Chapter 1, 2.1 and 2.

2 Quiz Notes

1.1 Identifying, Naming and Classifying Species

Species Concept:
- Concept scientists used to decide if 2 individuals are the same species
- 3 general species concepts:

Species Concept Description Advantages and Disadvantages

Morphological Species Concept
- Focuses on the morphology of an
organism.
- Concept relies on comparing
measurements and descriptions of
similar organisms (taking into
account that species vary and
change over time)
- Focuses on morphology (structure
and form of organisms)
Advantage: The concept is simple and
makes it the most widely used, especially
for plants
Disadvantage: how to decide how much
difference between individuals is too much
variation.

Biological Species Concept
- Concept focuses on similar
characteristics and ability of
organisms to interbreed in nature
and produce viable, fertile
offspring
- Meaning if 2 individual organisms
can mate naturally and make
offspring that can live and
reproduce, they are the same
species
Advantage: This species concept is widely
used by scientists
Disadvantage: Concept cannot be applied
in all cases (ex: when 2 populations are
physically separated, they don’t have
opportunity to interbreed in nature) Also
can’t apply to organisms who reproduce
asexually or who no longer reproduce

Phylogenetic Species Concept - Concept focuses on evolutionary Advantage: Concept can be applied to
Bact relationships among organisms extinct species. It also considers info about
eria - Uses DNA analysis relationships among organisms learned
Arch - Focuses on phylogeny from DNA analysis
Com aea (evolutionary history of species)
mon Disadvantage: Evolutionary histories are
not known for all species.
Anc
esto
r Naming Species:
- Binomial Nomenclature: is a naming system that has 2 parts
- The 1st word in the scientific name is the genus
- The 2nd word identifies the species
- The scientific name is italicized (1st word uppercase, second lower)
- Example: Homo sapiens
- When writing do the same but instead of italics, underline (Ex: Homo sapiens)
Classifying Species:
Taxonomy: branch of biology that identifies names and classifies species based on natural features
- A species is classified by one of 8 different categories (aka ranks)
- The name of each rank is called a taxon
- From most general to most specific:
Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
(Dear King Philip Cried Out For Goodness Sake)

Rank: Level in classification such as Domain or Kingdom

Taxon: A named group of organisms such as phylum Chordata or order Rodentia

1.2 Determining How Species Are Related

Anatomical Evidence of Relationship
Anatomical Structure:
- Anatomy is the study of structure and form (internal/external) of an organism
- Example: Looking at bone density between organisms

Homologous Structure:
- Structures that are similar between different species because they are inherited from a
common ancestor
- They are organs with the same structural patterns, but may look different or have
different functions

● Homology is similarity due to shared ancestry

● Analogy is similarity due to convergent evolution

Homologous Structures Analogous Structures

- The same or common ancestor - A different ancestor

- May/may not have the same function - Can have the same function
- Develop from similar embryonic tissue - Develop from different embryonic tissue
Psychological Evidence of Relationships
Physiology: Study of how the body works
- Physiological evidence shows similarities between how organs of different organ systems work,
which is indicative of an evolutionary relationship
- Ex: A blood protein found in blood of a horseshoe crab shows that it is more closely related to
spiders than crabs

DNA Evidence of Relationships

- DNA is a chain of nucleotides carry genetic information used in growth and development etc
- DNA sequences can be compared among species
- DNA has disproved past classifications of organisms
- Ex: Scientists used to think fungi was related to plants but DNA tells us that fungi is closer
related to animals

Phylogenetic Tree
- Scientists use a phylogenetic tree to show the evolutionary relationships between species
- A clade is a branch of the tree that shows all the organisms that share a common ancestor

1.3 Kingdoms and Domains

There are 3 domains and 6 kingdoms in which organisms can be grouped:

The 3 Domains
1) Bacteria
2) Eukarya
3) Archaea
● Eukarya contains the greatest biological diversity in the kingdom Protista
● Protista has lived longer than plants and animals so they had more time to evolve
The 6 Kingdoms
 1) Plantae (multicellular, eukaryotic)
2) Animalia (multicellular, eukaryotic)
3) Fungi (multicellular, eukaryotic)
4) Protista (unicellular, multicellular, and eukaryotic)
5) Bacteria (unicellular, prokaryotic)
6) Archaea (unicellular, prokaryotic)
Please Add Food Plates Back Away

Animalia
- Animals are multicellular, heterotrophic (can’t make their own food) eukaryotes,
- Unlike plants and fungi, animals don’t have a cell wall
- Animal bodies are held together by structural proteins (ie. collagen).
- Most animals reproduce sexually.

Plantae
- Plants are multicellular, eukaryotic producers (they create their own food).
- Plants can reproduce sexually and asexually.

Fungi
- Fungi are multicellular, eukaryotic decomposers.
- Like animals, fungi are heterotrophs
- Unlike animals, fungi do not ingest their food, instead they digest their food while it is still in the
environment by secreting powerful enzymes which break down complex molecules that the
fungi can absorb.
- Fungi produce spores through sexual or asexual life cycles

Protista
- Eukaryotes may be unicellular, multicellular and may be producers or consumers.
- Contains the organisms- protozoa, algae, slime molds, and water molds.
- Most protists are aquatic, and they are found almost anywhere there is water.
- Protists reproduce asexually through binary fission: duplicating their genetic material and then
splitting to form two daughter cells identical to the parent.

Bacteria
- Unicellular, prokaryotes, which may be producers, consumers or decomposers.
- Most bacteria are usually classified under this kingdom.
- Every major mode of nutrition and metabolism is represented among bacteria.
- They reproduce asexually through binary fission.

Archaea:
 - Unicellular, prokaryote
- Oldest group of organisms on Earth
- Share similar traits with Bacteria
- Extremophiles - “lovers” of extreme conditions.
- Extreme thermophiles (love very hot environments)
- Extreme halophiles (love highly saline environments)
- They reproduce asexually through binary fission

Autotroph: an organism that captures energy from the sun to produce its own energy-yielding food
Heterotroph: an organism that cannot make its own food and gets its energy from consuming other
organisms

The 2 Types of Cells

Prokaryotes:
- The first living organisms to evolve, they lack a membrane-bound nucleus
- It’s name actually means “before the nucleus”
- Represented by the kingdoms Bacteria and Archaea
- They reproduce by binary fission:
Eukaryotes:
- Larger, complex, membrane-bound nucleus
- Presence of a nucleus
- Contain organelles
- Reproduce in several ways including mitosis and meiosis

Cladograms
- A cladogram is a stylized diagram that looks like a series of Y’s or forks in a road.
- At each branch, or “Y” junction, novel characters of evolutionary origin are used to separate off
one group from the rest.

Dichotomous Key
- System for narrowing down organisms
Summary:
Domain Bacteria Archaea Eukarya

Kingdom Bacteria Archaea Protista Plantae Fungi Animalia

Example Staphylococcus Sulfolobus Amoeba Maple tree Mushroom Rabbit

archaea

Cell Type Prokaryote Prokaryote Eukaryote Eukaryote Eukaryote Eukaryote

# of cells Unicellular Unicellular Unicellular/ Multicellular Mostly Multicellular

Multicellular multicellular

Nutrition Autotrophs/ Autotrophs/ Autotrophs/ Autotrophs Heterotrophs Heterotrophs

Heterotrophs Heterotrophs Heterotrophs

Reproduction Asexual Asexual Asexual/ Sexual Sexual Sexual

Sexual

1.4 Classifying Types of Biodiversity

★ There are 3 important ways of studying biodiversity

Genetic Diversity:
The variety of heritable characteristics (genes) in a population of interbreeding individuals.
Ex: Different tail patterns of humpback whales

Species Diversity:
The variety and abundance of species in a given area.
Ex: Australia’s great barrier reef (contains so many different types species of coral and fish)

Ecosystem Diversity:
The variety of ecosystems in the biosphere
Ex: the variation in ecosystems, such as deserts, forests, grasslands, wetlands and oceans.

Gene Pools:
- Genetic diversity within a population is known as the gene pool
- It is the sum of all the versions of all the genes in a population.
- The larger the gene pool and genetic diversity, the better the chances of species survival despite
environmental pressures or changes
The health and sustainability of the biosphere can be measured by the richness of ecosystem
diversity.

Ecosystem Services:
the benefits experienced by species (including humans) that are provided by sustainable ecosystems.
Examples:
➔ Atmospheric gas supply
➔ Climate regulation
➔ Water supply
➔ Food production
➔ Waste treatment

Ecosystems with greater species diversity are more likely to provide important services reliably and are
also more resilient despite disturbances.
Examples of disturbances:
➔ Non-native species invasion
➔ Disease
➔ Charges in abiotic factor concentrations

★ The greater the lack of diversity, the more impact invasive species have on the ecosystem
★ Lack of diversity means more impact overall on diseases and plants growing

2.1 Viruses
Viruses do not belong to a kingdom and therefore are not considered to be alive

Viruses:
● Viruses are dependent on the internal workings of other cells. They cannot “live” independently
 outside of their host cell.
● Outside of a host cell, the virus will remain dormant.
● Viruses do not have:
○ A cellular structure
○ Cytoplasm
○ Organelles
○ Cell membranes
○ The ability to carry out life functions such as respiration
● A virus has a genome but can reproduce only within a host cell.
● VIrus can negatively affect the organism in which they have made their host.
● Examples of viruses include HIV, HPV, Polio and H1N1

Viral Structure
● The tiniest viruses are only 20 nm in diameter (smaller than a
ribosome)
● Even the largest viruses are barely visible with a light microscope.
● All viruses contain the following:
○ A protein shell enclosing the viral genome which is called
a capsid.
○ DNA (double or single stranded) or RNA (Double or single
stranded)
● Some viruses have accessory structures that help them infect their hosts.
● For example, a membranous envelope surrounds the capsids of influenza viruses and many
other viruses found in animals.
● These viral envelopes, which are derived from the membrane of the host cell, contain host cell
phospholipids and membrane proteins.

Lytic Cycle
- The typical replication of viruses is the lytic
cycle
- The term refers to the last stage of
infection, during which the host cell lyses
and releases the viruses that were
produced within the cell.
Lysogenic Cycle
- The lysogenic cycle replicates the virus’ genome without destroying the host. The viral DNA
attaches itself to the host cell’s chromosomes
- The virus may remain dormant within the host cell, only to later reactivate and instruct the host
cell to produce more viruses. (incubation time is longer)

Steps:
1. The viral genome enters the cell
2. Viral genome integrates into host cell genome
3. Host cell copies viral chromosomes
4. Cell divides, and virus chromosomes are transmitted to cells daughter cells
5. Daughter cells become parent cells, they divide and transmit viral chromosomes to new
daughter cells… and so on.

Retrovirus and Provirus

❖ A retrovirus contains an enzyme called transcriptase
❖ This enzyme causes the host cell to copy the viral RNA into DNA.
❖ The DNA then becomes a provirus that continues to produce new viruses without destroying
the cell (much different than the lytic cycle)
❖ This way the host cell is not damaged but the virus can still undergo a different type of
replication.
❖ Example: HIV

Prions
- Non viral disease-causing agents
- Cause severe deadly brain diseases

2.2 Archaebacteria and Eubacteria

Comparing Morphology:
➢ Most common forms in both bacteria and archaea are spheres and rods
➢ The spheres are called cocci and the rods are bacilli
➢ The 3rd is spiral shape
Anaerobic vs. Aerobic Environments
Aerobic
An aerobic organism requires oxygen for growth (obligate aerobes).
Anaerobic
An anaerobic organism is any organism that does not require oxygen.
It may react negatively or even die if oxygen is present (obligate anaerobes)

Comparing Nutrition
Methanogens (archaea)
- Only archaea go through methanogenesis which produces methane gas as a by-product
- Methane is the simplest organic compound but is a harmful greenhouse gas
- Methane-producing archaea live in the digestive tract of animals such as cattle

Cyanobacteria
- Some bacteria are photosynthetic- an example would be cyanobacteria
- Cyanobacteria produce oxygen and live in both fresh and saltwater
- They are responsible for much of the atmospheric oxygen on Earth

Comparing Habits
Extremophiles: Archaea have the ability to live in extreme conditions
Most bacteria are mesophiles (organisms that live in environments with moderate conditions)

Thermophile: “heat lovers”

Acidophile: “acid lovers

Halophile: “salt lovers”

Binary Fission
● Since bacteria and archaea lack nuclei, they cannot reproduce by mitosis or meiosis.
● Binary fission is an asexual form of reproduction, meaning it does not involve production of eggs
and sperm or mixing of genetic material from two individuals.
 ● Binary fission
produces daughter
cells that are
genetically
identical to the
mother cell.

Conjugation
- Some bacteria and archaea are able to exchange DNA by conjugation
- Process produces cells with new genetic combinations, providing a chance that they can better
adapt
- During conjugation one cell links itself to another cell via a bridging structure and transfers all or
part of their genetic code to the other cell.

Endospores
- Some species of bacteria can form a hard-walled structure, called an endospore, which protects
and stores the organism’s genetic material.
- Endospores will protect the bacteria from high temperatures, drying out, freezing, radiation and
toxicity.
- Endospores have not been found in archaea.

Gram Stains
● Gram stains are used to divide bacteria into two groups.
○ Gram-positive bacteria
○ Gram-negative bacteria
● Gram-positive bacteria have a thick protein layer on their cell wall and stain purple.
● Gram-negative bacteria have a thin protein layer on their cell wall and stain pink.