Taxonomy

Why is classification important?

To study the diversity of life, biologists use a classification system to name organisms and logically group them.

What is taxonomy?

A discipline of classifying organisms and assigning each organism a universally accepted name

Who was the first taxonomist and what did he do?

Aristotle.

He divided them into animals and plants, and then more specifically into air, sea and land.

What were the original classification used to name animals?

Common names were used to identify.

E.g. Seahorse, starfish.

What did Carolus Linnaeus do?

• Classify organisms and named by their physical structure

• Created the system of naming we use today.

• His classification system includes 7 levels.

• To avoid confusion, Carolus Linnaeus devised a naming system based on physical characteristics (structures)

What is a a group or level of organization called in taxonomy?

taxonomic category or taxon.

What is binomial naming. Give an example.

• Each species is assigned a 2-part scientific name

• Polar bear→ Ursus maritimus

State the order of classification for taxonomy

King - Kingdom

Phyllip - Phyllum

Came - Class

Over-Order

For - Family

Great - Genus

Spaghetti - Species

What are the 3 types of domains, and who introduced it?

Archaea, Bacteria, and Eukarya

Carolus Linnaeus

What are the rules of taxonomy and naming

• Every name should be unique

• A single language is used worldwide

• All animals are given a generic (common name) and a specific name in Latin (scientific name).

• First name is capitalized and is in italicized whole word

• Genus and species are used in the organism's name

What are the problems with traditional classification

• relies on body structure comparisons only

• Due to convergent evolution, organisms that are quite different from each other evolve similar body structures

Convergent evolution what is it? Give an example.

Process by which unrelated organisms independently evolve similarities when adapting to similar environments

Example: The barnacle and limpet are thought to be similar, but crabs and barnacles are related

What is Evolutionary Classification

Biologists now group organisms into categories that represent lines of evolutionary descent, not just physical similarities

Strategy of grouping organisms based on their evolutionary history.

Phylogeny

the presumed evolutionary history of an organism

What is a way to illustrate phylogeny

• The phylogeny of related organisms can be illustrated using a phylogenetic tree

Cladogram

A diagram that shows the evolutionary relationship among a group of organisms.

What are the 6 kingdoms, and why did they change from 3 to 6?

• Recently, as evidence about microorganisms continues to accumulate, biologists came to realize that the Kingdom Monera were composed of 2 distinct groups of bacteria.

• The 6-Kingdom system of classification includes kingdoms: 

Eubacteria	Archaebacteria	Protista
Fungi	Plantae	Animalia

Describe the structure of a virus

• Not cellular (No cytoplasm, membrane-bound organelles or cell membrane)

• Strands of nucleic acid(genetic material) encased within protein coat (Either DNA or RNA)

• Non-living, microscopic infectious substance

Label the following

Characteristics of a virus

• Reproduces inside host cell

• Not living = No cells

• Cause immune response in higher organism

  • Can cause disease or illness

• Antibiotics do not work with viral infections❌

  • Only antiviral and vaccines✅

Difference between virus and a living cell

Virus:

• No metabolic apparatus, do not digest or respire

• Not made of cells

  • No cell membrane

  • No nucleus or cytoplasm

• Virus solutions leave behind crystals when evaporated

• Only reproduces inside host

• Genes either made of DNA or RNA

• Can take over cell activity of hosts they invade

• Cause transmissible (contagious) disease

• Have same basic structure

• Core of nucleic acid is surrounded by protein

• All viruses have protein sheath around nucleic acid core

• x100 smaller than bacteria

Living Cell:

• Capable of independent reproduction

• Have cell membrane, cytoplasm and membrane-enclosed organelles

Examples of viruses and diseases

• Common cold, flu and cold sores

• Ebola, Avian Flue, AIDS and Covid-19

Give some examples of viruses that have drugs to slow their replication

• HIV

• Herpes

What is virulence

• Ability of virus to cause disease

What does more virulent mean and give examples

Faster reproduction

• Ebola, rabies

What does less virulent mean and give examples

Slower reproduction

• Common cold

How do DNA viruses infect host and give examples

• Infects host through chance encounter

• Once DNA insertion, no more extra steps to incorporate into human nucleus

• DNA viruses often find it easier to manipulate human cells because their larger, more stable DNA genomes

• Herpes

• Pox

Name a characteristic of DNA viruses

• Have same genetic material as humans

What do RNA use as their genetic material

• Use RNA as their genetic material or RNA intermediate to replicate

  • a RNA intermediate (mRNA) molecule that serves as a temporary copy of a DNA segment

What is a type of RNA virus and what do they do? Give an example

• Retroviruses (Reverse Transcript Viruses)

• Convert RNA into DNA before incorporating into host cell

• retrovirus turns into a provirus when its RNA genome is converted to DNA and integrated into the host cell's genome

• HIV

Example of RNA virus and what does it do?

• Rubella virus

  • Causes German Measles

What division cycle do RNA virus mostly replicate through?

Lytic

What do lysogenic viruses do?

• Remain dormant and incorporate into host cell's chromosomes

What do viroids do

• Are known to infect only plants

What do Bacteriophage do?

• Infect and replicate within bacteria

• "Bacteria eater"

Describe the stages of the virus lytic cycle

• Attachment

  • Virus must attach to protein receptors on cell wall or cell membrane of host

• Penetration

  • Virus must enter through cell membrane fusion or endocytosis

• Uncoating

  • Protein coat is worn away, exposing viral genome

• Replication and Assembly

  • Viral genome takes over host cell

  • Viral DNA is replicated

  • Creates more viruses

  • Occurs in cytoplasm

  • Host cell will use proteins to make new capsids to assemble viral particles

• Lysis

  • New virus particles rupture from host cell

Describe the lysogenic cycle

• Viral DNA enters cell and become permanently part of host cell's chromosomes

• DNA is now incorporated into host (Eukaryotic) DNA

  • Provirus

• If DNA of virus is incorporated into bacteriophage

  • Virus that infects bacteria

  • Prophage

• Many cases, genes aren't activated until later

  • Allows many generations of cells with viral instructions to be made

List the ways that viruses can be applied IRL

• To study basic mechanism of molecular biology

• Genetically modify organisms

• Virotherapy

• Biological insecticides

• Nanotech

• Potentially used to fight off super bugs

How could viruses be used to study basic mechanism of molecular bio

• DNA replication

• Protein syntheis

How could viruses be used for Virotherapy

• Uses viruses to treat bacterial infections and certain cancers

How could viruses be used for Nanotechnology

• Tools to stop or start genetic sequences needed in host cells

How could viruses be used to potentially used to fight off super bugs

• strain of bacteria that has become resistant to antibiotic drugs.

What are the different ways to spread viruses

Vectors

Airborne

Direction Contact

Fecal-oral

Sexually transmitted

How are they spread vectors

• Usually an animal that carries the virus

  • Rabies

How are they spread airborne

• Spread through air by people's coughing and sneezing

  • Respiratory complaints

  • Flu virus

How are they spread direction contact

• An infected person touches a surface, and another touches the same surface

  • Common cold

How are they spread fecal-oral

• Faeces particles contaminate hands, food and water

  • Gastroenteritis

  • Rotavirus

How are they spread sexually transmitted. Give an example

• Direct transfer of bodily fluids

  • HIV

Characteristics of bacteria

• Unicellular

• In every ecosystem + human body

• Prokaryotic

• Important decomposers

• Some pathogenic

What are some nutrient cycles that bacteria is important for?

Nitrogen cycle

Pathogenic

Ability of causing disease

Who first observed bacteria

Anton van Leeuwenhoek

What are the 2 scientists that discovered that bacteria caused many diseases

Robert Koch and Louis Pasteur

What did Paul Ehrlich do

He made the first antibiotic to treat bacterial disease used to treat syphilis

What is the cell wall of bacteria made of

Peptidoglycan

What’s so special about peptidoglycan

It’s unique to only bacteria

What is peptidoglycan

A compound of protein and carbohydrate

What other physical characteristic does bacteria have relating to morphology

Pili or flagella to move and interact with environment

What are the different shapes of bacteria

Bacillus

Coccus

Spirillus

Vibrio

Spirochaetes

Bacillus

Rod

Coccus

Sphere

Spirillus

Spiral

Vibrio

Boomerang

Spirochaetes

Tight coils

What are the prefixes to indicate the living arrangement for bacteria

Staphylo

Strepto

Staphylo

grape-like cluster

Strepto

a chain of bacteria

Gram Stain, what are they used for?

used to visualize bacterial cell wall structure

What affects how bacteria are classified as either gram-positive or negative?

Bacteria are classified as Gram-Positive or Gram-Negative based on the chemical and physical properties of their cell walls.

Gram-positive bacteria physical characteristics

Have a thick layer of peptidoglycan in their cell walls, which retains the crystal violet stain (appears violet/purple)

Thick cell wall

Gram-negative bacteria physical characteristics

Have a thinner peptidoglycan layer and an outer membrane, allowing the crystal violet to be washed out during the discoloration step (appear pink/red.)

Thin cell wall with peptidoglycan and lipoproteins

More common pathogen

How do bacteria reproduce

Reproduce asexually using the process of binary fission

What is conjugation

DNA exchange through a conjugation tube to another bacterium through a pilus

What is genomic DNA essential for

Essential for survival and reproduction of bacteria

What is Plasmid DNA

Small extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA

What are benefits to plasmid DNA, and name a characteristic

Provide genetic advantages to enhance survival

Can replicate independently

What are the phases of conjugation

• The donor cell attaches to a host cell with its pilus. Pilus draws the cells together

• Cells contact one another

• One strand of plasmid DNA transfers to the recipient

• The recipient synthesizes the complementary strand to become an F+ cell; the donor synthesizes a complementary strand, restoring its complete plasmid

What are the phases of bacterial growth

• Lag phase

• Log phase

• Stationary phase

• Death phase

Lag Phase

Bacteria adjusting to a new environment and growing slowly

Log Phase

Exponential growth

Stationary Phase

Bacteria have reached the carrying capacity of the environment

Death Phase

Logarithmic death of bacteria as nutrients get used up

Do all bacteria go through the WHOLE growth phase

No, only some

What are Endospores and what does it include

• Small spores that develop inside some bacteria.

• Includes the genetic material and a protective coat

When are endospores produced

• Produced during nutrient deprivation

• Cell is dormant and highly resistant, it preserves cell's genetic material in times of stress

Is Endospores biotic or abiotic

Biotic

How is bacteria categorized

Classified based on how they obtain energy

What are the different categories of Bacteria

Photosynthesizers, chemoautotrophs, heterotrophs

What is important about photosynthesizers

A significant fraction of the world’s photosynthesis is carried out by bacteria

What is an type of photosynethisers, and name some characteristics/facts

Cyanobacteria

• blue-green bacteria that contain chlorophyll in their cell membrane

• thought to have made the Earth’s oxygen atmosphere

What do chemoautotrophs do?

• Break down chemicals in soil and use them for nutrition

• Bacteria’s waste products act as fertilizer and help with agriculture

How many bacteria in a handful of soil

10 billion

Most of Eubacteria are what category of bacteria

Heterorophic

What’s special about heterotrophs

Primary decomposers that release nutrients back into the soils, which means they are also important to many nutrient cycles.

What are the different types of bacteria relating to respiration

• Obligate Aerobes

• Obligate Anaerobes

• Facultative Anaerobes

Obligate Aerobes

Must HAVE oxygen

Obligate Anaerobes

Must have NO oxygen

Facultative Anaerobes

Can grow with or without oxygen

What are different ways bacteria interact with other organisms

• Mutualism

• Parasitism

  • Pathogenic Bacteria

What happens in mutualism and give some examples

• an interaction where all parties benefit

• nitrogen-fixing bacteria in the soil as well as the naturally occurring bacteria in our gut