Biology Taxonomy Notes

Taxonomy

What is Taxonomy?

  • The science of naming and classifying organisms based on their characteristics.

Who Developed Taxonomy?

  • Carolus Linnaeus in the 1700s.
  • He grouped organisms by physical traits.

Taxa Order

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

Evidence of Evolution

  • Anatomical: Do the structures look the same?
  • Physiological: Do the proteins and enzymes in cells work the same?
  • DNA Evidence: How (genetically) closely related are the genes and proteins they're making?

Domains of Life

  • Bacteria, Archaea, Eukarya

Kingdoms of Life

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

Prokaryotes vs. Eukaryotes

  • Prokaryotes:
    • No nucleus (nucleoid)
    • Smaller and less complicated
    • Circular DNA
  • Eukaryotes:
    • Nucleus (no nucleoid)
    • Organelles
    • Nuclear membrane
    • Linear DNA

Nucleoid vs. Nucleus vs. Nucleolus vs. Nucleotide

  • Nucleoid = prokaryotic
  • Nucleus = eukaryotic
  • Nucleolus = organelle inside of nucleus
  • Nucleotide = basic building block of DNA

Prokaryotes

  • Bacteria and Archaea

Eukaryotes

  • Protists, fungi, plantae, animalia

Dichotomous Keys

  • Classification tool
  • Must use binary questions related to known species characteristics.

Species Concepts

  • Biological, morphological, phylogenetic

Biological Species Concept

  • Can successfully breed + produce fertile offspring.
  • Only applies to sexually reproducing organisms.

Morphological Species Concept

  • Comparing measurements/physical descriptions.
  • Often used in plants + asexually reproducing organisms.

Phylogenetic Species Concept

  • Evolutionary evidence between organisms - DNA studies or fossil evidence.

What are Species Concepts?

  • Used to classify organisms to see if species align with pre-discovered ones.

Binomial Nomenclature

  • 2 part scientific naming with Genus and species. Italicizes or underlined

Who Developed Binomial Nomenclature?

  • Carolus Linnaeus

Are Viruses Alive? Why?

  • No
    • Not cellular
    • Can't grow/develop on their own
    • Can't make protein/energy
  • Group of chemicals - needs a host

Physical Structure of Virus

  • Protein coat or capsid found on outside (protects the virus)
  • Nucleic acid/genetic material (RNA or DNA (not both)) inside core

What Can Viruses Infect?

  • Anything cellular, but very species-specific

How Do Viruses Reproduce?

  • Lytic and lysogenic cycle

How Does The Lytic Cycle Work?

  • Binds to cell using key
  • Injects DNA
  • Host DNA digested
  • DNA replication of virus using processed nucleotides from host cell
  • Makes proteins + energy from host cell to assemble the rest of the virus
  • Cell lyses (breaks) and releases new viruses

How Does The Lysogenic Cycle Work?

  • Attaches to cell with key
  • Inserts DNA
  • Integrates DNA into host without infecting it (or presenting)
  • Cell replicates and duplicates integrated genome
  • Can continue for years before switching to the lytic cycle suddenly and 'presenting'

How Can Viruses Be Helpful?

  • Attack bacteria that cause disease
    • Bacteriophages are used to destroy bacteria without infecting human cells
  • Can insert 'good genes' into people with genetic diseases
  • Introduce desired traits into plants/animals

What are Archea

  • Evolved from the first organisms on earth - primitive
  • Used to be grouped with bacteria - outdated

What Separates Archea From Bacteria

  • Cell walls have NO PEPTIDOGLYCAN (bacteria do)

Where Are Archea Found

  • Originally thought to only like extreme environments but can be found everywhere

What Are Bacteriophages?

  • Viruses that infect bacteria only

Archea Characteristics

  • Prokaryotes- nucleoid + no organelles
  • Anaerobic (don't need oxygen)
  • Don't photosynthesize - obtain energy from inorganic materials or the sun instead

Types of Archea

  • Methanogens, halophiles, thermoacidophiles

Methanogens

  • Methane-producing
  • Live in oxygen-free environment (sewage treatments, marshes, intestines of grass-eating animals)
  • Grow on CO2CO_2 & HH -> produce methane gas (as a waste product)

Halophiles

  • Salt-loving
  • Found in extreme saline environments (Dead Sea)

Thermoacidophiles

  • Can live in habitats of pH of 1 or 2
  • Found in hot sulfur springs, deep-sea ravines, volcanoes + mine drainage leaks

Archea Uses

  • Methanogens digest sewage + oil spills & produce Methanogens (alt energy source)
  • The most famous archea enzyme is obtained from Thermus aquatics - its heat resistance can be used in labs to make more copies of small samples of DNA

How to Classify Bacteria

  • Shape + colony groupings, cell wall structure, food & metabolism

Bacterial Shapes

  • Cocci, bacillus, spirillum

Cocci

  • Spherical bacteria

Bacillus

  • Rod-shaped bacteria

Spirillum

  • Spiral-shaped bacteria

Colony Shapes

  • (All bacteria are single-celled, but some can stick together)
  • Diplo, staphylo, strepto

Diplo

  • Pairs

Staphylo

  • Cluster (look like grapes)

Strepto

  • In chain

Types of Cell Wall Structure

  • Gram negative, gram positive

Gram Negative

  • Thin layer of the cell wall protein -> pink gram bacteria stain

Gram Positive

  • Thick layer of the cell wall protein -> gram bacteria stain purple

Bacteria Types of Food & Metabolism

  • Photoautotrophs, photoheterotrophs, chemoautotrophs, chemoheterotrophs

Photoautotrophs

  • Use light energy & photosynthesis to get energy, get C from CO2CO_2

Photoheterotrophs

  • Consume other organisms to get C and use light energy

Chemoautotrophs

  • Get energy by breaking bonds in inorganic materials (like ammonium or hydrogen sulfide)

Chemoheterotrophs

  • Get carbon and energy from eating organic molecules (like sugar and C+H)

How Do Bacteria Move?

  • Flagellum - whip-like tail
  • Cilia - tiny hairs on the surface of the cell (beat to move cell)

How Do Bacteria Reproduce?

  • Binary fission (asexually) or conjugation (sexually)

Binary Fission

  • Copies genetic info, splits into identical daughter cells

Conjugation

  • Bacteria plasmid DNA loop is transferred from one cell to another
  • DNA from the plasmid loop can integrate into other chromosome's DNA loop
  • (Sharing traits, cell #2 shops for bonus featured)

Endospores

  • Dormant cells show no signs of life
  • Highly resistant to high temperature, irradiation, strong acids, disinfectants (hard to get rid of)

How Are Bacteria Beneficial

  • More useful bacteria than harmful
  • Decomposes dead things
  • Helps organisms (us included) digest stuff
  • Help separate toxins in soil/water

What Domain Is Protista In

  • Eukarya

Kingdom Protista's Phylum

  • Protozoa, algae (or protophyta), molds

Protozoa Classes

  • Flagellates (zooflagellates)
  • Pseudopods (sarcodines)
  • Ciliates
  • Sporazoans

Algae Aka

  • Protophyta

Protophyta (Algae) Classes

  • Algae
  • Euglena
  • Diatoms
  • Dinoflagellates

Molds Classes

  • Smile molds
  • Water molds

Animal-Like Protists

  • Protozoa

Plant-Like Protists

  • Protophyta (algae)

Fungus-Like Protists

  • Molds

Protista Characteristics

  • Eukaryotes
  • Most are aerobic (require oxygen)
  • Most are single-celled
  • Live in moist environments

How Many Species Are In Protista

  • Over 200k

Protozoan Characteristics

  • Heterotrophs (ingest other organisms or dead organic matter)
  • Unicellular
  • Animal-like fungi

How Are Protozoans Classified?

  • How they move and live

Flagellates

  • The motorboats

Flagellates Aka

  • Zooflagellates

Flagellates Characteristics

  • Free-living
  • Found in fresh or marine habitats
  • Flagella to move (whip-like extension)
  • Can cause disease

Flagellates Examples

  • Giardia lamblia - causes upset stomach - common in Lake Ontario

Pseudopods

  • The blobs

Pseudopods Aka

  • Sarcodines

Pseudopods Characteristics

  • Most are free-living
  • No cell wall
  • Move using pseudopods
  • Engulf bits of food by phagocytosis
  • Reproduce using binary fission

Phagocytosis Meaning

  • Flowing around and over food particles to absorb

Heterotroph Meaning

  • Must consume other living things

Autotroph Meaning

  • Can make its own food

What Are Pseudopods

  • Cytoplasmic extensions that act as feet

Ciliates

  • The hairy ones

Ciliates Characteristics

  • Live in both fresh water and marine habitats
  • Move by beating cilia (tiny hairs)
  • Typically reproduce by binary fusion but occasionally use conjugation

Ciliates Examples

  • Paramecium

Sporazoans

  • The parasites

Sporazoans Characteristics

  • Non-motile, don't move on their own
  • Must live inside a host

Sporazoans Example

  • Malaria

Malaria

  • A disease caused by mosquitoes implanting parasites in the blood

Protophyta (Algae) Characteristics

  • Plant-like protists
  • Autotrophic - photosynthetic
  • Can be multicellular, unicellular, or live in colonies

Algae (Class) Characteristics

  • Either unicellular or multicellular
  • Photosynthetic, have chlorophyll
  • Can be red, green, or brown
  • No roots, stems, or leaves
  • Limited movement

Euglena Characteristics

  • Aquatic
  • Move around like animals
  • Photosynthetic in light, heterotrophic in dark!
  • Reproduces with binary fission

Diatoms Characteristics

  • Shells made of silica, glass-like
  • Photosynthesis pigments called carotenoids make golden colors

What Are Diatoms Used For

  • Can be a bug repellent

Dinoflagellates Characteristics

  • Spin around using 2 flagella
  • Form toxins that can kill animals and sometimes people

Responsible For Red Tides

  • Dinoflagellates

Molds Characteristics

  • Fungi-like protists
  • Heterotrophic - feed on dead plants/animals
  • Live in cool, damp habitats
  • Have cell walls
  • Reproduce with spores

Fungi Characteristics

  • Evolutionarily closer to animals than plants
  • Cell wall made of chitin
  • Eukaryotic
  • Heterotrophs
  • Mostly multicellular

Molds (Protists) vs. Molds (Fungi)

  • Protista: single-celled, live in colonies
  • Fungi: multicellular

Fungi Unicellular

  • Yeast

Fungi Are Classified By How They Make Sexually Reproduced Spores

  • (Rapidly changing with DNA analysis)

Saprophyte

  • Feed by extracellular digestion
  • Release enzymes into surrounding & absorb food
  • Live on or near their food

Fungi Way They Eat

  • Saprophyte (type of digestion)

Fungi Structure

  • Hyphae, mycelium

Hyphae

  • The network of filaments makes up the body of fungi
  • Hyphae frowning in different direction get different names

Mycelium

  • branching network of hyphae that Grow together underground

Fungi Reproduction

  • Alternate between asexual and sexual per generation

Fungi Asexual Reproduction

  • Spores
  • Fragmentation

Spores

  • Can be produced by mitosis
  • Windblown reproductive cells that can grow into new organisms in suitable environments
  • Type of fungi asexual reproduction

Fragmentation

  • Pieces of hyphae break off & grow into new mycelium
  • Asexual reproduction

Fungi Sexual Reproduction

  • In conditions unfavorable (Hot/dry), fungi use mating to produce more genetically diverse spores
  • Occurs when two haploid hyphen (of opposite types (+ & -) fuse to form a diploid zygospore

Zygospore

  • Have thick spore walls to protect from harsh conditions
  • Can form new fungi

Imperfect Fungi Group

  • No sexual phase
  • Cheese molds, penicillin

How Are Fungi Important?

  • Help recycle nutrients
  • Decomposers in C & N cycles

Non-Vascular Plants Examples

  • Mosses, liverworts, hornworts

Non-Vascular Plants Characteristics

  • No vascular system - nutrients, waste + water move through cells by osmosis/diffusion
  • Growth limited
  • No true leaves, roots, or stems

How Do Non-Vascular Plants Reproduce?

  • Need moist environments so gametes can swim together for reproduction

3 Major Adaptions For Life On Land (Plants)

  • Protection from drying out
  • Vascular system
  • Better structures to hold plants up and catch the sun better

What Are Stems + Leaves Used For

  • Protection from drying out, vascular system, hold plant to catch energy better

What Are Roots Used For

  • System of vessels, absorbs minerals and water from soil/ground

First Vascular Plants

  • Ferns

Seeds How Are The Important

  • Adaption to improve reproductive success
  • Let plants reproduce sexually without water

Seeds Types

  • Gymnosperms and angiosperms

Gymnosperms

  • Naked seeds, no fruit (pinecones)

Angiosperms

  • Flowering plants
  • Seeds protected by fruit (apples) Meant to Attract pollinators (bees)

Earliest Photosynthetic Organisms

  • Plant-like Protista (algae/protophyta)

Where Does Most Of Photosynthesis Occur?

  • Ocean!

Yeast reproduce through?

  • Budding

Bryophytes

  • Nonvascular plants

How Is Binomial Nomenclature Important?

  • Names individual organisms while recognizing the genus and species they belong to so we have some background information

Saprotrophs

  • Feed on dead organisms

Chemotrophs

  • Organisms that obtain energy from chemicals

Heterotrophs

  • Organisms that cannot make their own food

Autotrophs

  • Organisms that make their own food

Phototrophs

  • Obtain energy from light

Obligate Anarobes

  • Must live in the absence of oxygen

Do Plant Cell Walls Contain Chitin?

  • No

Earliest Land Plants - Approx 500 Million Years Old

  • Evolved from green Algae

Saprophyte vs Phagocytosis

  • Saprophytes live on or hear their food source, release enzymes into surrounding and absorb food
  • Phagocytosis is when an organism flows over/around the food source to absorb it

How Do Pseudopods Reproduce

  • Binary fission

How Do Ciliates Reproduce?

  • Typically binary fission and sometimes conjugation

How Do Euglena Reproduce?

  • Binary fission

Carotenoids

  • Photosynthesis pigment that makes diatoms a golden color

Flows Over To Absorb

  • Phagocytosis

Feed By Extracurricular Digestion

  • Saprophyte

Fungi Cell Wall Made Of

  • Chitin