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Since most things at the macro level are determined by the expression of genes, studying those genes directly is the most exact way of comparing organisms. Since all living things are made of cells and since all cells perform a few of the same basic functions, all living things contain at least a few of the same genes that govern these basic functions. Some of these genes are called housekeeping genes because, as vacuuming and dishwashing are necessary for any household, these genes are necessary for the smooth operation of any cell. 

The most widely studied housekeeping genes do not actually encode a protein, but instead they encode ribosomal RNA (rRNA). rRNA is used by all known living organisms to synthesize proteins from messenger RNA (mRNA). Even if the proteins being created are very different from one organism to the other, the process for making them is very similar. Once an evolved method works, it will probably remain that way in all future generations.  Since all organisms possess genes for rRNA, we can compare their rRNA sequences to look for differences caused by mutations. When scientists compare the rRNA sequences from two different organisms, they are looking for how many "words in the sentence" have been changed. The more nucleic acids are different between the two sequences, the more changes have occurred. Scientists then attempt to confirm this estimate with other data, such as fossils and carbon dating. This information allows systematists to create a chronological order of events, each event represented as a new branch emerging from a node on a phylogenetic tree. This new scientific field is called molecular systematics.

The first difference is that the clades based on the type of coelom are gone. That's because biologists had logically assumed that animals without a coelom came first, followed by a pseudocoelom, and then a true coelom. However, when the genetic data were analyzed, systematists found that the acoelomate worms actually evolved from animals with more complex bodies, becoming simpler over time. This process is known as reversal. It occurs when a trait reverts to an earlier form, creating another kind of homoplasy.

The protostomes are now divided into two new clades, the Lophotrochozoa and the Ecdysozoa. The lophotrocozoa clade includes mollusks (Phylum Mollusca), segmented worms (Phylum Annelida), and several aquatic creatures with a ciliated ring of tentacles around their mouths. Ecdysozoa are all organisms that molt. ("Ecdysis" is the Greek word for molting.) 

 

Classification

"Troph" means nourishment or food in Greek. Next, remember that auto- and hetero- pertain to carbon sources and chemo-and photo- pertain to energy sources. Autotrophs are autonomous/independent of other organisms; they do not rely on others to create organic compounds but can do it on their own. Heterotrophs get their carbon by digesting organisms (either autotrophs or their fellow heterotrophs) that already contain organic compounds. Chemotrophs are like batteries; they get their energy from chemicals. Phototrophs are like solar panels; they get their energy from the sun.

Prokaryotes v. Eukaryotes

We've tossed these words around already, but now we'll really unpack them. The root "karyon" comes from the Greek word for nucleus. "Pro" means "before" and "eu" means "true." Therefore, the major distinction between prokaryotes and eukaryotes is that the former organisms do not have a nucleus and the latter ones do. 

The nucleus is one type of membrane-bound organelle. Prokaryotes aren't just lacking nuclei; they don't have any organelles. Both prokaryotes and eukaryotes have plasma membranes and most prokaryotes have cell walls, which they share with some eukaryotic cells, like plants.

Prokaryotes are haploid, meaning they only have a single copy of their genes, which is contained within a circular molecule of DNA. Prokaryotes reproduce asexually, whereas eukaryotes usually reproduce sexually and are always diploid, meaning they have two different copies (alleles) of each gene. That said, prokaryotes could share some of their genes with non-offspring in what is called horizontal gene transfer. This is a more primitive, less complete way of increasing the genetic diversity within a population.

The final difference we'll consider is size. Prokaryotes are almost always unicellular. Only a few species can create colonies containing cells with different tasks. The simplest eukaryotes are also unicellular, but most eukaryotes are multicellular once they get past the awkward fertilization stage. 

Human egg cells are among the largest cells on Earth. They tend to be somewhere over 100 μm in diameter, which is about the size of the period at the end of this sentence. Adults are made of 60-90,000,000,000,000 (trillion) cells. 
 

Metabolic Options

All living things need energy to survive. This energy fuels the reactions that build the molecules that they need and recycle the ones that they don't need.  

Organisms can either get their energy from chemical compounds, in which case they're called chemotrophs, or they can capture it from sunlight, giving them the name phototrophs. All organisms also need a source of carbon atoms to make most of the molecules in their bodies. When an organism's carbon source is the organic molecules of other organisms, it is called a heterotroph. Heterotrophs must consume other organisms, which is why they are often called consumers. When an organism is able to use (inorganic) carbon dioxide to create its own organic molecules, it is called an autotroph. Autotrophs are also called producers because they can produce their own carbon compounds.Based on their needs for both energy and carbon, we can combine these terms and classify organisms into four categories.

1) Chemoheterotrophs need organic molecules as a carbon and an energy source. We, for example, eat plants and animals, which are made up of organic molecules. We then digest those molecules by breaking their bonds, which releases energy that can be harnessed and used to do work. Breaking down large molecules has the added benefit of creating many smaller molecules that can then by reworked and made into the proteins and other molecules that we need. All animals are chemoheterotrophs.

2) Photoheterotrophs get their carbon from other organisms but also get their energy from the sun. This means that they must somehow digest or decompose matter from other organisms but they have chlorophyll or other pigments that can capture energy from the sun. Purple non-sulfur bacteria are fun examples that use a purple pigment to absorb sunlight instead of chlorophyll, which is green.

3) Photoautotrophs capture energy from the sun to make their own organic molecules out of inorganic molecules, like carbon dioxide. In this way, photoautotrophs are the least dependent on other organisms. Unicellular photoautotrophs were probably the first form of life on Earth. Almost all plants are photoautotrophs.

4) Chemoautotrophs are quite special because they can use inorganic molecules both to make organic molecules and as an energy source. Therefore they can survive in weird, extreme environments, like deep in the ocean where the sun doesn't shine. They use carbon dioxide as a carbon source and they oxidize molecules like ammonia (NH3) and hydrogen sulfide (H2S) for energy. Most archaea are chemoautotrophs.
 

Domain Bacteria

All members of the Domain Bacteria are prokaryotic. Under the Domain Bacteria, there is a single Kingdom, also called Bacteria. Within that kingdom, there are more than 20 recognized phyla. They are generally classified based on their shape, the characteristics of their cell walls, and their type of metabolism.

Pathogenic bacteria are the ones everyone thinks of when they hear the word "bacteria." They're the ones that can get us sick. They cause everything from mild stomach upset and severe food poisoning to deadly spinal meningitis. They can also cause epidemics, especially chlamydia, tuberculosis, and cholera. The bacterium Yersinia pestis was the cause of the Black Death plague that decimated Europe's population in the mid-14th century (and wiped out large portions of the Middle East and Asia, too). Luckily, antibiotics and good hygiene are generally effective against bacteria. 

Bacteria are small, microscopic, but just because we can't see something doesn't mean that it isn't there. In fact, there are more than 10 times as many bacterial cells in your body than human cells. Some bacteria help our bodies to digest our food, develop our immune systems, and keep "bad bacteria" and other microscopic organisms in check.

Bacteria are a very diverse group of organisms. Most of them are chemoheterotrophs. If they decompose dead matter, they are called saprotrophs. The ones that feed off of living matter (like the ones inside of us) are not necessarily pathogenic, but some are. Other bacteria are photoautotrophs, like cyanobacteria, or photoheterotrophs, like purple nonsulfur bacteria. They contain chlorophyll or other pigments that can trap the energy contained in sunlight. Iron bacteria are one type of chemoautotrophic bacteria. They form that brownish residue around the insides of toilet tanks. They're harmless but they sure don't look nice.

Domain Archaea

All archaea are also prokaryotic. They were originally thought to be the most ancient, living life form, which is where they get their name (think "archaic").  They were also thought to be a type of bacteria, which is understandable because they are often rod- or sphere-shaped, just like bacteria. They are also prokaryotic, like bacteria. But molecular systematics has recently shown us that they are more similar to eukaryotes than bacteria are, suggesting that bacteria are actually the more ancient organisms.

We also now know about some of their genetic and biochemical differences with bacteria, which we have summarized for you below 

Archaea

• No peptidoglycan* in cell walls

• Different phospholipids in cell membranes

• 3 RNA polymerases, like eukaryotes

• Ribosomes similar to eukaryotic ribosomes

Bacteria

• Peptidoglycan* in cell walls

• Different phospholipids in cell membranes

• One RNA polymerase

• Ribosomes not so similar to eukaryotic ribosomes

* Peptidoglycan is a repeating macromolecule (polymer) made of amino acids and sugars that form an interconnecting web that gives bacterial cell walls structure and strength.

Archaea are generally classified into five phyla (Crenarchaeota, Euryarchaeota, Korarchaeota, Nanoarchaeota, and Thaumarchaeota). Since these tiny cells are often hard to find and study, there isn't always agreement on which organism belongs where. 

Methanogens like to live in places that are void of oxygen because their cellular respiration is anaerobic. They can be found in swamps and in the guts of many animals, including us. As their name suggests, they produce methane gas as a byproduct of their respiration. 

Extreme halophiles love to live in environments that are very salty, like the Dead Sea in Israel/Jordan or the Great Salt Lake, UT. The water in these places can be ten times as salty as regular ocean water. Due to osmosis, if these little cells didn't have some intense protections, their insides would be sucked right out of them.

Extreme thermophiles like it hot (> 113 ºF/45 ºC). They are usually found in hydrothermal vents in the ocean or in hot springs like those in Yellowstone National Park. The record for bearing the heat stands at 248 ºF/121 ºC. Most proteins denature (or unfold) at high temperatures. Since most of the structure and function of a cell comes from proteins, these tiny creatures have to have super special proteins that can withstand that kind of heat without losing their function. 

Rings of golden color formed by mats of bacteria and archaea that love the heat of Great Prismatic Spring, Yellowstone National Park. The center of the spring is so blue because it is pure, sterile water. It is so hot in the center that no living things are found there.

We owe much of what we know about molecular biology to a bacterium. Polymerase chain reaction (PCR) is a technique used in every molecular biology lab in the world. It allows a small section of DNA to be copied over and over again to create enough of it to study. The reaction requires a DNA polymerase that can withstand temperatures high enough to separate the double strands of the DNA template (~205 ºF/96 ºC). Such a polymerase was found and isolated from a bacterial thermophile called Thermus aquaticus. 

Domain Eukarya

As we move through the kingdoms within the eukaryotic domain, cells begin to work together in tissues to perform specialized tasks. Then the tissues begin to work together as organs and the organs and tissues work together in organ systems. Social animals specialize and work together in communities, adding the final level of collaboration to the hierarchical nature of life. Remember that each of these advances is an adaptation, which also means that they represent new categories being formed within our taxonomic hierarchy.

Kingdom Protista

Protists are are usually microscopic and unicellular but that's where their similarities end. They are, of course, eukaryotic, too, since they belong to the Domain Eukarya. They are actually thought to be direct descendants of the earliest eukaryotes and fungi, plants, and animals.  Though they are usually unicellular, some live together in colonies of loosely connected cells and others are made up of many cells. Some are even made of a single cell with multiple nuclei. In order to move, some push their cell mass around and extend it to create "fake feet" (pseudopods) for pulling themselves forward; others use long, rope-like structures (flagella) that whip around to propel them through their environments; and others have hair-like cilia covering their little bodies to push them through liquids.

Eating—or obtaining nutrients—is also accomplished in many different ways. Some protists are photoautotrophs, like plants and algae, because they contain chloroplasts and undergo photosynthesis. Some are more like heterotrophic fungi because they digest food outside of themselves and then absorb the nutrients. Others remind us of animals because they actually take food particles into their bodies and digest them there.  Kelp looks like a plant but is a kind of brown algae and is one of the largest organisms in Kingdom Protista.

Kingdom Fungi

Fungi are usually decomposers (chemoheterotrophs) that break down dead things. Fungi are an important worker, together with bacteria, in any compost pile. Without these decomposers, your beloved pile of grass and leaves in the back yard would just sit there and never become the rich fertilizer you wants for the garden.  All fungi are made of eukaryotic cells whose cell walls contain complex carbohydrates, usually chitin. Fungi are generally considered to be yeast or molds, depending on whether they are unicellular or multicellular.  Yeasts are found all over the place: in dirt, on plants, on our skin, and in our bodies. They are also responsible for making bread and alcoholic beverages, and even some medicines.  Molds begin as unicellular spores that begin to replicate, creating long, branching filaments (hyphae) that allow them to penetrate food sources. These filaments then mature into tangled webs (mycelia). 

Reproduction in fungi is varied. It usually happens through the creation of spores, but this can happen both sexually (through meiosis) and asexually (through mitosis) in the same organism, though not at the same time. Creating the spores sexually has the advantage of producing genetic variety, but it isn't as fast as asexual spore formation. Spores are hard to kill. If a fungus feels threatened, it's going to quickly make asexual spores and hope that its descendants will live to see a better day. 

There are five distinct phyla in this kingdom: Chytridiomycota, Zygomycota, Glomeromycota, Ascomycota, and Basidiomycota. Scientists who study fungi are called. Mycologists.

Kingdom Plantae

All plants are eukaryotes and most plants are photoautotrophs, but there are exceptions to most biological rules.  A few plants are actually carnivorous, and thus photoheterotrophs, like the Venus fly trap. They are still capable of obtaining nutrients from the air and soil, but they tend to live in places with nutrient-poor soil.

All plant cells are surrounded by a plasma membrane, which is then surrounded by a stiff cell wall. The cell wall gives structure and support to the plant, helping it to stand upright. It's an advantage for a plant to stand tall. There is less competition for space in the ground. giving the advantage to catch more rays of sun, which is necessary for photosynthesis.  Most plants get tall enough that they need a way to transport water and nutrients from their roots in the soil up to their top parts. They have vascular tissues that are analogous to our blood vessels, except they are tougher and there is no heart to pump liquids through. They actually have two different sets of vessels: xylem that carry water and dissolved inorganic minerals and phloem that carry dissolved organic molecules like sugar. Both of these tissues contain the polymer lignin to strengthen and support them.

All plants have the same life cycle, called alteration of generations. Alternation of generations basically involves a diploid phase and a haploid phase. Different plants spend different portions of their lives in each phase and the structures and mechanisms used in each phase vary with phyla.


Plant life cycle: alternation of generations

Plants can be classified into five broad categories, each containing a few phyla. Nonvascular bryophytes (Phyla Bryophyta, Hepatophyta, Anthocerophyta) include mosses, liverworts, and hornworts. These short plants are so short that they don't need the vascular network that other plants need. They also don't have real roots, leaves, or stems. All together, that means they need to live in moist environments. You may have heard that moss only grows on the north side of trees and that's true-ish. In lands north of the equator, the sun will never directly shine on the north side of a tree so it will tend to be cooler and more moist on that side so there will tend to be more moss there. However, if you're in a cool, moist climate like Washington State, it probably doesn't matter which side of the tree you're on. The moss will be happy anywhere.

There are two big groups of vascular plants: those with seeds and those without. The vascular seedless plants (Phyla Lycopodiophyta, Pteridophyta) may not have had seeds but they have all of the other "normal" trappings of a plant, like roots, leaves, and stems.  Vascular seeded plants are then divided into two more groups: those with "naked" seeds (the gymnosperms) and those with fruit surrounding their seeds (the angiosperms). Fruit is actually the wall of a plant's ovary nourishing and protecting its developing seed(s).

Gymnosperms include the Phyla Coniferophyta, Cycadophyta, Ginkgophyta, Gnetophyta. The first phylum is the conifers: evergreens with their seeds in cones. The cycads and some of the Gnetophyta also bear their seeds in cones. Ginkgo biloba trees (the only living species in the Ginkgophyta phylum) and some of the plants in Gnetophyta have seeds that look something like berries but they aren't made from the ovary wall or they would be classified as angiosperms.

Angiosperms are just one big phylum, Anthophyta. The ovaries of angiosperms mature into a thick coating around the seeds, which we technically call fruit. This is not your typical "fruits and vegetables" fruit, though. Angiosperms include wheat, corn, and cacti, to name just a few "non-fruits." The fruits of angiosperms help to protect and disperse the seeds. When eating fruit, most animals besides humans don't bother to spit out the seeds. So, the seeds travel through the gut of the animal for a while as it wanders in search of more food. Eventually, the seeds are deposited on the ground again, leaving the animal from the end opposite that through which they came in as waste material.

Kingdom Animalia

These guys are all eukaryotes. They are all multicellular in their adult forms and have the most complex body plans of all organisms on Earth. Some are more complex than others, but they all have their cells arranged and working together in tissues, which work together to create organs, which work with other organs and tissues to create organ systems. 

This sponge is nicknamed a Venus Flower Basket but its scientific name is Euplectella aspergillum.

All animals can reproduce sexually, but a few have some creative alternatives. Some simple animals, like sponges, can reproduce asexually by creating a new adult from a fragment that breaks off from a parent organism. Some animals, including sponges, are hermaphrodites, meaning that a single organism can produce both eggs and sperm. In sponges, a given organism will only produce one type of gamete at a time. Fertilization happens when its gametes are released and fuse with those of a sponge producing the opposite kind of gamete. Other hermaphrodites, like Ctenophores (comb jellies), are capable of fertilizing their own gametes because they produce both eggs and sperm simultaneously. 

Among some of the most important developments of animals are those that protect their young as they mature. The location of both fertilization and embryonic development have much to do with the survival of young animals and is a useful characteristic to look for when classifying animals.   

Most amphibians reproduce in the water. Females lay many jelly-like eggs in a mass. Males then release their sperm in the water nearby. Because fertilization is external to the animals, many of the eggs will go unfertilized and the ones that do get fertilized are left to develop on their own in the water where they are very vulnerable to hungry prey. That is why so many eggs are laid in the first place: very few will become adults. 

In birds, fertilization is internal and therefore more successful. Eggs, either fertilized or unfertilized are laid with a hard, protective shell; the mother watches over and warms the eggs until they hatch. In placental mammals, fertilization and embryonic development occur within the protective environment of the mother's uterus. This gives the young their best chance for survival. Because it takes so much energy from the mom, usually only a few offspring are born at a time. 

All animals are chemoheterotrophs. They usually take food into their bodies and digest it there. Sugars and starches are broken down and combined with oxygen to generate ATP, or energy.  Proteins are broken down into amino acids and recycled to create the proteins needed by each particular cell at any given moment. Most animals move around to find their food – mobility is an important adaptation—but a few, like sponges and coral, are sedentary. They have to sit and wait for their food to come to them. They have filters that let water through but capture the tiny food particles floating in the water. Most animals also have a highly developed nervous system and muscle system, which they use not only to get from point A to B but also to find and ingest food and water, react to predators or falling trees.