Assignments and Term Paper

1. Assignments and Term Paper • Grading altered • 10% for assignments – once a week, presentations twice a week. • 5% for term paper – groups of 4 • 25% quizzes • 25% mid-term • 35% final exam

2. Lecture 2 Variety of Life • Classification of living organisms • Methods of classification • Different kingdoms of living organisms: Monera, Protista, Fungi, Plantae, and Animalia.

3. Classification of Living Organisms • At least 1.7 million species of living organisms have been discovered. • Taxonomy (Gr. taxis, "arrangement, order", nomos, "law") is the science of classification (Latin, classis, "a class", facere, "to make"). • Two branches, naming an organism, or nomenclature and placing it in a group, systematics. • The Role of Taxonomy :  1. Taxonomy works out for us a vivid picture of the existing organic diversity of the earth. 2. Taxonomy provides much of the information permitting a reconstruction of the phylogeny of life. 3. Taxonomy reveals numerous interesting evolutionary phenomena.

4. Nomenclature • Without a set of international rules to follow, the results of taxonomy would be confusing at best. • International Code of Zoological Nomenclature (ICZN). • The Linnaean Hierarchy. • Nomenclature based on a binomial system devised by the Swedish naturalist Carl Linnaeus in 1758. • The scientific name of an organism consists of a collective generic name, beginning with a capital letter, and a specific or species name, in lower case letters. E.g Homo sapiens

5. Linnaeus Hierarchy Arranged as a hierarchy, with largest group at the top: Kingdom Phylum Class Order Family-category including 1 genus or a group of genera of common phylogenetic origin, which is separated from other families. Genus-category containing a single species, which is separated from other taxa by behaviour, morphology, or some other characteristics. Species-group of closely related organisms capable of interbreeding to produce fertile offspring. Drastic differences

6. How are they classified?

7. Reductionist Principle Chemicals Cells How similar is the DNA? What type of cell is it? Nutrition? Movement? Coordination/sensory system? Anatomy? Embryonic development? Tissues Organs Systems Organism Population Community Ecosystem

8. Methods of Classification • Homology - shared characteristics inherited from a common ancestor. • The more recently two species have shared a common ancestor, the more homologies they share. • Study of homologies was limited to anatomical structures and pattern of embryonic development. • Since the birth of molecular biology, homologies can now also be studied at the level of proteins and DNA by : • DNA-DNA Hybridization • Chromosome Painting • Comparing DNA Sequences

9. Molecular Homology • Protein sequencing provides a tool for establishing homologies from which genealogies can be constructed and phylogenetic trees drawn. Example : Hemoglobins Human beta chain 0 Mouse 27 Gorilla 1 Gray kangaroo 38 Gibbon 2 Chicken 45 Rhesus monkey 8 Frog 67 Lamprey 125 Dog 15 Sea slug (a mollusk) 127 Horse, cow 25 Soybean (leghemoglobin) 124 Number of amino acid differences between the beta chain of humans and the hemoglobins of the other species. In general, the number is inversely proportional to the closeness of kinship.

10. Domains of Life • Until comparatively recently, living organisms were divided into two kingdoms: Animalia and the Plantae. • Animals fed on organic material – heterotrophic • Plants synthesis own organic material from inorganic material – auxotrophic. • In the 19th century, evidence began to accumulate that these were insufficient to express the diversity of life. • Scheme in widest current use divides all living organisms into five kingdoms.

11. Early View 2 Kingdoms Whittaker’s View 5 Kingdoms Plants Animals Fungi Animals Plants Algae Protoctista Copeland’s View 4 Kingdoms Monera (prokaryotes) Animals embryophytes algae Protoctista Monera

12. Three Domains of Life • All cellular organisms fall into two natural groups, prokaryotes and eukaryotes. • Pro, before; karyon, nucleus DNA is not enclosed by a nuclear membrane and lies free in the cell. • Eu, true; karyon, nucleus evolved from prokaryotes. • Recent work, however, has shown that the Prokaryotae are now divided into two domains, the Bacteria and the Archaea. • No one of these groups is ancestral to the others

14. ProkaryotesIntroduction to Bacteria • Bacteria are often maligned as the causes of human and animal disease. • The actinomycetes, produce antibiotics such as streptomycin and nocardicin; others live symbiotically in plants and animals (including humans). Bacteria put the tang in yogurt; bacteria help to break down dead organic matter; bacteria make up the base of the food web in many environments. • Are of such immense importance because of their extreme flexibility, capacity for rapid growth and reproduction, and great age - the oldest fossils known, nearly 3.5 billion years old, are fossils of bacteria-like organisms.

15. Most bacteria may be placed into one of three groups in response to oxygen: Aerobic bacteria thrive in the presence of oxygen and require it for their continued growth. Anaerobic bacteria cannot tolerate gaseous oxygen, such as those bacteria which live in deep underwater sediments, or those which cause bacterial food poisoning. Facultative anaerobes, which prefer growing in the presence of oxygen, but can continue to grow without it. Most bacteria may be placed into one of two groups depending on what they use as a source of energy: Heterotrophs derive energy from organic compounds that they must take in from the environment -- this includes saprobic bacteria found in decaying material. Auxotrophs fix carbon dioxide to make their own food source light energy (photoautotrophic), e.g the cyanobacteria, green sulfur bacteria, purple sulfur bacteria, and purple nonsulfur bacteria or by oxidation of nitrogen, sulfur, or other elements (chemoautotrophic). The sulfur bacteria use hydrogen sulfide as hydrogen donor, instead of water like most other photosynthetic organisms.   Classification of Bacteria

16. Structure of Bacteria • Prokaryotic - lack the membrane-bound nuclei their DNA forms a tangle known as a nucleoid. • DNA is not organized into linear pieces, the chromosomes, bacterial DNA forms loops. • Bacteria contain plasmids, or small loops of DNA, that can be transmitted from one cell to another, either in the course of sex (yes, bacteria have sex) or by viruses. • This ability to trade genes with all comers makes bacteria amazingly adaptible; beneficial genes, like those for antibiotic resistance, may be spread very rapidly through bacterial populations. • Bacteria do not contain membrane-bound organelles such as mitochondria or chloroplasts, as eukaryotes do. However, photosynthetic bacteria, such as cyanobacteria, may be filled with tightly packed folds of their outer membrane. The effect of these membranes is to increase the potential surface area on which photosynthesis can take place.

17. Bacterial Cell Membrane • The cell membrane is surrounded by a cell wall in all bacteria except one group, the Mollicutes, which includes pathogens such as the mycoplasmas. • The composition of the cell wall varies among species and is an important character for identifying and classifying bacteria. • Danish bacteriologist developed a staining procedure to look for differences in the cell wall. The Gram Stain. • If a bacteria has a thick cell wall made of peptidoglycan (carbohydrate polymers cross-linked by proteins); it will retain a purple colour when stained with a dye known as crystal violet, and is known as Gram-positive. • If a bacteria has a double cell wall, with a thin inner wall of peptidoglycan and an outer wall of carbohydrates, proteins, and lipids it will not stain purple with crystal violet and is known as Gram-negative.

18. Introduction to the Archaea • The Domain Archaea wasn't recognized as a major domain of life until quite recently. • In the late 1970s discovery of an entirely new group of organisms, by Dr.Carl Woese and his colleagues at the University of Illinois. They were studying relationships among the prokaryotes using DNA sequences, and found that there were two distinctly different groups. • Those "bacteria" that lived at high temperatures or produced methane clustered together as a group well away from the usual bacteria and the eukaryotes. • Because of this vast difference in genetic makeup, Woese proposed that life be divided into three domains: Eukaryota, Eubacteria, and Archaebacteria. He later decided that the term Archaebacteria was misleading, and shortened it to Archaea.

19. Archaeans • Inhabitants 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 (such as the ones pictured above), 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.

20. The Eukaryotae • The Eukaryota include the organisms that most people are most familiar with - all animals, plants, fungi, and protists. • Share properties such as a nucleus, cytoskeletons, and internal membranes. • Eukaryote DNA is divided into linear pieces called chromosomes (unlike bacterial DNA, which forms loops).

21. Assignment • Read pp 52-76 • Give the Linnaeus Classification for segmented worms and human beings. • Why have both these living organisms been placed in the same kingdom of Animalia?