Classification: Exploring and Organizing Life’s Diversity

History of Classification Aristotle (384-322 B.C.) developed the “first” system Based on how an organism looks Plants and animals Plants were divided into herbs, shrubs and trees Animals were divided based on physical characteristics System was flawed Bats were considered birds because they had wings Whales were considered fish because they had fins Fungi were considered plants Bacteria and other microorganisms were not included Didn’t know they existed

Carolus Linnaeus Born Carl von Linné (1707-1778) Developed a system based on physical similarities Called taxonomy Developed a system for naming organisms that is still used today Called binomial nomenclature 2-word naming system using Latin words The first word is the genus (closely related species) The second word is the specific epithet.

Rules for Scientific Names 1st word is capitalized 2nd word is lowercase Both words are italicized (if typed) or underlined (if hand-written) Examples: Homo sapiens Canis familiaris Pinus virginiana Yersinia pestis

What is wrong with these names? Homo Sapiens homo sapiens Homo sapiens

Advantages of Binomial Nomenclature It is universal The same scientific names are used everywhere on Earth The scientific name tells you about the organism Where it is found, what it does, who discovered it, or identifying characteristics It shows relationships Organisms of the same genus will have the same first word

Taxonomy Science of naming and classifying organisms 8 Levels Domain Kingdom Phylum Class Order Family Genus Species Did King Philip Come Over For Great Spaghetti? Domain is the least specific (most different organisms grouped) Species is the most specific (only one type of organism)

For Us (Guaranteed Test Question ) Domain: Eukarya Kingdom: Animalia Phylum: Chordata Class: Mammalia Order: Primata Family: Hominidae Genus: Homo Species: sapiens Everyone alive can make perfectly healthy, hearty soup

Domains and Kingdoms There are 3 Domains and 6 Kingdoms of life Bacteria Archaea Eukarya Kingdoms in each domain Domain: Bacteria Kingdom: Bacteria Domain: Archaea Kingdom: Archaea Domain: Eukarya Kingdoms: Protista. Fungi, Plantae, Animalia

Cladistics More recent attempt to group Earth’s biodiversity Groups organisms based on Evolutionary relationships Separates organisms based on derived characteristics Much more accurate and insightful Shows real relationships, not perceived ones Recently, based more upon DNA than characteristics

Cladogram

Dichotomous Keys A tool used to identify an organism Consists of a series of dichotomous statements (2 differing statements)

Characteristics of Living Things In order to be alive, something needs to do all of the following: Be made up of one or more cells, containing DNA Obtain and use energy Grow and develop Growth=get bigger Develop=changes throughout life Reproduce Respond to the environment If something lacks even one of these things, it is not living

Viruses Viruses are NOT living things They lack most of the characteristics of living things They do not grow and develop They can only reproduce using other organism’s cells They can not obtain or use energy They are not made of cells They do, however, affect living things greatly Can be pathogenic Cause disease (cold and flu) VIRAL DISEASES CANNOT BE TREATED WITH ANTIBIOTICS

Prions Prions are infectious proteins (Also not living things) Found in air, and cause host’s proteins to fold improperly Causes diseases such as Bovine Spongiform Encephalopathy (Mad Cow Disease) and Creutzfeldt- Jakob Disease (human form) Causes misshapen proteins in the brain Brain develops holes and resembles a sponge Prion diseases are nearly always fatal, as the body has no way to fight them https://www.youtube.com/watch?v=aP-ShyyHiIc https://www.youtube.com/watch?v=lS9jKVM7ZXo

Types of cells There are 2 cell types Prokaryotic Eukaryotic Lack a nucleus and other organelles Only organelles they have are ribosomes Both Domain Bacteria and Domain Archaea Eukaryotic Have a nucleus and organelles Only Domain=Eukarya

What are Prokaryotes? Single-celled organisms Very tiny Cannot be seen without a microscope Our microscopes are not powerful enough Lack a nucleus and most other organelles Most numerous organisms on Earth Extremely important organisms.

Classification and Evolution Prokaryotes are split into 2 Domains Domain Bacteria Domain Archaea Everything else on Earth is in Domain Eukarya Prokaryotes were the first living things to evolve, around 3.8 billion years ago Only living things on earth until 2 billion years ago Until 1970s, Archaea were considered to be bacteria (called Archaebacteria) As more was learned about them, they were given their own domain because they are VERY different from bacteria

Domain Bacteria Made up of bacteria Only 1 kingdom-Bacteria Most abundant living things on Earth. Live in almost every environment Air Ocean Soil Intestines Estimated number of bacteria on earth: 5x1030 You have 10 times more bacterial cells than human cells!

Classification of Bacteria Thousands of bacterial species exist. Many are classified by shape. Others are classified based on the color that they stain (Gram staining)

Bacterial shapes Baccili: Cocci: Spirilla Rod shaped Sphere-shaped Spiral-shaped

Structure of Bacterial Cells Bacterial cells are surrounded by a plasma membrane Most also have cell walls Surrounding the membranes and cell wall (if present) is a capsule, which further protects the cells Inside of the bacterial cell is cytoplasm, similar to eukaryotic cells Floating in the cytoplasm are ribosomes and plasmids (small sections of DNA) There is no nucleus Instead, there is a Nucleoid (area with DNA) and may be plasmids (circular DNA) to be exchanged with other bacteria Bacterial cells also may contain whip-like structures called flagella Also have hair-like protrusions called pili that allow them to attach to objects

Structure of Bacterial Cells

How do bacteria get energy? Some are photosynthetic Others decompose organic matter Some can use chemicals from the environment to do a process similar to photosynthesis (called chemosynthesis) Mutualism Getting resources from other species, while providing some service to that species (+/+) Parasitism Stealing resources from host organisms (+/-)

Bacteria and People You may think that bacteria’s purpose is to make us sick For some bacteria, this is true For many others, it is not Benefits of Bacteria Create medicine, such as vaccines Help us digest foods and get vitamins Decompose wastes Fix Nitrogen into usable forms for plants Make foods such as cottage cheese, yogurt, cheese, and many more.

Dark side of Bacteria Mycobacterium tuberculosis (Tuberculosis) Some bacteria can lead to disease Clostridium tetani Tetanus aka Lockjaw Affects muscles (including the heart). Leads to muscle spasms, and can be fatal. Escherichia coli (E. Coli) Many strains exist in human intestines in a commensalism relationship. However, some can cause food poisoning. Transmitted by fecal-oral route. WASH YOUR HANDS AFTER USING THE BATHROOM!!! Mycobacterium tuberculosis (Tuberculosis) Second deadliest infectious disease (After HIV/AIDS). Yersinia pestis “The Bubonic Plague” or “The Black Death Killed over 1/3 of the European Population between 1347 and 1353

A child and a portrait of a soldier affected with tetanus

Spread of the Black Death

Controlling Bacteria Bacteria in food and water can be killed by cooking at a high temperature Bacteria on surfaces can be killed with cleaning products such as bleach or Lysol Antibiotics can be used to kill bacteria that are harming humans Effective against bacterial infections such as strep throat, sinus infections, ear infections, pneumonia, etc. However, there is a problem

Antibiotic Resistance in Bacteria Some bacterial species are evolving resistance to antibiotics. https://www.youtube.com/watch?v=znnp-Ivj2ek The antibiotic kills those that are not resistant, but leaves the one that are resistant Example: Clostridium difficile A common bacteria that causes diarrheal disease in hospitals. Hospitals, due to their obsessive cleaning procedures, have selected for resistant strains. Patients are being infected at a high rate, while staying in hospitals.

Genetic Diversity in Bacteria Bacteria reproduce asexually (without sex) Called binary fission One bacteria replicates its DNA and then splits Makes clones-identical copies Benefit: Quick, little energy used, don’t need a mate Disadvantage: No genetic diversity Susceptible to extinction Conjugation is a way bacteria can increase genetic diversity Exchanging all or part of a plasmid with another bacteria No longer identical

Domain Archaea Only 1 Kingdom Prokaryotes Called Archaea Prokaryotes First discovered in extreme environments Originally classified as bacteria As more was learned about them, they were found to be VERY different from bacteria Their cell wall is more similar to Eukaryotes than bacteria They were given their own Domain and Kingdom Very little is known about these organisms

Archaea: Tiny but Tough Many archaea are extremophiles Organisms that have evolved to live in extreme conditions. Example: Hydrothermal vents in the ocean (picture) are very acidic and hot. Would kill most organisms, yet archaea thrive. 4 types of extremophiles Halophiles-Survive in very salty water (Dead sea) Hyperthermophiles- Survive at high heats Some archaea can survive up to 122° C (252° F) Acidophiles-Live in highly acidic environments (like near volcanoes) Alkaliphiles-Live in very basic environments

Where else do they live? Archaea do not only live in extreme environments They are found nearly everywhere on Earth. Including in humans (many are found in the human belly button!) Around 4 % of human microbiome The microorganisms that live on or in us They are also important decomposers, and part of Nitrogen cycle Many archaea also form symbiotic relationships None are known parasites Most form mutualistic relationships Archaea in cattle gut help break down grass and straw, and get nutrients in return

Eukaryotes Cells contain a nucleus and other organelles 1 Domain: Eukarya 4 Kingdoms: Protista Plantae Fungi Animalia

Kingdom Protista Not a great classification Includes any organism that is eukaryotic but is not a plant, animal, or fungus Not a lot in common, besides being eukaryotic Some are autotrophic, others are heterotrophic Some are unicellular, others are multicellular Some are parasitic, some are producers, some are consumers Will likely be broken into several kingdoms in the future

Kingdom Plantae The plants Mostly autotrophic Most are multicellular Many contain chloroplasts Most are multicellular Contain cell walls

Kingdom Fungi Fungi Heterotrophic Have cell walls composed of chitin Molds, mushrooms, yeast Heterotrophic Many are decomposers Have cell walls composed of chitin Most are multicellular A few, such as yeast, are unicellular

Kingdom Animalia The animals Multicellular heterotrophs Lack cell walls Very diverse 36 phyla Differentiated based on symmetry, body organization (cells to organ systems), and embryonic development Vertebrates and invertebrates