Origin and Diversification of Life:

Origin and Diversification of Life: MICROBES

Unit 12: Concepts • Taxonomy (E) • The 6 Kingdoms (I) • Origins of Life (C) • Microbes (I) • Bacteria • Archaea • Protista • Viruses (C)

Essential question 1.1: On what basis are organisms now classified?

Carolus Linnaeus created a system of classification that organized species into taxa that formed a hierarchy or set of ordered ranks. Kingdom, Phylum, Class, Order, Family, Genus, Species Linnaean Classification Good Place to employ a mnemonic device King Philip Came Over From Geneva Switzerland

Hierarchies • Each group will contain less individuals until only one is described. • Are camels more closely related to Llamas or Giraffes? Why? • Llamas because they are in the same family and Giraffes are only in the same order.

Each species is a assigned a two-part scientific name. First word is capitalized. Second word is lowercased. When typed, the name is italicized. When handwritten the name is underlined. Examples Ursusmaritimus Felisconcolor Pavocristatus TWO NAME SYSTEM NAMING Binomial Nomenclature

CanisFamiliaris feliscatus PANTHERA LEO CANIS lupus Describe what is wrong each name below then rewrite one of the binomial names correctly Second name capitalized First name not capitalized All Caps is incorrect All caps for first word is incorrect Which two of the above are most closely related? Why? Canis lupus and Canisfamiliaris

Classification wasn’t always easy Classify the following organisms into 2-5 groups

I. Aristotle made the first classifications based on structural analogies (legs, wings, etc.). • 2,000 years ago, this made sense, since scientists were not aware of natural selection and the evolutionary process. • Today, this is illogical, considering their vastly different ancestry. • Birds were classified with bees (wings). • Spiders were classified with bears (legs).

II. Analogous traitsarise from different ancestry, but currently serve the same function- these result from convergent evolution. • Despite being composed of different structures, the wings of bats, birds and butterflies have adapted convergently for the same purpose - flight. • Since the structures are different, they do not demonstrate ancestral relatedness, just similar selection pressures because of common behaviors!

Convergent Evolution:Example: Mammals that feed on ants or termites. • Some organisms have lived in different places or times, but in similar environments. They start with different structures but have similar selection pressures. Over time, through the mechanisms of evolution, distantly related organisms develop similar structures and characteristics.

Question:How are analogous traits different from homologous traits? Cite an example for each. • Analogous traits arise due to the same selection pressures on different/non-related populations thereby developing similar anatomical parts using different genes. • Homologous traits arise due to populations that share common ancestry responding to different selection pressures thereby developing different anatomies from similar genes.

Evolutionary Classification • Grouping species into larger categories that reflect lines of evolutionary descent rather than overall similarities and differences. • A cladeconsists of a single common ancestor and all of the groups that have descended from that ancestor. • Information concerning common ancestry is used to link clades together into a diagram called acladogram. Learn how to construct cladograms

Following the numbered slides on this page you can see how cladograms can be constructed. • First splitting event. • Continued speciation leads to more branches. • Entire histories and degrees of relatedness can be shown on one cladogram.

Essential question 2.1: How can each of the 6 kingdoms be described using a set of essential vocabulary?

6 kingdoms make up 3 Domains • Originally there were only 2 kingdoms. • Plants and Animals • As we have learned more about the life on this planet we have redefined our kingdoms. • We now recognize the following • Eubacteria, Archaea, Protista, Fungi, Plant and Animal.

Key Characteristics of Life • All known organisms on Earth fall into one of the domains/kingdoms based on 4 characteristics. • Cell Type – • Prokaryotic vsEukaryotic • Cell Structures– • Cellwalls,chitin,chloroplasts • Number of Cells– • Unicellular vs Multicellular • Nutrition– • Autotroph vs Heterotroph

What does it mean to be a… • Heterotrophic eukaryote with cell walls made of chitin • Write a basic description for a fungus. • How would you describe an archaean? • If you found a multi-celled autotroph that had a cell wall of cellulose, nuclear envelope, and chloroplasts you would classify it as a… • Unicellular prokaryote with no peptidoglycan Plant

The Tree of Life • We follow the same rules of Evolutionary Classification to organize the kingdoms. When all combined we refer to this cladogram as theTree of Life.

Essential Question 3.1 • What 3 explanations exist for the appearance of the Earth’s first forms of life?

Origin of Life • Over the course of time as Humans have pondered the origin of life we have ultimately arrived at 3 possible explanations. Biologically we will explore one of these options. In the next few slides the reason for that should become clear. • Abiogenesis – Life from non-living chemicals • Creation – Involves a supernatural being • Cosmic Ancestry – Extra terrestrial origin

Why Abiogenesis? • Science is the building and organizing of knowledge in the form of testable explanations and predictions. • Creation is built upon religious beliefs that a supernatural being willfully crafted life. This belief is common among most cultures on Earth and many have their own variation of this belief. Creation is not testable so it does not fall within the context of a science class. • Cosmic ancestry is the belief that life traveled to the Earth as a passenger riding comets or meteorites. While providing an interesting debate about life beyond Earth it only moves the question of how life began to an earlier time and location.

Abiogenesis • If we trace the speciation found in the fossil record back far enough we find only bacteria. • The question that remains is how did that bacteria come into being. • Scientists have identified 4 stages along the path to the first cell from nonliving matter.

Stage 1:Organic Monomers Video link • Simple organic molecules called monomers, evolved from inorganic compounds prior to the existence of cells. • Amino acids and nucleotides are both examples of monomers. • Amino acids build proteins and nucleotides build strands of DNA or RNA. • Experiments have shown that these building blocks can be created abiotically. Key Scientists/Experiments: Primordial soup Hypothesis Alexander Oparin; JBS Hldane Stanley Miller; Harold Urey Iron-Sulfur world hypothesis Günter Wächtershäuser

Stage 2:Organic Polymers • Organic monomers were joined to form organic polymerssuch as RNA, DNA, proteins and fatty acids. • Small polypeptide chains have been shown to have enzymatic properties. • RNA can be both a substrate and an enzyme. • Abiotic polymerization of protein and RNA have been demonstrated through experimentation. Key Scientists/Experiments: Protein-First Hypothesis Sidney Fox RNA-First Hypothesis Thomas Cech; Sidney Altman (Nobel 1989) Iron-Sulfur world hypothesis Claudia Huber

Stage 3:Protocells • Organic polymers became enclosed in a membrane to form the first protocells or probionts. • The first cell membranes were probably fatty acids instead of phospholipids. • Fatty acids form micelles that have been shown under proper conditions to create vesicles. Key Scientists/Experiments: Coacervate Droplets: Alexander Oparin Liposomes: Alec Bangham Membrane first hypothesis: David Deamer;

Stage 4:Living Cells • Probionts acquired the ability to self-replicate and undergo protein synthesis. • The two leading theories contend that eitherRNA or proteins existed in the probionts first. • This fourth stage requires both.

L.U.C.A. • While the waters surrounding Abiogenesis are certainly not crystal clear they do provide a consistent picture that the stages could work in nature and can be reproduced in the lab. • Exactly how and when the pieces first came together will likely remain a mystery lost to deep time. • One thing we will see is how theLastUniversalCommonAncestor left a legacy of self replication and descent with modification.

Question:What are the four stages that must have occurred for life to have form Abiotically? • In order for life to occurred abiotically we must have had the formation of organic monomers from the chemicals available in the oceans of Earth. These monomers must have polymerized to have made the polymers necessary to form probionts. These probionts needed to become self replicating in order to be considered alive. This process required specific environments and long periods of time. Many of these stages have been recreated in laboratory experiments under controlled situations.

2.1BYA Multicellularity 1.4BYA The Tree of Life - During the Precambrian time, 1 the first cell or cells give rise to 2 bacteria and 3 archaea; 4 the first eukaryotic cell evolves from archaea. 5 Heterotrophic protists arise when eukaryotic cells gain mitochondria by engulfing aerobic bacteria, and 6 photosynthetic protists arise when these cells gain chloroplasts by engulfing photosynthetic bacteria. 7 Animals (and fungi) evolve from heterotrophic protists, and 8 plants evolve from photosynthetic protists.

Cenozoic Mesozoic Humans Paleozoic Colonization of land Origin of solar system and Earth Animals Prokaryotes 4BYA 1BYA Proterozoic Archaean Multicellular eukaryotes 2BYA 3BYA Atmospheric oxygen Single-celled eukaryotes

Essential Questions 4.1 & 4.2 • How are microbes identified and classified? • How are microbes important to humans and the environment we live in today?

Kingdom Bacteria • All bacteria are prokaryotes. • Prokaryotes are the simplest and most abundant form of life on Earth. • Prokaryotes are small, contain a single circle of DNA and lack a nuclear membrane. • Bacteria come in 3 general shapes formed by cell walls. Many contain a large flagellum. (plural-flagella)

Identifying Bacteria • Bacteria commonly come in three forms. • Rod-shaped - bacilli • Spiral - spirillaor spirochetes (large spiral) • Spherical - cocci Lactobacilli: rod-shaped Enterococci: spherical Spirochaeta: spiral

Question:How many of you ingested bacteria this week? sour cream buttermilk olives sauerkraut vinegar sourdough bread yogurt cheese Anything that has been sitting out for more than a few minutes!

Identification continued • Sometimes bacteria can be identified solely by the shape and color of their colonies. • One technique used in microbiology labs to identify bacteria is to test for the presence of a thin peptidoglycan layer and a membrane coating. The membrane and thin layer of peptidoglycan prevents a particular stain from adhering to the cell. This technique is called gram staining (next slide) and is named for biologist Hans Gram.

Gram Staining

Importance of bacteria • Prokaryotes were responsible for creating the properties of the atmosphere (cyanobacteria)and soil for over 2 billion years. • Prokaryotes make many important contributions to the world’s ecosystems, including playing key roles in cycling carbon and nitrogen. • Bacteria are often overlooked by people due to their size but have large roles in our daily lives. We will look at some areas where bacteria intersect with the Human lives. • Beneficial bacteria • Pathogenic bacteria

Bacteria with Human Benefits • Bacteria are used in the production of yogurts, cheeses, pickles, sauerkraut, soy sauce and vinegar. • A bacterial coating known as your “normal flora” occupies every inch of your body making it difficult for harmful bacteria to attack. • Bioremediation: use of bacteria to remove pollutants from water, air, and soil. • Psuedomonas - clean up oil spills • Thiobacillus - extract lead / mercury from mine runoff

Bacteria can be Pathogens • A pathogen is general term used for any microbe that causes disease in a plant or animal host.

List 3 ways that bacteria impact your life. 1. Pathogens – Causing disease 2. Food manufacturing – Cheeses, yogurts etc.. 3. Bioremediation – Oil spills etc…

Kingdom Archaea • While Archaeans are very different from bacteria they are nearly identical upon visual inspection: • Unicellular prokaryotes • Cell walls, flagella, and DNA look similar but are biochemically and physiological very different. • Archaeans environments typically are very different than bacteria leading to their being named extremophiles. • Non pathogenic – No known disease causing Archaeans have been found.

Archaea are extremophiles. • Methanogensare anaerobic and produce methane gas. They are chemoautotrophs usingH2to change CO2into CH4 (Methane). • Found in swamps/marshes (Swamp gas) • Intestines of mammals (Flatulence) • Thermoacidophileslive in extremely hot/acidicconditions(above 80C and below pH 2).Have different membranes and walls than bacteria and eukaryotes to prevent denaturing. • Hydrothermal vents / hot springs. • Halophileslive in salty environments (12-15%, ocean only 3.5%)like the Great Salt Lake, the Dead Sea and hypersaline soils.

Origin and Diversification of Life: