UNIT I UNITY DIVERSITY OF LIFE Hillis Chp

UNIT I – UNITY & DIVERSITY OF LIFE Hillis – Chp 1, 19, 20 (pgs. 392 -406), 22 Big Campbell ~ Ch 1, 18, 27, 28, 31 Baby Campbell ~ Ch 1, 10, 16, 17

Biology is. . .

I. “THE STUDY OF. . . “ – EXPERIMENTAL DESIGN Inquiry-based

I. EXPERIMENTAL DESIGN, cont • Types of Experiments o Comparative, Observational, Controlled • Setting up a Controlled Experiment o Clearly defined purpose o Valid, clear hypothesis Ø Testable statement or prediction Ø Do not use “I think …”, “My hypothesis is …”, etc! Ø Often written in “If …, then …” format but not required o Control Group Ø Benchmark or standard for comparison o Experimental or Test Group(s) Ø Only one factor can be changed in each test Ø Independent (Manipulated) Variable Ø Dependent (Responding) Variable

I. EXPERIMENTAL DESIGN, cont • Important Considerations o Controlled variables (aka control variables, constants) must be monitored Ø Additional factors that could change from one set-up to another o Sample Size o Potential sources of error o Is it repeatable? • Presentation of Data o Concise & Organized Ø Tables

I. EXPERIMENTAL DESIGN, cont o Graphs Ø Format ü Descriptive title ü Key ü Units must be evenly spaced (line break) and labeled ü Use at least half of available space ü Use a RULER!!! Ø DRY MIX ü Ø Types of Graphs ü Continuous Independent Variable (time) → _Line_ Graph ü Discrete Independent Variable → _Bar__ Graph ü Part of a Whole → ___Pie___ Graph

I. EXPERIMENTAL DESIGN, cont o Graphs, cont § For Height Lab … v Mean v Median v Mode v Range v Histogram Ø Ø Normal Distribution?

I. EXPERIMENTAL DESIGN, cont o Data Analysis Ø Null Hypothesis v“Statement of No Effect” v States that any differences in data sets are due to random errors that cannot be eliminated in experimental design/protocol v. For example, § There are no significant differences between predicted and observed data. § There are no significant differences between control group data and test group data. Ø Alternate Hypothesis – it is formulated to describe the effect that we expect our data to support. Ø Statistical Analysis – Supports or refutes null hypothesis

I. EXPERIMENTAL DESIGN, cont v Standard Deviation Ø

I. EXPERIMENTAL DESIGN, cont v Standard Error of the Mean

I. EXPERIMENTAL DESIGN, cont Examine the data below showing two different experiments in which the heart rate of 10 different individuals was measured in beats/minute. Study A Study B 68 68 70 84 76 90 62 60 70 92 72 58 74 64 67 66 68 78 70 86

I. EXPERIMENTAL DESIGN, cont Calculate the standard deviation for each data set. Study A Study B 68 68 70 84 76 90 62 60 70 92 72 58 74 64 67 66 68 78 70 86

I. EXPERIMENTAL DESIGN, cont • Is there is a significant difference between the average heart beat/minutes in the two data sets? Construct a graph to illustrate.

I. EXPERIMENTAL DESIGN, cont • Conclusion o Evaluate hypothesis Ø Was it supported, refuted, or were results inconclusive? o Assess experimental design Ø Was there only one independent variable? Ø Were sources of error minimized? Ø Controlled variables/constants Ø Repeatable? • Theory

II. UNITY OF LIFE • Form vs. Function • Characteristics of Life o All living things are made of _cells_. § Prokaryotic § Eukaryotic

II. UNITY OF LIFE, cont. • Characteristics of Life, cont o Living things obtain and use energy. o Living things respond to their environment. o Living things grow and develop. o Living things maintain homeostasis. o Living things are based on a universal genetic code. o Living things reproduce. o As a group, living things evolve.

III. HIERARCHY OF LIFE o Organization of Life Biosphere Ecosystem Community Population Organism § organ system § organ § tissue § cell Ø Organelle Ø Molecule Ø Atom Ø Ø Ø

III. HIERARCHY OF LIFE, cont • Classification of Life v Domain v Kingdom v Phylum v Class v Order v Family v Genus v Species

III. HIERARCHY OF LIFE, cont • A Closer Look at Classification § Domain _Archaea_ Ø Kingdom __Archaebacteria__ § Domain _Bacteria_ Ø Kingdom _Eubacteria__ § Domain __Eukarya__ Ø Kingdom _Protista___ Ø Kingdom __Fungi___ Ø Kingdom __Plantae___ Ø Kingdom __Animalia___

IV. CHALLENGING THE BOUNDARIES OF LIFE • Viruses. . . Living or Nonliving? Ø Discovery of Viruses § First isolated by Ivanowsky in 1890 s from infected tobacco leaves § Crystallized by Stanley in 1935 – proved viruses were not cells Ø Not capable of carrying out life processes without a host cell Ø Parasites

IV. BOUNDARIES, cont • Viruses, cont Ø Structures found in all viruses: § Viral genome v DNA or RNA. v May be single-stranded or doublestranded § Protein coat v Known as a capsid v Made up of protein subunits called capsomeres.

IV. BOUNDARIES, cont • Viruses, cont Ø Structures/adaptations that may be present: § Viral envelope v Typically derived from host cell membrane o Exception is Herpes virus, synthesized from nuclear envelope of host cell v Aid in attachment. Envelope glycoproteins bind to receptor molecules on host cell v Most viruses that infect animals have envelope § Tail – Found in some viruses to aid in attachment

IV. BOUNDARIES, cont

IV. BOUNDARIES, cont • Viruses, cont. Ø Bacteriophage § Infect bacteria § Bacterial Defense Mechanisms v. Restriction Enzymes v. Coexistence

IV. BOUNDARIES, cont – Viral Replication 1. Virus enters; is uncoated; releases viral genome and capsid proteins 2. Host enzymes replicate the viral genome 3. Host enzymes replicate viral genome 4. Viral genomes and capsids self-assemble into new viral particles; exit the cell

IV. BOUNDARIES, cont – Viral Replication Viral Entrance into Host Cell

IV. BOUNDARIES, cont – Viral Replication LYTIC CYCLE 1. Lytic Cycle – Results in death of host cell.

IV. BOUNDARIES, cont – Viral Replication LYSOGENIC CYCLE

IV. BOUNDARIES, cont – Human Viruses • DNA Viruses o No envelope Ø Papilloma Virus q Warts, cervical cancer o With envelope Ø Smallpox Virus - cowpox Ø Herpesvirus q. Herpes simplex I and II – cold sores, genital sores q. Epstein-Barr virus – mono, burkitt’s lymphoma q. Varicella zoster – shingles, chicken pox

IV. BOUNDARIES, cont – Human Viruses RNA Viruses

IV. BOUNDARIES, cont – Human Viruses • RNA Viruses o No envelope ØRhinovirus – common cold o Envelope ØCoronavirus - SARS ØFilovirus – Ebola (hemmorrhagic fever) ØInfluenza virus - flu ØHIV § Belongs to a group of viruses known as _Retroviruses__ § Contain RNA, reverse transcriptase v. Converts _RNA_ to _DNA_

IV. BOUNDARIES, cont – HIV Ø A Closer Look at Human Immunodeficiency Virus § Infects WBCs known as Helper T cells § Can reside in lysogenic-like cycle for years § Active, symptomatic = AIDS

IV. BOUNDARIES, cont – HIV, cont

IV. BOUNDARIES, cont • Viroids o Single, circular RNA molecule; lack protein o Parasitize plants • Prions o o Infectious proteins; lack nucleic acid Cause Mad Cow Disease, Creutzfeldt-Jakob Disease Very long incubation period No treatment

V. THE DIVERSITY OF LIFE Kingdom Type of Cell Structures Nutrition Description Archaebacteria • • Cell wall not made of _______ Mostly ________ “_______ bacteria”; require ______ conditions Eubacteria • • Cell wall made of ________ Mostly ________ Ubiquitous; _____; may be pathogenic Protista • • Mostly ____ May have cell wall, Auto or hetero chloroplasts, flagella Fungi • • Mostly ____ Cell wall made of ______; no _______! Plantae • • Cell wall made of Strictly All non-motile ______; all ________ have chloroplasts (_______) Animalia • • Never have ____________; chloroplasts “_______”; very diverse “kingdom” Strictly All non-motile; _______________ (_______) Strictly All _______________ during life cycle; (_______) most complex

IV. THE DIVERSITY OF LIFE Kingdom Type of Cell Structures Nutrition Description Archaebacteria • Prokaryotic • Unicellular Cell wall not made of peptidoglycan Mostly heterotrophic “Ancient bacteria”; require harsh conditions Eubacteria • Prokaryotic • Unicellular Cell wall made of peptidoglycan Mostly heterotrophic Ubiquitous; decomposers; may be pathogenic Protista • Eukaryotic • Mostly uni May have cell wall, Auto or hetero chloroplasts, flagella “Junk Drawer of Life”; very diverse “kingdom” Fungi • Eukaryotic • Mostly multi Cell wall made of chitin; no chloroplasts! Strictly heterotrophic (absorption) All non-motile; decomposers Plantae • Eukaryotic • Multicellular Cell wall made of cellulose; all have chloroplasts Strictly autotrophic (photosynthesis) All non-motile Animalia • Eukaryotic • Multicellular Never have cell walls or chloroplasts Strictly heterotrophic (ingestion) All motile during life cycle

VI. PROKARYOTES – A CLOSER LOOK

VI. PROKARYOTES, cont • Archaebacteria Ø Examples include methanogens, thermoacidophiles, halophiles Ø Taq DNA polymerase

VI. PROKARYOTES, cont Eubacteria Ø Ubiquitous Ø May be pathogenic Ø Most are harmless • Classification Ø Shape § Cocci § Bacilli § Spirilla Ø Gram Stain Reaction § Positive § Negative

Gram + Streptococcus pneumoniae

Gram - Neisseria gonorrhoeae – gram negative; coccus shaped E. coli – gram negative; rod-shaped

VI. PROKARYOTES – EUBACTERIA, cont • Nucleoid region • Plasmids • Asexual reproduction Ø Binary fission

VI. PROKARYOTES – EUBACTERIA, cont • Adaptations Ø Capsule § Adherence § Protection § Associated with virulence Ø Pili § Adherence § Conjugation Ø Endospore § Bacterial “hibernation” Ø Motility (flagella, slime,

Spore formation – adaptation seen in some bacteria that allows them to survive adverse conditions. A hard, protective wall forms around the DNA of the bacteria – and the bacteria can survive for centuries. When favorable conditions return, the spores revive, and the bacteria is able to revive and germinate. Ex. Bacillus anthracis; Clostridium botulinum Bacillus anthracis

VI. PROKARYOTES – EUBACTERIA, cont • Adaptations, cont Ø Quorum Sensing/Biofilms § Fairly recent discovery § Bacteria exchange chemical communication signals § Multicellularity? ? ? Ø “Sexual Reproduction” § Genetic Recombination Occurs by: § Transformation § Transduction § Conjugation

§ Transformation – external DNA incorporated into cells – can come from dead bacteria

• Transduction – transfer of genes between a bacteria and a virus vector – the virus inserts new genes into the bacteria…. This method is used in biotechnology to create bacteria that produce valuable products such as insulin.

• Conjugation – a form of sexual reproduction in which there is a direct transfer of a plasmid from one bacteria to another (through pili) before the bacteria divides – results in offspring with new genes/traits. - Plasmid - smaller ring of DNA that functions in antibiotic resistance or metabolism; replicates independently of the entire DNA

VI. PROKARYOTES – EUBACTERIA, cont • Metabolism o Nitrogen fixation Ø Conversion of atmospheric nitrogen (N 2) to ammonium (NH 4+) o Metabolic Cooperation Ø Biofilms o Oxygen relationships Ø Obligate aerobes Ø Facultative anaerobes Ø Obligate anaerobes

VI. PROKARYOTES – EUBACTERIA, cont Bacterial Pathogenesis • Koch’s Postulates – Criteria for bacterial disease confirmation Ø The microorganism is found in all individuals with the disease. Ø The microorganism can be cultured from the host. Ø The isolated organism will produce disease when injected into another host. Ø The organism can be isolated from the newly infected host. • “Normal Flora” • Some bacteria are opportunistic pathogens Ø Normal residents of host; cause illness when defenses are weakened • Toxin Production Ø Exotoxins - Bacterial proteins that can produce disease w/o the prokaryote present (botulism, cholera) Ø Endotoxins - Components of gram negative membranes (typhoid fever, Salmonella food poisoning)

VI. PROKARYOTES – EUBACTERIA, cont • Bacterial Pathogenesis, cont Ø Examples v Clostridium sp. v Staphylococcus v Streptococcus v Neisseria sp. v Mycobacterium tuberculosis v Legionella pneumophila

EUKARYOTES

VII. KINGDOM PROTISTA • • Very diverse All _Eukaryotic_ Mostly _Heterotrophic_ Classified according to eukaryotic kingdom protist is most like, nutrition Ø Animal-like § Ingestive § Protozoans Ø Plant-like § Photosynthetic § Algae, kelp, seaweed § Very impt aquatic producers; phytoplankton Ø Fungus-like § Absorptive

VII. KINGDOM PROTISTA, cont Protist Phylogeny. . . For now!

VII. KINGDOM PROTISTA, cont • Important Protozoans Ø Zooplankton § Important component of aquatic food chains Ø Human Pathogens § Entamoeba o Intestinal pathogen o Associated with dirty, stagnant water o Moves, feeds using pseudopods § Giardia o Lack mitochondria, cell walls o Live in fresh water; flagellated o Intestinal pathogens

VII. KINGDOM PROTISTA, cont • Important Protozoans, cont Ø Plasmodium § Belong to Apicomplexa ü All parasitic, non-motile § Cause malaria § Vector = Anopheles mosquito § Resistance seen in _____ _Individuals heterozygous for sickle cell anemia_ Ø Toxoplasma

VIII. KINGDOM FUNGI

VIII. KINGDOM FUNGI, cont • Absorptive heterotrophs; release exoenzymes Ø Decomposers (saprobes) Ø Parasites Ø Mutualistic symbionts (lichens) • Primarily reproduce asexually • Classified according to reproductive structures • Include mushrooms, bracket fungi, puffballs • Yeast Ø Unicellular Ø Reproduce asexually; budding Ø May be pathogenic

VIII. KINGDOM FUNGI, cont • Specialized Fungi Ø Molds § Used to be classified as Deuteromycota or “Imperfect Fungi” § No known sexual stage § Penicillium Ø Lichens § Mutualistic relationship with algae or cyanobacterium § Sensitive to air pollution Ø Mycorrhizae § Mutualistic relationship found in 95% of all plants