UNIT I

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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

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Biology is . . .
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I. THE STUDY OF . . . EXPERIMENTAL DESIGN
Inquiry-based
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I. EXPERIMENTAL DESIGN, cont

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

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I. EXPERIMENTAL DESIGN, cont

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

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I. EXPERIMENTAL DESIGN, cont

• Graphs
• Format
• Descriptive title
• Key
• Units must be evenly spaced (line break) and
  labeled
• Use at least half of available space
• Use a RULER!!!
• DRY MIX
• Types of Graphs
• Continuous Independent Variable (time) ?
  _Line_ Graph
• Discrete Independent Variable ? _Bar__ Graph
• Part of a Whole ? ___Pie___ Graph

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I. EXPERIMENTAL DESIGN, cont

• Graphs, cont
• For Height Lab
• Mean
• Median
• Mode
• Range
• Histogram
• Normal Distribution?

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I. EXPERIMENTAL DESIGN, cont

• Data Analysis
• Null Hypothesis
• Statement of No Effect
• States that any differences in data sets are due
  to random errors that cannot be eliminated in
  experimental design/protocol
• 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.
• Alternate Hypothesis it is formulated to
  describe the effect that we expect our data to
  support.
• Statistical Analysis Supports or refutes null
  hypothesis

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I. EXPERIMENTAL DESIGN, cont

• Standard Deviation

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I. EXPERIMENTAL DESIGN, cont

• Standard Error of the Mean

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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
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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
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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.

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I. EXPERIMENTAL DESIGN, cont

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

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II. UNITY OF LIFE

• Form vs. Function
• Characteristics of Life
• All living things are made of _cells_.
• Prokaryotic
• Eukaryotic

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II. UNITY OF LIFE, cont.

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

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III. HIERARCHY OF LIFE

• Organization of Life
• Biosphere
• Ecosystem
• Community
• Population
• Organism
• organ system
• organ
• tissue
• cell
• Organelle
• Molecule
• Atom

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III. HIERARCHY OF LIFE, cont

• Classification of Life
• Domain
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• Species

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III. HIERARCHY OF LIFE, cont

• A Closer Look at Classification
• Domain _Archaea_
• Kingdom __Archaebacteria__
• Domain _Bacteria_
• Kingdom _Eubacteria__
• Domain __Eukarya__
• Kingdom _Protista___
• Kingdom __Fungi___
• Kingdom __Plantae___
• Kingdom __Animalia___

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IV. CHALLENGING THE BOUNDARIES OF LIFE

• Viruses . . . Living or Non-living?
• Discovery of Viruses
• First isolated by Ivanowsky in 1890s from
  infected tobacco leaves
• Crystallized by Stanley in 1935 proved viruses
  were not cells
• Not capable of carrying out life processes
  without a host cell
• Parasites

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IV. BOUNDARIES, cont

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

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IV. BOUNDARIES, cont

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

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IV. BOUNDARIES, cont
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IV. BOUNDARIES, cont

• Viruses, cont.
• Bacteriophage
• Infect bacteria
• Bacterial Defense Mechanisms
• Restriction Enzymes
• Coexistence

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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
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IV. BOUNDARIES, cont Viral Replication
Viral Entrance into Host Cell
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IV. BOUNDARIES, cont Viral Replication
LYTIC CYCLE

• 1. Lytic Cycle Results in death of host
  cell.

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IV. BOUNDARIES, cont Viral Replication
LYSOGENIC CYCLE
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IV. BOUNDARIES, cont Human Viruses

• DNA Viruses
• No envelope
• Papilloma Virus
• Warts, cervical cancer
• With envelope
• Smallpox Virus - cowpox
• Herpesvirus
• Herpes simplex I and II cold sores, genital
  sores
• Epstein-Barr virus mono, burkitts lymphoma
• Varicella zoster shingles, chicken pox

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IV. BOUNDARIES, cont Human Viruses
RNA Viruses
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IV. BOUNDARIES, cont Human Viruses

• RNA Viruses
• No envelope
• Rhinovirus common cold
• Envelope
• Coronavirus - SARS
• Filovirus Ebola (hemmorrhagic fever)
• Influenza virus - flu
• HIV
• Belongs to a group of viruses known as
  _Retroviruses__
• Contain RNA, reverse transcriptase
• Converts _RNA_ to _DNA_

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IV. BOUNDARIES, cont HIV

• 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

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IV. BOUNDARIES, cont HIV, cont
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IV. BOUNDARIES, cont

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

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V. THE DIVERSITY OF LIFE
Kingdom Type of Cell 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, chloroplasts, flagella Auto or hetero _______________________ very diverse kingdom
Fungi Mostly ________ Cell wall made of ____________ no ______________! Strictly _______________ (______________) All non-motile _______________
Plantae Cell wall made of ____________ all have chloroplasts Strictly _______________ (______________) All non-motile
Animalia Never have _____ ____________ chloroplasts Strictly _______________ (______________) All ___________ during life cycle most complex
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IV. THE DIVERSITY OF LIFE
Kingdom Type of Cell 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, chloroplasts, flagella Auto or hetero 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
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VI. PROKARYOTES A CLOSER LOOK
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VI. PROKARYOTES, cont

• Archaebacteria
• Examples include methanogens, thermoacidophiles,
  halophiles
• Taq DNA polymerase

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VI. PROKARYOTES, cont

• Eubacteria
• Ubiquitous
• May be pathogenic
• Most are harmless
• Classification
• Shape
• Cocci
• Bacilli
• Spirilla
• Gram Stain Reaction
• Positive
• Negative

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Gram
Streptococcus pneumoniae
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Gram -
E.coli gram negative rod-shaped
Neisseria gonorrhoeae gram negative coccus
shaped
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VI. PROKARYOTES EUBACTERIA, cont

• Nucleoid region
• Plasmids
• Asexual reproduction
• Binary fission

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VI. PROKARYOTES EUBACTERIA, cont

• Adaptations
• Capsule
• Adherence
• Protection
• Associated with virulence
• Pili
• Adherence
• Conjugation
• Endospore
• Bacterial hibernation
• Motility (flagella, slime,

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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
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VI. PROKARYOTES EUBACTERIA, cont

• Adaptations, cont
• Quorum Sensing/Biofilms
• Fairly recent discovery
• Bacteria exchange chemical communication signals
• Multicellularity???
• Sexual Reproduction
• Genetic Recombination Occurs by
• Transformation
• Transduction
• Conjugation

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• Transformation external DNA incorporated into
  cells can come from dead bacteria

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• 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.

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• 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

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VI. PROKARYOTES EUBACTERIA, cont

• Metabolism
• Nitrogen fixation
• Conversion of atmospheric nitrogen (N2) to
  ammonium (NH4)
• Metabolic Cooperation
• Biofilms
• Oxygen relationships
• Obligate aerobes
• Facultative anaerobes
• Obligate anaerobes

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VI. PROKARYOTES EUBACTERIA, cont

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

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VI. PROKARYOTES EUBACTERIA, cont

• Bacterial Pathogenesis, cont
• Examples
• Clostridium sp.
• Staphylococcus
• Streptococcus
• Neisseria sp.
• Mycobacterium tuberculosis
• Legionella pneumophila

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EUKARYOTES
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VII. KINGDOM PROTISTA

• Very diverse
• All _Eukaryotic_
• Mostly _Heterotrophic_
• Classified according to eukaryotic kingdom
  protist is most like, nutrition
• Animal-like
• Ingestive
• Protozoans
• Plant-like
• Photosynthetic
• Algae, kelp, seaweed
• Very impt aquatic producers phytoplankton
• Fungus-like
• Absorptive
• Slime Molds

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

• Important Protozoans
• Zooplankton
• Important component of aquatic food chains
• Human Pathogens
• Entamoeba
• Intestinal pathogen
• Associated with dirty, stagnant water
• Moves, feeds using pseudopods
• Giardia
• Lack mitochondria, cell walls
• Live in fresh water flagellated
• Intestinal pathogens

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VII. KINGDOM PROTISTA, cont

• Important Protozoans, cont
• Plasmodium
• Belong to Apicomplexa
• All parasitic, non-motile
• Cause malaria
• Vector Anopheles mosquito
• Resistance seen in _________
• _Individuals heterozygous for
• sickle cell anemia_
• Toxoplasma

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VIII. KINGDOM FUNGI
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VIII. KINGDOM FUNGI, cont

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

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VIII. KINGDOM FUNGI, cont

• Specialized Fungi
• Molds
• Used to be classified as Deuteromycota or
  Imperfect Fungi
• No known sexual stage
• Penicillium
• Lichens
• Mutualistic relationship with algae or
  cyanobacterium
• Sensitive to air pollution
• Mycorrhizae
• Mutualistic relationship found in 95 of all
  plants