia (Barnacles): they are the only sessile group in this phylum.

+ Class Decapoda (Crabs, Lobsters, Shrimp, Crayfish, Krill): An elongated abdomen and telson ( for swimming)followed by cephalothorax. They are capable of crawling forward slowly.

- Echinodermata : All marine. They have pentaradial symmetry while their larvae have bilateral symmetry. They have CaCO3 endoskeleton. Also, they have vascular system and associated tube feet.

+ Class Asteroidea (Sea Star) : Marine animals. They have central disc and five tubular feet.

+ Class Holothuroidea (Sea cucumbers) they have bilateral symmetry and pentaradial structure. However, they lack endoskeleton and used the thickened epidermis as a protective covering.

+ Class Ophiuroidea (Brittle Stars): they have a small, round disc with five distinct arms which are easily broken. These arms are flexible and used to move in snake-like motion.

+ Class Echinoidea (Sea Urchin, Sand dollar): They have flattened test and short spines.

Some Representative Classes of the Phylum Chordata:


 * Chondrichthyes: cartilaginous fish
 * Osteichthyes: bony fish
 * Sauropsida: reptiles
 * Amphibia: amphibians
 * Aves: birds
 * Mammalia: mammals (mammalary gland)

Plants
Plants belong to the Plantae kingdom. The Plantae kingdom consists of over 300,000 species of multicellular autotrophs that convert sunlight into usable chemical energy through the process known as photosynthesis. Essential to photosynthesis are the pigments chlorophyll-a and b that absorb the light energy. All plants have cell walls made of cellulose. Plants' life cycle involves an alternation of generations in which diploid plants (2n) give rise to haploid plants (n), which through a sexual process, produces diploid plants again. All land plants can be divided into two categories: bryophytes (non-vascular plants) and tracheophytes (vascular plants).

All plants have a life cycle that alternates between a diploid organism and a haploid organism. The diploid form of the life cycle is called the sporophyte, which contains two sets of genetic DNA while the haploid form of the life cycle is the gametophyte, comprising of only one set of DNA. As a result, this phenomenon of a life cycle which switches between a diploid and a haploid organism is called an alternation of generations. The haploid gametophyte cells reproduce through mitosis to form the gametes of the plant, the egg and sperm; when they are fertilized, they form the diploid zygote, which becomes the diploid sporophyte. Later, when the diploid sporophyte reproduces by meiosis, haploid reproductive cells are developed as the gametophytes.

Nonvascular Plants

Bryophytes are thought to be the first land plants. They do not have lignin-impregnated cells and are limited in size because of this. They also lack roots and have structures called rhizoids instead which are somewhat similar. Bryophytes are mainly in the gametophyte (haploid) phase for the majority of their life cycle. This group mainly consists of liverworts, hornworts, and mosses.

Nonvascular plants lack cells that are joined together that function together to transport nutrients and water throughout the whole plant. As a result, these plants are unable to grow tall, giving them the nickname ‘ground hugging plants’ since they only grow close to the ground and form carpets of mosses. The gametophyte stage dominates the life cycle of nonvascular plants, and the sporophyte grows on top of the gametophyte. Some nonvascular plants are bisexual, and they produce both male and female gametophytes. Mosses require a film of water in order for the sperm to get to the egg for fertilization and reproduction. As a result, many mosses are found in environments that remain moist, allowing for ideal moss reproduction. The Sphagnum moss is a collection of moss in the environment that forms a bog, which holds a lot of water. Because of this, sphagnum mosses are oftentimes used in soil fertilizers to help the sandy soil retain more water.

The sporophytes of nonvascular plants are usually attached on top of the gametophyte and it contains three distinct parts, the foot, the seta, and the capsule. The foot is responsible for attaching to the gametophyte, but more importantly, its main function is to absorb nutrients from the gametophyte. The seta is a stalk that is able to transport these nutrients to the capsule. The capsule uses these nutrients to produce spores through meiosis, which will fertilize the eggs and reproduce more moss. One evolutionary adaptation that nonvascular plants have obtained is the use of the peristome, which is a structure that opens and closes based on the environment to allow the spores to be discharged from the capsule. When the environment is dry, the peristome opens, allowing the spores to travel far by the wind, and when the environment is wet, the peristome closes until stronger gusts of winds are present.

Vascular Plants

Tracheophytes tend to be larger and more complex than bryophytes. Unlike the bryophytes, the tracheophytes contain the xylem and phloem, which are used to transport water and sugars throughout the plant. Tracheophytes are mainly in the sporophyte (diploid) phase for the majority of their life cycle. This group consists of ferns, conifers, and flowering plants.

Vascular plants contain the key vascular tissues, xylem and phloem, that allow them to grow taller. On the contrary to nonvascular plants, these plants have dominant sporophytes instead of gametophytes, and the sporophyte is no longer dependent on the gametophyte for nutrients. Vascular plants have roots that absorb nutrients from the soil and transport them to the rest of the plant. Xylem is the plant tissue that is responsible for transporting water and nutrients from the soil to the whole plant. The cell walls of this tissue are strengthened by lignin. The second tissue, phloem, is responsible for transporting the amino acids, sugars, and organic products to other parts of the plant to allow it to grow. With these vascular tissues, plants were able to grow taller and stronger, giving the plant support for more sunlight. As more plants were able to grow taller, they competed to grow taller than each other in order to get more sunlight and produce more sugars and starches. Additionally, these taller plants were able to disperse their spores farther, allowing the population to spread into new environments.

The sporophytes of vascular plants evolved roots and leaves that helped the plant produce more sugars. The roots helped anchor the plant into the ground by forming a huge network of branching roots in the soil. This helped the plant absorb more nutrients from the soil. The leave evolved, allowing the plant to capture more sunlight and produce photosynthesis and producing sugars for itself to grow taller. These seedless vascular plants dominated the forests, growing to hundreds of feet competing for sunlight. Ferns were a dominant plant that was abundant in many varieties.

The seed plant can be divided into two categories, gymnosperms and angiosperms. Seed plants contain a seed, which is the whole ovule which is an embryo that is packed with a food supply and encased in a protective coating. This allows the seed to be dispersed farther distances and still have the nutrients to thrive. Unlike vascular plants, seed plants do not need water in order for fertilization to occur. Gymnosperms have seeds that are exposed and are not enclosed in chambers, such as pine trees, gingko trees, and cycads. Angiosperms are plants with flowers. The reproductive part of the plant is called the flower, and when it is fertilized, it becomes the fruit. Flowering plants have evolved over time in order to increase their chances of getting fertilized by animals or other forces of nature. For examples, some flowering plants evolved red petals, which stand out to birds’ eyes. As a result, when the birds reach with their beaks for the nectar in the flower, the pollen is rubbed onto the bird to be transported to different flowers for fertilization. Another example is that flowers have evolved to have light colored and fragrant flowers, attracting nocturnal animals to pass the pollen on to other flowers for fertilization.

Fungi
Fungi is a member of the kingdom Fungi includes molds, mushrooms, and mildews. Most of fungi are photosynthetic and are either saprotrophic or parasitic. This class of Eukaryotes are heterotrophic and is comprised of hyphae (which forms mycelium) and has cell walls made of chitin. The reproduction of fungi usually involves spores made in specialized structures. Examples of fungi would be yeasts, molds, and mushrooms. They are actually closely related to animals than to plants in the evolution sense. But in studies, fungi are classified under botany. Reproduction can be sexual or asexual. Asexual reproduction generally involves the formation of spores while sexual reproduction involves the production of complex structures. Fungi are divided into four clades base on the sexual structure:

- Zygomycota : are mostly terrestrial but some live in soil or on decaying plants. The hyphae lack septa ( cross wall) so the mycelium is multinucleate mass. Examples of this clade are Rhizopus, Pilobus, and etc.

- Ascomycota : are most diverse. These fungi asexually reproduce through conidia. Sexually, two mating strains come together and form asci within ascocarp. In each ascus, eight ascospores are produced. Yeast, which is a unicellular type, is an example of this clade. Furthermore, Penicillium is used in modern medicine is another example of this clade.

- Basidiomycota : don't have asexual structure. Sexually reproduce by basidiospore, which are located in basidiocarp. Example of this clade is mushroom.

- Chytridiomyota

Fungi can live in a wide range of habitats. But of course, different species lives in various habitats. There are about 70,000 species that are formally found, but the actual number of fungi species is still unknown.

Fungi perform the most important task for ecosystems. They are decomposers, returning nutrients they absorb back into the ground for circulation. Without fungi, there would be a shortage of nutrients in the soil, and plants and entire ecosystems would be completely different. Mycorrhizae is a mutual relationship between a fungi and a plant. The fungi’s hyphae either penetrate the roots of a plant or grow close to the roots of a plant. As a result, the fungus helps absorb nutrients for the plant, and the plant receives sugars from the plant as well. Together, they both benefit from this relationship. This relationship helps the plant increase its intake of nutrients, allowing it to grow taller and faster. In an experiment between a plant and a plant with a beneficial relationship with a fungus, the plant with the fungus grew to a taller height over the same period of time.

Another beneficial relationship is between a fungus and an ant. The ants gather leaves for the fungus while the fungus digests the leaves and produces sugars that the ants can eat. In this case, both the fungus and the ant depend on each other. The ant cannot eat the leaves, and the fungus cannot reach the leaves. As a result, this relationship helps the fungus and the ant thrive together.

Human uses many fungi as food and medicine.



Protists
Protists are eukaryotic microorganisms that are unicellular, colonial, or multicellular; but the one specific property that sets them apart from each other in Eukarya domain is that they don't have specialized tissues. They do not have any of the distinctive characters of plants, animals, or fungi. All algae except blue-green algae, protozoans, and other organisms that were thought to be fungi have now been correctly identified in the kingdom Protista. The organisms usually composed of Protists are characterized by their ability to photosynthesize (like algae), produce molds (mildews, slime molds and water molds), and forage. Algae and other photosynthetic protists are of higher importance to our lives mainly because they produce a substantial amount of oxygen. They thrive only in aquatic environments. Some protists have flagella that are involved in locomotion. They reproduce in several ways: Isogamy, in which the motile gametes are the same size. Anisogamy, in which the female gametes are larger than the males. Lastly, oogamy, in which the larger female gametes are none motile and the males are motile. The Protists are divided into 12 divisions. This was based on modes of nutrition, pigments, carbohydrate food reserves, flagella, cell wall components, and the environment in which they live in. Protists are an important part of the food chain. For example, kelp beds are one of the most productive ecosystems on the earth.

a. Stramenopila: include diverse autotrophs and heterotrophs possess two flagella : one flagellum has numerous hair-like projection and the other is smooth, lacking hair.

- Bacillariophyta (diatoms): live in fresh and salt water. They possess chlorophyll a and b and carotenoids ( they have golden color). They contribute oxygen to atmosphere. Diatoms live in a silica shell and resembles an agar plate.

- Phaeophyta (brown seaweed): live in temperate water. They possess chlorophyll a and c and brown pigment fucoxanthin. Their cellwall are made of cellulose and algin. For example, macrocystis.

b. Rhodophyta: marine seaweed. They have chlorophylls a and d and pigment phycobilins. They have red color.

c. Chlorophyta (green algae): unicellular and colonial. They have chlorophylls a and b. Cell wall is made of cellulose and stores starch. Examples of this class are Spirogyra and Desmids.

d. Euglenozoa - Euglenophyta : one or two anterior flagella. They can be autotrophic or heterotrophic. Example: Euglena.

-  Kinetoplastida : have single large mitochomdrion along with kinetoplastid which store DNA. They are symbiotic or pathogenic. Example: Trypanosoma gambiense.

-  Trychonympha : Beneficial endosymbionts that develops mutualistic relationship with termites.

e. Alveolata:

-  Dinoflagellata : Found in marine waters. They have paired flagella lying in grooves which give mobility. Example: Ceratium.

-  Apicomplexa : Parasitic and none motile as adults. Examples: Plasmodium vivax ( cause malaria)

-  Ciliophora : Move by cilia and have large macro-nucleus and micro-nuclei.They are holotrophic. Most of them are single-celled organisms. Example: Paramecium, Vorticella.

f. Protists with Pseudopodia: they have pseudopodia which are used in locomotion and feeding.

-  Amoebozoa  (Amoebas): live in marine and fresh water or in soil. They have no fixed body and lack the shell.

- Radiolaria : live in ocean. They are enclosed by porous tests of silica dioxide. Using axopodia to feed and slowly move.

- Cercozoans (forams): live in marine, enclosed by coiled tests of CaCO3.