Classification & Microorganisms: Chapter 17-19

Taxonomy

the science of naming and classifying organisms

Taxon

a group of organisms in a classification system

Species

a group of organisms that can breed and produce offspring that can reproduce

Binomial nomenclature

a system that gives each species a two-part scientific name using Latin words

Genus

the first part of the binomial nomenclature, which includes one or more physically similar species that are thought to be closely related
EX: "Quercus" includes more than 500 species of oak trees

Linnaean system of classification

-7 levels (taxa)
-From most general to most specific: Kingdom, phylum, Class, Order, Family, Genus, Species

genetic research

Today, scientists use ___ ___ to help classify living things in the Linnaean Classification System. Previously, it was based on physical characteristics.

Phylogeny

The evolutionary history for a group of species
-shown as branching tree diagrams
-shows how different groups of species are related to each other

Cladistics

classification based on common ancestry
-most common method is to make evolutionary trees
-goal is to place species in the order in which they descended from a common ancestor

Cladogram

Evolutionary tree that proposes how species may be related to each other through common ancestors

derived characters

The traits that can be used to figure out evolutionary relationships among a group of species are those that are shared by some species but are not present in others
-cladograms are made by figuring out which ___ ___ are shared by which species
----the mo

Molecular clocks

models that use mutation rates to measure evolutionary time

Mitochondrial DNA (mDNA)

DNA found only in mitochondria
-The mutation rate of this is about 10x faster than that of nuclear DNA, which makes this a good molecular clock for closely related species (species of the same kingdom or phylum)
-always inherited from the mother

Ribosomal RNA (rRNA)

Ribosomes contain this
-useful for studying distantly related species, such as species that are in different kingdoms or phyla
-When studying the relationships among species over longer time scales, it is best to use a molecule that has a lower mutation r

Animalia and Plantae

The original two kingdoms were...

Animalia, Plantae, Protista, Archaea, Bacteria, Fungi

The six kingdoms are...

Bacteria, Archaea, and Eukarya

The three Domains are...

Bacteria

This domain includes single-celled prokaryotes in the kingdom Bacteria
-one of the largest groups of organisms on Earth
-can be classified by many traits, such as their shape, their need for oxygen, and whether they cause disease

Archaea

Organisms in this domain are single-celled prokaryotes
-known for their ability to live in extreme environments (deep sea vents, hot geysers, Antarctic waters, and salt lakes)
-classified in the kingdom Archaea

Eukarya

This domain is made up of all organisms with eukaryotic cells (have a distinct nucleus and membrane-bound organelles)
-may be single celled (protists) or colonial (some algae) or multicellular (humans)
-this domain includes the kingdoms Protista, Plantae,

colonial

Algae in the domain Eukarya are...

Nucleus (or lack thereof) and cell wall

If you come across an unusual single-celled organism, what parts of the cell would you study in order to classify it into one of the three domains?

Virus

an infectious particle made only of a strand of DNA or RNA surrounded by a protein coat (PATHOGEN)

Bacteria

one-celled microorganisms that can also cause infection (PATHOGEN)

Pathogen

Any living organism or particle that can cause an infectious disease is called an infectious agent, or __

reproduce

Are viruses living things? Unlike cells, they cannot ____ on their own. They need living cells to help them reproduce and make proteins. They are also much smaller than cells.
-not given a place in the Linnaean system of biological classification

Viroids

Infectious particles that cause disease in plants
-made of single-stranded RNA without a protein coat
-Has even less in common with living things than do viruses
-passed through seeds or pollen (PATHOGEN)
-can stunt the growth of plants

Prion

Infectious particle made only of proteins that can cause other proteins to fold incorrectly
-when proteins misfold, the protein will not work properly (PATHOGEN)
-infectious, yet have no genetic material
-mad cow disease

Virus, Bacteria, Fungus, Viroid, Prion, Protist

list pathogens

Capsid

A single viral particle (virion) is made up of genetic material surrounded by a protein shell called, ___

virus

The structure of a ___ includes genetic material (DNA or RNA), a capsid, and an envelope (lipid) (only on some)

Virion

A single viral particle

Lipid envelope

The protective outer coat of a virus, from which spiky structures of proteins and sugars may stick out
-some viruses attach to host cells by these spikes

Viruses

___ can only reproduce after they have infected host cells

Host cell specificity

the virus won't be able to infect the cell if it doesn't connect properly
-each type of virus can infect only certain hosts
-a virus identifies its host by fitting its surface proteins to receptor molecules on the surface of the host cell, like a key fitt

Bacteriophages

Viruses that infect bacteria
EX: E. coli (commonly found in intestines of mammals)

endocytosis

Viruses that infect Eukaryotes
-may enter the cell by ____
-HIV

Lytic infection

An infection pathway in which the host cell bursts, releasing the new viral offspring into the host's system, where each then infects another cell
-builds new viruses right away
-takes control of the host's own DNA, turning on the genes necessary to copy

Lysogenic infection

A phage combines its DNA into the host cell's DNA, forming a new set of genes called a prophage
-a trigger (stress) can activate the prophage, which then uses the cell to produce new viruses or it can remain as a permanent gene
-dormant
-does not destroy

prophage

DNA of a bacteriophage inserted into a host cell's DNA

Influenza, SARS, Common Cold, HIV

Examples of viral infections (4)

epidemic

a rapid outbreak of an infection that affects many people

vaccine

substance that stimulates the body's own immune response against invasion by microbes

retrovirus

a virus that contains RNA and uses an enzyme called reverse transcriptase to make a DNA copy

pathogens

Vaccines are made from weakened ____
-made from the same pathogen that it is supposed to protect against
-weakened versions of the virus, or parts of the virus
-vaccines cause a mild immune response

vaccines

Often, the only way of controlling the spread of viral disease is through ___

Prokaryotes

Includes bacteria and archaea
-are the most widespread and abundant organisms on Earth
-grouped based on their need for oxygen

Obligate anaerobe

Prokaryotes that cannot live in the presence of oxygen
EX: they live in marshes, at lake bottoms, in intestines, archaea that produce methane gas

Archaea

Some ___ are able to grow at temperatures greater than 100 degrees C

Obligate aerobes

Prokaryotes that need the presence of oxygen in their environment
EX: pathogens like Tuberculosis and leprosy

Facultative aerobe

Prokaryotes that can survive whether oxygen is present in their environment or not

Bacilli

Rod-shaped bacteria

Spirilla (Spirochetes)

Spiral-shaped bacteria

Cocci

Spherical bacteria

Plasmid

small piece of genetic material that can replicate separately from the prokaryote's main chromosome

Flagellum

a long, whiplike structure outside of a cell that is used for movement

Pili

Prokaryotes contain these structures that are thinner, shorter, and often more numerous than flagella. They help prokaryotes stick to surfaces and to other prokaryotes

Bacteria vs. Archaea

Bacteria vs. Archaea
structural: B: (bacilli, spirilaa, cocci) and A: (many shapes)
molecular: B: (circula DNA [plasmids]), flagella, pili [hair]) and A: (same)
----different cell walls and membranes

conjugation

prokaryotes can exchange parts of their chromosomes through a hollow bridge of pili formed to connect two or more cells (like sexual reproduction)

endospore

a specialized cell with a thick, protective wall
-to form: the bacterium copies its chromosome and produces a wall around the copy
-helps the bacterial DNA survive harsh conditions such as drying out, temperature change, and disinfectants

peptidoglycan

Bacteria have a polymer, called ___ in their cell walls
-the amount of this polymer is an important characteristic of bacteria

cell wall

Because of their ___ ___ differences, archaea are often not affected by medicine used to treat bacterial infection

Gram staining

used to identify types of bacteria
-identifies the amount of a polymer, called peptidoglycan, that is present in the cell walls
-this result is either gram positive (thicker peptidoglycan layer and stained purple) or gram negative (thin layer of peptidogl

Beneficial roles of prokaryotes

Prokaryotes provide nutrients to humans and other animals
Prokaryotes play important roles in ecosystems
-help ferment food (yogurt, cheese, soy sauce, etc)
-in ecosystems: help decompose, return nutrients

Bioremediation

a process that uses microbes and other living things to break down pollutants. For example, some types of bacteria can digest oil, which is helpful for cleaning up oil spills and other industrial accidents

toxin

a poison released by an organism

Diseases

____ invade tissues and release toxins to make you sick

antibiotic

chemicals that kill or slow the growth of bacteria
-stops the bacteria from making cell walls
-used to fight bacterial disease
-because viruses also lack cell walls, antibiotics do not work on viral infections

Bacterial disease examples

Anthrax, Whooping Cough, Bubonic Plague

protist

eukaryote that is not an animal, a plant, or a fungus
-may be single celled or multicellular, microscopic or very large
-different ways of moving around and of responding to the environment
-some reproduce asexually while others reproduce both asexually a

food

Protists are divided into 3 types based on how they get their ___
-Animal-like
-Plant-like
-Fungus-like

Animal like protists

protists that can move around, consume other organisms, and their cells lack chloroplasts
-Zooflagellates - flagella (termite gut)
-pseudopod - "false foot" (amoeba/foraminifera)
-Ciliates - cilia (paramecium)
-Sporozoa - "floaters

protozoa

describes the many phyla of animal-like protists

Pseudopod

means "fake foot", is a temporary extension of cytoplasm and plasma membrane that helps protozoa move and feed

Cilia

short, hairlike structures that cover some or all of the cell surface and help the organism swim and capture food

Lifecycle of the malaria parasite

1) when an infected mosquito bites a human, it transmits Plasmodium sporozoites that enter the liver, where they develop
2) the developed parasites leave the liver and enter red blood cells, where they reproduce asexually until the red blood cells burst
3

algae

Photosynthetic plantlike protists

Plant like protists

-can be single celled or multicellular
-autotrophic
-
Euglenoids
: swim with 1-2 flagella, autotrophic and heterotrophic, freshwater
-
Dinoflagellates
: swim with 2 flagella, Noctiluca (bioluminescent), produce red tides (occur when changes in ocean curre

Life cycle of Single-celled Green Algae

SEXUAL:
-Mitosis produces many haploid gametes
-Gametes fuse, forming a diploid zygote
-Meiosis occurs within the zygote producing four haploid cells that will grow and mature
ASEXUAL:
-the cell divides by mitosis
-the daughter cells develop flagella and

slime molds

eukaryotic organisms that have both fungus-like and animal-like traits
-divided into 2 phyla : plasmodial and cellular

plasmodial slime molds

this type of slime mold lives as a single mass of cytoplasm that is actually a large single cell with many nuclei
-can grow as large as a meter or more in diameter
-move like giant amoeba as it absorbs bacteria and nutrients from decaying matter
-"dog vom

cellular slime molds

this type of slime mold is common in soil
-each spore released by this type of slime mold becomes a single amoeba-like cell

water molds

fungus-like protists that are made up of branching strands of cells
-common in freshwater habitats
-decomposers or parasites of plants/fish
-one type causes disease, resulted in the Great Potato Famine

chitin

a tough polysaccharide that is also found in the shells of insects and their close relatives

plants vs. fungi

plants vs. fungi
P-(contain chlorophyll and photosynthesis) F-(no chlorophyll and gets food by absorbing it from environment)
P-(true roots, leaves, and stems) F-(no roots, leaves, or stems)
P-(plant cell walls made of polysaccharide cellulose) F-(fungal

fungi

general characteristics of ___
-mycelium (underground hyphae)
-hyphae (long string from underground to top of fungus)
-fruiting body (reproductive parts)

hyphae

bodies of multicellular fungi are made of long strands called...

mycelium

-hyphae often group together in long tangled masses to form a mycelium
-an underground network of hyphae in fungi
-vegetative part of a fungus
-may produce fruiting bodies

fruiting body

a reproductive structure of a fungus that grows above ground
-mushrooms are one type

primitive fungi

Group of fungi:
-AKA chytrids
-the smallest and simplest group
-mostly aquatic, have flagella
-some are decomposers, while others are parasites of protists, plants, or animals

sac fungi

Group of fungi:
-EX: yeasts, morels, and truffles
-diverse group that all has a sac (ascus) in common that contain spores for reproduction
-Ascomycetes

bread molds

Group of fungi:
-Zygomycetes
-molds on spoiled food
-fungi used to ferment foods like soy sauce
-get food by decomposing dead or decaying matter
-Mycorrhizae

Mycorrhizae

mutualistic partnerships between fungi and the roots of certain plants
-help plants to take inorganic nitrogen from the soil and convert it to nitrates and ammonia, which the plants use

club fungi

Group of fungi:
-fruiting bodies are club shaped
-mushrooms, puffballs, bracket, or shelf fungi
-Basidiomycetes

budding

Asexual reproduction in fungi
-through simple fission or through ___

club

Sexual reproduction in fungi (___ fungi)
1) nuclei fuse within basidia to form zygots
2) zygotes undergo meiosis to form spores
3) spores are dispersed by wind
4) spores grow into hyphae of opposite mating types underground
5) a mycelium grown underground

bread molds

Sexual reproduction in __ __
1) gametes of different mating types form at the tip of hyphae
2) the gametes fuse and a zygospore forms. It has a thick wall and can remain dormant for a long time
3) a zygote produces a sporangium
Asexual reproduction in __

sporangia

spore forming structures found in fungi and algae

sac

Sexual reproduction in __ fungi
1) joining of 2 mycelia that are different mating types
2) the joined hyphae grow into the aboveground fruiting body
3) a sac develops at the tip of each hyphae within the fruiting body
4) inside the sac, haploid spores for

fungi

3 major roles of ___
1) fungi as decomposers
----decompose dead and decaying matter, return
nutrients
2) fungi as pathogens
----disease-causing, obligate pathogens (always
cause disease)
3) fungi as mutualists (both organisms benefit)
----lichen (relation

lichen

a mutualistic relationship between a fungus and algae or photosynthetic bacteria

mycorrhizae

-mutualistic associations between plant roots and soil fungi
-more than 80% of plants have this on their roots