Classification.pdf

School Natural Sciences Department Life Sciences Instructor Dr. Ashish Gupta Course Code BIO-108 Course Title Animal Sciences I Credits (L:T:P) 2:0:1 Contact Hours (L:T:P) 2:0:3 Prerequisites Biology at 10+2 level...

School Natural Sciences Department Life Sciences Instructor Dr. Ashish Gupta Course Code BIO-108 Course Title Animal Sciences I Credits (L:T:P) 2:0:1 Contact Hours (L:T:P) 2:0:3 Prerequisites Biology at 10+2 level All branches at School of Natural Major Core for Sciences Major Elective for NA RECOMMENDED TEXT BOOKS 1. Barrington, E.J.W. (1979) Invertebrate Structure and Functions. II Edition. E.L.B.S. and Nelson. 2. Barnes, R.S.K., Calow, P., Olive, P.J.W., Golding, D.W. & J.I., Spicer (2002) The Invertebrates: A New Synthesis. III Edition. Blackwell Science. 3. Modern Text Book of Zoology: Invertebrates Prof. R.L. Kotpal 4. Moore: An Introduction to the Invertebrates, Cambridge University Press, 2001 5. Textbook of Invertebrate Zoology G.S. Sandhu & H. Bhaskar, 2004. 6. Dhami, P.S. & Dhami, J.K. Non-chordate Zoology. R. Chand & Co 7. Jordan, E.L. and P.S. Verma, 2010, Invertebrate Zoology, S. Chand & Co Ltd., Ram Nagar, New Delhi. Evaluation for BIO-108 course- Dr. Ashish Gupta (Ist half of the semester)- 50% Dr. Anindita Chakrabarty (IInd half of the semester)- 50% Evaluation- Mid-term exam- 30% Presentation/report- 10% Practical exam- 10%  Estimates on the number of Earth's current species range from 2 million to 1 trillion, of which about 1.74 million have been databased thus far and over 80 percent have not yet been described. What are classification systems? Why do we need them? How do we classify living organisms?  Carolus Linnaeus (1707–1778) In his Systema Naturae, first published in 1735, Carolus Linnaeus distinguished two kingdoms of living things: Animalia for animals and Plantae (Vegetabilia) for plants. He classified all living organisms into two kingdoms based on the observable traits such as – mode of nutrition and locomotion (mobility). 1. Plants and animals were divided into two kingdoms not abruptly but based upon specific characters. 2. It initiated systematic methods to classify the living organisms. More and more characters were, later, taken into consideration for development of better methods. LIMITATIONS  It grouped unicellular & multi-cellular organisms together, for example, Chlamydomonas & Spirogyra were placed together under algae.  There is no proper distinction between prokaryotes and eukaryotes. Like in the case of bacteria without a nuclear envelope and cellular organelles are placed in the plant kingdom.  No defined place for fungi. These organisms live by decomposing and absorbing waste organic matter rather than preparing their own food like green plants. But, given the only options to choose i.e. either from plants or animals, we may still call them plants because they are fixed and have a spread out appearance.  Some protozoans like Euglena possess characters of both plants and animals, and did not fall into either kingdom.  All other organisms such as green plants, mosses and multicellular seaweeds, moulds and mushrooms, lichens, minute-colored or colorless unicellular organism and bacteria were lumped together in the plant kingdom.  In the system both photosynthetic & non-photosynthetic organism are placed together in the kingdom plantae. For example the fungi lack chlorophyll and are saprophytic in nature, they are placed in the plant kingdom. Organisms like the lichens do not fall either in the animal or plant kingdom.  It did not mention some acellular organisms like viruses and viroids.  BINOMIAL NOMENCLATURE Scientific name (consists of two Latin words) Genus Species (generic name) (species epithet) Species is the basic unit of classification. Organisms that share many features in common and can breed with each other and produce fertile offspring are members of the same species. Related species are grouped into a genus (plural- genera). The rules for writing scientific names Father of modern taxonomy - Both words are italicized or underlined  Swedish botanist, physician, and zoologist. - Genus is always written first and is capitalized  Who formalised binomial nomenclature, the modern system of naming organisms.  Two-word Latin name to identify and name - Species is written second and is always lower case any species. - Both names are in Latin or Latinised - Two different organisms cannot have same name - The species name has to be different within genus Chose the correct one- Homo sapiens Homo Sapiens Sapiens homo Homosapiens homo sapiens Homo sapiens H. SAPIENS H. sapiens Homo sapiens Homo sapiens Robert Harding Whittaker (December 27, 1920 – October 20, 1980) was a distinguished American plant ecologist who first to proposed the five-kingdom taxonomic classification and divided the world's biota into the Animalia, Plantae, Fungi, Protista, and Monera in 1969. The main criteria for classification used by him include cell structure, thallus organisation, mode of nutrition, reproduction and phylogenetic relationships. Merits of Five Kingdom Classification This system of classification is more scientific and natural. It is the most accepted system of modern classification as the different groups of animals are placed phylogenetically. The prokaryotes are placed in a separate kingdom as they differ from all other organisms in their organization. As the unicellular organisms are placed under the kingdom protista, it has solved many problem related to the position of organisms like euglena. The fungi totally differ from other primitive eukarytotes hence, placing the group fungi in a status of kingdom is justifiable. The kingdom Plantae and Animalia shows the phylogeny of different life styles, in the five kingdom classification, they are more homogeneous group than the two kingdom classification. This system of classification clearly indicates cellular organization and modes of nutrition, the character which have appeared very early in the evolution of life. Demerits of Five Kingdom Classification This system of classification has drawbacks with reference to the lower forms of life. The Kingdom of Monerans and the Protists include diverse, heterogenous forms of life. In both the kingdoms there are autoptrophic and hetertrophic organisms. They also include organisms which have cells with cell wall and cells without cell wall. Organisms like the unicelluar green algae like volvox and chlamydomonas have not been included under the Kingdom Protista because of their resemblance to other greeen algae. In this system of classification viruses have not been given proper place. Discoverer of third domain of life, the Archaea  Carl Richard Woese was an American microbiologist and biophysicist.  The three-domain system is a biological classification introduced by Carl Woese in 1977 that divides cellular life forms into archaea, bacteria, and eukaryote domains.  In particular, it emphasizes the separation of prokaryotes into two groups, originally called Eubacteria (now Bacteria) and Archaebacteria (now Archaea) on the basis of differences in 16S rRNA genes. To reflect these primary lines of descent, he treated each as a domain, divided into several different kingdoms. Woese initially used the term "kingdom" to refer to the three primary phylogenic groupings, and this nomenclature was widely used until the term "domain" was adopted in 1990  Woese is famous for defining the Archaea in 1977 by phylogenetic taxonomy of 16S ribosomal RNA, a technique pioneered by Woese which revolutionized the discipline of microbiology.  At Illinois, Woese examined the nucleotide sequences of 5S ribosomal RNA (a component of ribosomes, which build proteins) from different organisms.  He quickly realized that ribosomal RNA is an ideal chronometer for measuring evolutionary distances between living things. It has a slow mutation rate, performs an identical function in all organisms and, because ribosomal RNA interacts specifically with a multitude of proteins, the genes encoding it are unlikely to jump between individuals of different species. rRNA, an evolutionary chronometer  To create his evolutionary tree of life, then, Woese would need to choose a gene that was present in every known organism, one that was copied from generation to generation with a high degree of precision and mutated very slowly, so he would be able to track it over billions of years of evolution.  “By tracking these gene sequences over time, he could calculate the evolutionary distance between two organisms and make a map of how life on Earth may have evolved.” Some of the most ancient genes are those coding for molecules known as ribosomal RNAs. In ribosomes, parts of the cell that float around the soupy cytoplasm, proteins and ribosomal RNA, or rRNA, work together to crank out proteins.  Woese had several different rRNA molecules to choose from in the various subunits, which are classified based on their length. At around 120 nucleotides long, 5S rRNA wasn’t big enough to use to compare lots of different organisms. On the other end of the spectrum, 23S rRNA was more than 2300 nucleotides long, making it far too difficult for Woese to sequence using the technologies of the time. The Goldilocks molecule—long enough to allow for meaningful comparisons but not too long and difficult to sequence—was 16S rRNA (~1500 bp) in prokaryotes and its slightly longer eukaryotic equivalent, 18S rRNA.  Certain parts of the 16S rRNA molecule mutate at different speeds. Changes to 16S rRNA are, on the whole, still extremely slow (humans share about 50% of their 16S rRNA sequence with the bacterium E. coli), but one portion mutates much more slowly than the other. It’s as if the 16S rRNA clock has both an hour hand and a minute hand. The very slowly evolving “hour hand” lets biologists study the long-term changes to the molecule, whereas the more quickly evolving “minute hand” provides a more recent history. What makes rRNA (or another sequence) a good ‘chronometer’? 1. It is universally distributed across group chosen – all organisms have rRNA 2. It is functionally similar between organisms – rRNAs all participate in protein synthesis 3. Its sequence changes slowly - good for looking across long periods of time 4. The rRNA sequences can be aligned, or matched up, between 2 organisms 5. Other sequences that can be used are the large rRNA subunit, or the gene for cytochrome c oxidase, ferredoxin. Refined methods in classification led to the three domain, six kingdom classification system  The organisms are classified into domains based on the cell type.  Domain is a taxonomic category above the kingdom level  Domain is further subdivided into six kingdoms based on the cell structure & method of nutrition.  DNA evidence proved that bacteria & archaea are very different.  Domain 1 - Bacteria (Prokaryotes)  Domain 2 - Archaea (Ancient Prokaryotes)  Domain 3 - Eukarya (All Eukaryotes) Phylogenetic tree of life The Archaea (archaebacteria) Archaea constitute a domain of single-celled microorganisms. These microbes (archaea; singular archaeon) are prokaryotes, meaning they have no cell nucleus. The cell walls of Archaea contain no peptidoglycan. Archaea were initially classified as bacteria. Archaeal cells have unique properties separating them from the other two domains of life, Bacteria and Eukarya. Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably the enzymes involved in transcription and translation. Habitat of archaea Archaeans include inhabitants of some of the most extreme environments on the planet. Some live near rift vents in the deep sea at temperatures well over 100 degrees Centigrade. Others live in hot springs or in extremely alkaline or acid waters. They have been found thriving inside the digestive tracts of cows, termites, and marine life where they produce methane. They live in the anoxic muds of marshes and at the bottom of the ocean, and even thrive in petroleum deposits deep underground.  Methanococcus jannaschii Kinds of Archaebacteria Halococcus Pyrolobus fumarii, which holds the upper temperature limit for life at 113 °C (235 °F) and was found living in hydrothermal vents. Electron micrographs of Pyrolobus fumarii (Blöchl et al. 1997) Species of Picrophilus, which were isolated from acidic soils in Japan and are the most acid- tolerant organisms known—capable of growth at around pH 0 Bacteria (also known as eubacteria or "true bacteria") Eubacteria can be found almost everywhere and kill thousands upon thousands of people each year, but also serve as antibiotics producers and food digesters in our stomachs. The Bacteria possess the following characteristics-  Bacteria are prokaryotic cells. Unicellular. Naked DNA. No membrane bound organelles.  The cell walls of Bacteria, unlike the Archaea and the Eukarya, contain peptidoglycan.  Bacteria are sensitive to traditional antibacterial antibiotics but are resistant to most antibiotics that affect Eukarya.  Bacteria contain rRNA that is unique to the Bacteria as indicated by the presence molecular regions distinctly different from the rRNA of Archaea and Eukarya.  Bacteria include mycoplasmas, cyanobacteria, Gram-positive bacteria, and Gram-negative bacteria. Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the cell wall. Peptidoglycan serves a structural role in the bacterial cell wall, giving structural strength, as well as counteracting the osmotic pressure of the cytoplasm. The peptidoglycan layer is substantially thicker in Gram-positive bacteria (20 to 80 nanometers) than in Gram-negative bacteria (7 to 8 nanometers), with the attachment of the S-layer. The Eukarya (eukaryotes)  Eukarya have eukaryotic cells. Both unicellular & multicellular. It contains membrane bound organelles.  Like the Bacteria, they have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages. Not all Eukarya possess cells with a cell wall, but for those Eukarya having a cell wall, that wall contains no peptidoglycan.  Eukarya are resistant to traditional antibacterial antibiotics but are sensitive to most antibiotics that affect eukaryotic cells.  Eukarya contain rRNA that is unique to the Eukarya as indicated by the presence molecular regions distinctly different from the rRNA of Archaea and Bacteria. The Eukarya are subdivided into the following four kingdoms: 1. Protista - Protista are simple, predominately unicellular eukaryotic organisms. The simplest form of eukaryotes exhibiting both autotrophic and heterotrophic mode of nutrition. Examples includes slime molds, euglenoids, algae, and protozoans. 2. Fungi- Fungi are unicellular or multicellular organisms with eukaryotic cell types. The cells have cell walls but are not organized into tissues. They do not carry out photosynthesis and obtain nutrients through absorption. Examples include sac fungi, club fungi, yeasts, and molds. 3. Plantae - It includes all the plants that are non-motile,multicellular and eukaryotic organisms with their cell walls made up of cellulose. Plants are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and have cell walls. They obtain nutrients by photosynthesis and absorption. Examples include mosses, ferns, conifers, and flowering plants. 4. Animalia - Animals are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and lack cell walls. They do not carry out photosynthesis and obtain nutrients primarily by ingestion. Examples include sponges, worms, insects, and vertebrates. ‘Biomolecules’  Watson and Crick Solved the DNA Structure in 1953 They discovered that: The Phosphate Backbone was on the outside Nitrogen Bases on the inside Determined rules of base pairing- -Hydrogen bonding between AT, GC James Watson Francis Crick -Width of a purine-pyrimidine pair 5 end Antiparallel nature of strands Hydrogen bond 3 end 1 nm They proposed DNA has a double helix structure ( Although their work was based on X-ray 3.4 nm Crytallographic work of Rosalind Franklin) Since the two strands of DNA are complementary each strand acts as a template for building a new strand in replication 3 end 0.34 nm 5 end The molecules of Life Biomolecules Home reading 1. What is rRNA and why was did scientists choose it as an Evolutionary Chronometer? 2. What are 'extremeophiles'?