Diversity Unit Review

Why do we classify organisms?//

  • To divide and organize them
  • To create a universal classification and name to avoid confusion between different cultures and languages

\\Phylogeny//

  • Evolutionary history, including relationships with other organisms based on past ancestors

\\Taxonomy//

  • Is the identification, classification, and naming of species

\\Carlos Linnaeus//

  • Father of Taxonomy
  • Developed the system for naming species: Binomial Nomenclature

\\Taxon//

  • (pl. taxa)
  • Particular classification of an organism at each rank level
  • (i.e phylum Chordata or order Rodentia)

\\Binomial Nomenclature//

  • Two-part naming structure
  • An organism’s scientific name or species name has two parts
  • Genus part + Species name

\\Rules for writing Binomial Nomenclature//

  • The scientific name is italicized, with the genus name capitalized, and the species is in lowercase
    • I.e Homo sapiens
  • When the name is written by hand, both parts are underlined
    • I.e Homo sapiens

\\Organism//

  • A life form, with multiple functions, put together

\\Species//

  • A group of organisms that can interbreed in nature and produce fertile offspring

\\Domain//

  • Broadest, most inclusive rank
    • Bacteria
    • Archaea
    • Eukarya

\\Kingdom//

  • Second most general rank
  • Includes six different taxa (animals, plants, protists, bacteria, fungi, archaea)
  • Incredible structural diversity (internal and external forms) within the kingdom

\\Classifcation of Kingdoms//

  • When classifying only kingdom rank, the following characteristics can be used
    • Number of cells (unicellular or multicellular
    • Cell wall material (if present)
    • Nutrition (autotroph or heterotroph)
    • Autotroph: captures energy from sunlight/abiotic substances
    • Hetereotroph: obtains energy by consuming other organisms
    • Primary means of reproduction (asexual or sexual)

\\The 6 Kingdoms//

  • Bacteria
  • Archaea
  • Animalia
  • Plantae
  • Protista
  • Fungi

\\Levels of Organization(ranks)//

  • Domain
  • Kingdom
  • Phylum
  • Class
  • Order
  • Family
  • Genus
  • Species

\\Prokaryotic Cell//

  • (before the nucleus)
  • No membrane-bound nucleus
  • Simpler internal cell structure
  • No membrane-bound organelles
  • Only organelles or ribosomes, which are not membrane-bound
  • Usually smaller, and simpler

\\Eukaryotic Cell//

  • (true nucleus)
  • Membrane-bound nucleus
  • More complex internal cell structure
  • Usually larger (up to 1000x)
  • Membrane-bound organelles

\\Dichotomous keys//

  • Many scientists use classification manuals to identify organisms
  • Usually, it involves completing a two-part question or dichotomous key
  • The key is constructed so that a series of choices must be made, and each choice leads to a new branch of the key
  • If the choices are made accurately, the end result is the correct name of the organism being identified

\\Virus//

  • It is a non-cellular particle made up of DNA or RNA and a capsid that can invade a living cell; host specific
  • Not considered living since they cannot live outside of cells
    • Dependent on the internal physiology of cells
    • Are not cellular and this lack cytoplasm, organelles, and cell membranes
  • A virus must infect a host cell in order to be functional

\\Capsid//

  • A protein coat that wraps around a virus

\\Viral Size//

  • Range in size from 30nm to 300nm

\\Viral Shapes//

  • Polyhedral
  • Helical
  • Enveloped
  • Complex
    • P.H.E.C

\\Polyhedral//

  • Many-Sided (Refers to capsid)
  • Examples include:
    • Poliovirus, rhinovirus, adenovirus

\\Helical//

  • Nucleic acid is enclosed in a hollow cylindrical capsid
  • Examples include:
    • Tobacco mosaic virus, rabies

\\Enveloped//

  • Contains a membrane coat surrounding the capsid
  • Usually roughly spherical, but highly pleomorphic
    • Can be helical of polyhedral
  • Examples include:
    • Influenza virus, Herpes simplex virus

\\Complex//

  • A combination that usually contains additional structural components attached
  • Best shape
  • Examples include
    • Bacteriophage, poxvirus

\\Bacteriophage//

  • A virus that infects bacteria

\\Lytic Cycle//

  1. Attachment
  • The virus attaches to the body of the cell
  1. Entry / Injection
  • The virus invades a hostel cell and injects is viral DNA or RNA into the host cell
  1. Replication
  • The host cell makes copies of new viral proteins and nucleic acids
  1. Assembly
  • New viral particles are put together
  1. Lysis and Release
  • New viral particles are related to the environment when the cell is lysed and are able to invade new cells
  • (When symptoms start)
    • Quicker incubation period

\\Lysogenic Cycle//

  • Some viruses can remain dormant inside a cell
  • They are called latent viruses
    • They may remain inactive for long periods of time, possibly even years
  • In this cycle, the viral DNA joins the host chromosome and a provirus(prophage) is formed
  • Viral DNA joins with the chromosome DNA
  • Later they activate to produce new viruses in response to an external signal or trigger
  • At that point, they go into the lytic cycle
    • Examples: HIV and Herpes

\\Retrovirus//

  • A type of lysogenic virus
  • Enveloped viruses with an RNA genome
  • Replicate via a DNA intermediate (enzyme reverse transcriptase) to convert RNA into DNA
  • The viral DNA enters the chromosomes of the host cell, forming a provirus
  • When the host cell divides by mitosis it replicates the provirus along with its own DNA
  • The process can continue for years with no harm to the host
  • At any time, the provirus can separate from the host chromosomes and complete the more damaging lyric cycle
  • Examples:
    • Human immunodeficiency virus (HIV), and herpes simplex virus

\\Connection to human health//

  • Some virus infections can be prevented by making vaccines
  • Our bodies make antibodies when exposed to the vaccine to fight the virus
  • (Memory Cells)

\\Viruses and Biotechnology//

  • Viruses are not entirely bad
  • Can be useful tools in biotechnology
  • Biological role (Artificial):
    • They can be used to make many copies of desirable genes
    • Can be used in medicine for ‘gene therapy to repair bad genes

\\Prions: Non-Viral Disease-Causing Agents//

  • Disease-causing proteins that become harmful when they change molecular shape
  • They cause deadly brain diseases such as Creutfeldt-Jacob disease (CJD), or Mad Cow Disease

\\Bacteria//

  • Smallest independently living organisms
  • The most abundant living organism
  • Can be beneficial (majority) or disease-causing
  • Can live in different environments

\\Characteristics of Math//

  • Unicellular (some many stick together in colonies)
  • Prokaryotic
  • Have a single circular DNA loop (no chromosomes)
  • May contain an additional loop called a plasmid DNA
  • Have small ribosomes (compared to eukaryotes)
  • Have a cell wall made of a material called peptidoglycan

\\Bacteria Size//

  • Can range in size, usually between 0.2 and 10um
  • Larger than viruses, smaller than eukaryotic cells

\\Bacteria Shape//

  • Cocci
    • Round
    • Coccus(s)
  • Bacilli
    • Rod-Shaped
    • Bacillus

\\Spiral Bacteria//

  • Vibrios
    • Curved Rods
  • Spirilla
    • Helical shape and fairly rigid bodies
  • Spirochetes
    • Helical shapes and flexible bodies

\\Other Bacterial Shapes//

  • Star-Shaped Bacteria
  • Rectangular Bacteria
  • Pleomorphic Bacteria
    • They can change their shape and contort
    • No characteristic shape

\\Bacteria Colonies//

  • Diplo
    • Pairs(2)
  • Tetrad (Not a prefix)
    • Groups of 4 (cocci)
  • Sarcinae (Not a prefix)
    • Groups of 8 (cocci)
  • Strepto
    • Chain
  • Staphylo
    • Grape-like clusters (cocci)

\\Bacteria Movement//

  • Flagella
    • Singular Flagellum
    • “Tail-like” projection that helps push the bacterium (similar to a tadpole); most motile bacteria move like this
    • They can have one or more flagella
    • Spiral bacteria use internal like flagella; they twist along an internal axis and move
    • (similar to a screw)
  • Gliding bacteria
    • The mechanism is not quite clear but they just glide over surfaces

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\\Gram State Classification//

  • Some bacteria can be classified on the cell wall’s response to Gram Stain
    • Gram Stains (crystal violet) show differences in amino acids and sugar molecules
  • Gram-positive
    • A thick wall composed of many layers of peptidoglycan
    • The thick wall blocks the escape of the crystal violet iodine complex
    • Stains purple
  • Gram-negative
    • A thin layer of peptidoglycan
    • Can not retain the dye
    • Stains pink
    • Larger in number and more diverse

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\\Bacterial Growth//

  • Bacteria grow exponentially in “ideal” conditions
    • Unlimited food and space

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\\Zone of Inhibition//

  • Normal Growth
    • Cloudy areas around the disc
  • Inhibited Growth
    • Less cloudy areas around growth
  • Total inhibition
    • Clear areas around the disc show an absence of growth

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\\Bacteria Reproduction//

  • Binary Fission
    • Form of asexual reproduction
    • DNA duplicates
    • Cell divides
    • Daughter cells separate
  • Conjugation
    • Form of sexual reproduction
    • DNA(normally from a plasmid) passes from one bacterium cell to another via a structure called a pilus
    • Produces new genetic combinations

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\\Plasmids//

  • Are small DNA loops that contain genes different from those of the chromosome
  • They can split from the chromosome and rejoin it
  • Can be transferred through conjugation, resulting in new genetic combinations and is an agent for increasing biodiversity
  • Plasmids are important in genetic engineering

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\\Antibiotic resistance//

  • Through the process of conjugation, a bacterium can acquire the gene (from a plasmid DNA) that allows it to become resistant to an antibiotic

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\\Gas Exchange//

  • Oxygen requirements for bacteria vary
  • Aerobe
    • Requires oxygen
    • E.x Genus - Corynebacterium - skin
  • Obligate Anaerobe
    • Die when exposed to oxygen
    • E.x genus- Clostridium - large intestine
  • Facultative Aerobes
    • Use oxygen when present, but can grow without it
    • E.x Genus - Escherichia - large intestine
  • Bacteria are mesophiles -organisms that occupy moderate (less extreme) conditions

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\\Biological Role of Bacteria//

  • Plant Growth (fix nitrogen)
  • Decomposition (organic materials)
  • Food Digestion (symbiotic bacteria - human gut)
  • Human food (cheese, yogurt)
  • Photosynthesis: bacteria are producers in food chains

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\\Endospores: Protecting Genetic Material//

  • Some species of bacteria can form endospores
    • Hard-walled structures that protect and store the organism’s genetic material
    • Resistant to high temperatures, drying out, freezing, radiation, and toxic chemicals
    • When suitable conditions return, the endosphere germinates back into an active bacterium
    • So far not found in Archaea
    • Examples:
    • Clostridium Tetani
    • Clostriudium Botulinum

\\Archaea Cell Type//

  • Prokaryotic (no nucleus)
  • Unicellular

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\\Archaea Cell Structure//

  • Cell wall, no peptidoglycan
  • The cell membrane contains unusual lipids that can withstand high and low temperatures
  • Similar shapes to bacteria
  • Some form aggregations(like colonies)

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\\Archaea Methods of Reproduction//

  • Reproduce by binary fission and conjugation

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\\Archaea Biological Role//

  • Some archaea produce methane

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\\Connection to Human Health Archeaea//

  • None
    • This type of organism is rarely in contact with humans

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\\Characteristics of Archaea//

  • Live in an aerobic (oxygen-rich) or anaerobic (oxygen-poor) habitats
  • Arcahae are extremophiles
    • Organisms that live in extreme environments

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\\Thermophiles//

  • Endure temperatures over 100C (e.g hot springs, deep sea vents)

\\Acidophiles//

  • Endure low pH levels (e.g mine drainage lakes, volcanic craters)

\\Halophiles//

  • Endure salt concentration of about 20% (e.g salt lakes)

\\Methanogens//

  • Anaerobes that live in the depths of swamps and sewage, and the digestive tracts of animals give off methane

\\Psychrophiles//

  • Live in unusually cold temperatures

\\Thermoacidophiles//

  • Live in environments that are both hot and acidic

\\Types of Arcahea//

  • Thermophiles
  • Acidophiles
  • Halophiles
  • Mathanogens
  • Psychrophiles
  • Thermoacidophiles
  • TAHMPT

Animal-Like Protists

  • Unicellular Eukaryotic
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