EXAM 1 Systematics and Phylogeny - Bio 2 Dr. Ortega

Systematics

The branch of biology that deals wth classification of organisms

Classification of organisms

Based on shared characteristics such as morphology, DNA, ecology, and similar behaviors

Anthrax

disease is caused by a bacteria and can be sent in a powdery form for bio terrorism and leads to difficulty breathing and even death - LETHAL - and can effect humans and animals

Situation that happened with Anthrax Disease

Letters were sent out containing anthrax, because this, those exposed died.

Five people died

(Flyer that states "Special Reward up to $2.5 million)

How many letters were believed to be sent out?

7

How many infections did this cause?

22 infections; but 5 people died

Anthrax

Dormant bacteria that was mailed out, isolated, and particular genes had their own nucleotides sequenced

How were the sequences obtained?

From thousands of samples worldwide

The mailed strain of Anthrax

"Ames Strain"

Ames Strain

Very lethal bacterium strain that was used for bio-defense research purposes

Where was the Ames Strain found?

In a cow farm in IOWA farm and then it was moved to the pentagon because it was very toxic

Bruce E. Ivins

62 year old man that worked for the government's bio-defense labs in Maryland. He was the main suspect pertaining to the letters that were sent out. FBI was going to lay charges on him, but he committed suicide before being questioned (so we'll never really know)

Phylogens

development of species/organisms; process by which taxon appears

taxon

group or level of organization into which organisms are classified

Branch for vascular plants

From fossil records- Ferns, then Pine Trees, then Sunflowers.

We know this is the correct order because the pine trees contain pollen which is only found in sunflowers.

Are fossil records complete?

No, this is why they rely on other types of evidence to establish the best hypothesis of evolutionary relationships.

Branch for apes

From DNA data it's known that through time gorillas evolutionists into chimpanzees, and then into humans

Cladistics

A phylogenetic classification system that uses shared derived characters and ancestry for grouping taxa.

derived characteristics

characteristics that appear in recent parts of a lineage but not in its older members.

inherited from the most recent common ancestor of the group

ancestral characteristics

similarity that arose prior to the common ancestor of the group

Synapomorphies

Shared derived characters

outgroup

group that does not possess any of the derived characteristics but has all ancestral traits

Do all mammals have hair?

YES

Why do you think when we evolved to humans we became bipedal?

cause we learned to use tools with our hands

Polarize

first step of cladistics; used to determine if the characters are ancestral or derived in each ancestor using the outgroup as a reference

Cladogram

Diagram that depicts a hypothesis of evolutionary relationships among a group of organisms

clades

group of species that share a common ancestor as indicated by the possession of shared derived characters.

also defined as synapomorphies - derived characters shared by clade members

sister species

two species that are each other's closest relatives

Homoplasy

a shared character state that has not been inherited from a common ancestor. There are two kinds: convergent evolution and evolutionary reversal

convergent evolution

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

Example: fins for the animals that live in the ocean, or wings for birds to fly. whales and penguins do not share a common ancestor, but both have flippers as limbs

evolutionary reversal

The reappearance of an ancestral trait in a group that had previously acquired a derived trait.

principle of parsimony

favors the hypothesis that requires the fewest assumptions/steps/synapomorphies

Classification

how we place species and higher groups into the taxonomic hierarchy (Genus, Family, class, etc)

monophyletic

ALL descendants came from one common ancestor

paraphyletic

Pertaining to a group of taxa that consists of a common ancestor and some, but not all, of its descendants.

polyphyletic

pertaining to a group of taxa that includes distantly related organisms but does not include their most recent common ancestor

Deep Time

geological time that is divided into 4 eons: Hadean, Archean, Proterozoic, and Phanerozoic

4.5 billion years ago

Earth was formed as a hot mass of molten rock

As it cooled, chemically-rich oceans were formed from water condensation

3.5 billion years ago

life originated on Earth in the Archean

After

The first terrestrial colonization happened ______________ the Cambrian Explosion

500 million years ago

Cambrian explosion

Cambrian explosion

rapid diversification of most major animal groups marking the start of the Paleozoic era.

happened in AQUATIC environments.

Cyanobacteria

Bacteria that can carry out photosynthesis

Extremely Important Development

O2 in the atmosphere interacted with ultraviolet (UV) radiation from the sun and formed O3 (Ozone)

Ozone

O3; critical because it reduces the mutation rate caused by UV light

3 monophyletic domains of life

Eubacteria

Archaea

Eukaryotes (has 6 supergroups identified within eukaryotes)

prokaryotes

paraphyletic (Eubacteria and Archaea)

eukaryotes

monophyletic

plants

have 3 different DNA

humans

have 2 different DNA

Endosymbiosis

a mutually beneficial relationship in which one organism lives within another (but typically behave as a single organism)

Two critical endosymbiosis

mitochondria and Chloroplasts

Mitochondria

are the descendants of a "Hybrid" microorganism involving prokaryotes

purple sulfur bacteria

does photosynthesis by oxidizing hydrogen sulfide to release as sulfur

Rickettsia

parasite bacteria that uses oxygen to oxidize sugars to produce ATP (aerobic respiration).

This bacteria becomes the mitochondria.

aerobic respiration

Respiration that requires oxygen

Chloroplasts

Are derived from cyanobacteria.

two independent endosymbiosis events involving eukaryote and prokaryote cells.

red and green algae

a eukaryotic cell with mitochondria that engulfed cyanobacteria (makes one red and one green algae)

brown algae

originated when a eukaryotic cell engulfed a red alga

Hierarchical System of Classification

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

Carolus Linnaeus

(1707-1778) Founder of taxonomy, the branch of biology concerned with naming and classifying organisms. Developed two part system of naming organisms.

Synapomorphies

provides a new perspective to the Linnaean classification system

Two part naming system

cursive/italicized, first word is capitalized (type) and second word (species) is lowercase.

Taxonomy

The scientific study of how living things are classified

- classification level is called a Taxon (plural = taxa)

"Margarita" Cat (classifications and synapomorphies)

1. Class- mammalia- Mammary glands and hairs

2. Order- carnivora- presence of carnassial teeth

3. Family- felidae- skull with short rostrum and facial area and short inflated braincase

4. Genus- felis- small felines, cannot roar because of unique throat stucture

5. Species- margarita- Large ear pinnae and reduced weight and size

Virus

A tiny, nonliving particle that invades and then reproduces inside a living cell.

Virus structure

nucleic acid core surrounded by a capsid (protein cover)

- some viruses also have an envelope (lipids + proteins)

- NO Cytoplasm (a virus is not a cell)

nucleic acid core

the innermost part of a virus that is either DNA or RNA (can't be made of both)

- can be single stranded, double stranded, circular, or linear

Genome

all of an organism's genetic material

Viruses are classified by their genome

RNA viruses (COVID is a single stranded RNA virus)

DNA Viruses

Retroviruses

Retroviruses

Genes encoded by RNA, but include DNA intermediates (but really RNA viruses)

-REVERSE TRANSCRIPTASE

-HIV = 2 single stranded RNAs

Virion

Virus outside of the cell that is metabolically inert

reverse transcriptase

Will synthesize DNA using viral RNA as a template

Only found in RETROVIRUSES

each type of virus has a

limited host range

Limited host range

exact fit is required for a virus to adsorb to a host cell

tissue tropism

inside a host the virus may only infect certain tissues

Viruses can...

Remain dormant or latent for YEARS

viral genome

tricks host cell into making viruses

Viruses lack

Their own ribosomes, nucleotides, amino acids, and most of the enzymes for protein and nucleic acid synthesis

Bacteriophage

A virus that infects bacteria; called "phage"

- E. Coli infecting

lysogenic cycle

a viral reproductive cycle in which the viral DNA is added to the host cell's DNA and is copied along with the host cell's DNA

- virus and host coexist

lytic cycle

A type of viral replication cycle resulting in the release of new phages by killing the host cell.

-Kills host

HIV (human immunodeficiency virus)

The infectious agent that causes AIDS. HIV is a retrovirus.

-targets immune system cells (CD4+, Helper T cells, and Macrophages). Without these cells the body cannot fight back.

- 7% of the population is HIV resistant because they have a protein mutation that doesn't allow the allow the bacteria to penetrate.

AIDS

acquired immunodeficiency syndrome

-first reported in the USA in 1981

-originated in Africa in 1950s

provirus

A viral genome that is permanently inserted into a host genome.

-integrates in genome of CD4+ cells

CD4+ helper T cells

Cells that protect against infections and activate the body's immune response. HIV kills these cells, so a high count usually means better health.

HIV infection cycle

Attachment, Entry through fusion pore, Replication, Assembly, Release

In attachment

Viral gp120 glycoproteins attaches to CD4 proteins on a CD4+ and macrophage cells

HIV Virus - attachment

Coreceptors (proteins of human immune system cell) like CCR5 affect likelihood of entry

- individuals with a particular mutation for this protein (CCR5) are resistant to HIV

HIV virus - Replication

Virus uses reverse transcriptase to convert virus RNA to double stranded DNA

-Enzyme is extremely ERROR PRONE

-mutations are common

-difficult to combat with drugs or vaccines

HIV virus - assembly

Making many copies of virus

HIV virus - release

New virus exit by budding

AIDS treatment

Antiviral drugs that can target viral entry, genome replication, integration of viral DNA, and maturation of HIV proteins

- but HIV has high mutation rate so drug resistance can become a problem

combination therapy

combinations of drugs used to eliminate viruses

HAART (highly active antiretroviral therapy)

Combination of drugs effective against AIDS

Coronavirus taxonomy

- order /

- suborder /

- family /

- subfamily /

- 4 genera = alpha, beta, gamma, delta coronavirus

Betacoronavirus

SARSr-Cov

COVID

RNA virus

spike proteins

protruding structures of virus that are recognized by antibodies

Spike protein and COVID cycle

- binds to ACE2 RECEPTOR protein found outside of human cells

- Virus enters inside the cell

-vRNA released and use as a template to make new viruses