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//

Attachment

The virus attaches to the body of the cell

Entry / Injection

The virus invades a hostel cell and injects is viral DNA or RNA into the host cell

Replication

The host cell makes copies of new viral proteins and nucleic acids

Assembly

New viral particles are put together

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

\\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

\\Bacterial Growth//

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

\\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

\\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

\\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

\\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

\\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

\\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

\\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)

\\Archaea Methods of Reproduction//

Reproduce by binary fission and conjugation

\\Archaea Biological Role//

Some archaea produce methane

\\Connection to Human Health Archeaea//

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

\\Characteristics of Archaea//

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

\\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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