Name the Classification system

Domain, kingdom, phylum, order, family, genus, specific epithet,

Problems with the classification

• No real criteria define the levels

• 2) Does not show evolutionary relationships

What is a species?

• Species concepts-

• Morphology Species Concept (Linnaeus)-

  • Based on anatomical similarities and differences.

• Cons- How much anatomical variations is required to justify having a new species

• Pros- good for naming new species in fossils- where that's all we’ve got to go on.

Biological Species Concept-

• if 2 organisms can produce viable (living), fertile offspring, then they’re the same species.

For a new species to arise, a couple of events must occur: (2)

• ew species to arise, a couple of events must occur:

  • 1) Reproductive Isolation- two segments of a population are separated; they can no longer mate with each other. The gene pool is also split into 2.

  • 2) Genetic Divergence- the 2 gene pools accumulate different mutations in different places(chromosomes) and at different rates.

    • If the 2 populations are reintroduced, they no longer recognize each other as potential mates.

    • *When they no longer recognize each other, that’s when we say they’re 2 different species.

• Mechanisms of Reproductive Isolation-prevents fertilization (5 types)

• 1) Mechanical isolation- reproductive parts don’t go together anymore. EX: plant- pollen can't stick to stigma.

• 2) Temporal isolation- Different breeding season.

• 3) Behavioral isolation- Different courtship rituals.

• 4) Ecological isolation- different habitats and niches.

• 5) Game mortality- “mating” occurs. External fertilization. Gametes can’t survive

Post- Zygotic barriers means

•  fertilization does occur.

 Reduced hybrid fertility

• Offspring are viable but sterile.

 Hybrid breakdown-

• Offspring are viable and fertile, BUT the 2nd generation is sick and dies.

  • Pros- great for classifying animal which are limited in the ability to hybridize (cross breed)

  • Cons- Not so great for other organisms (plants, bacteria) which have fewer limitations in the ability to hybridize.

  • Artificial decrease in diversity. may lose conservation status

True or false, Sometimes, Geology can cause Reproductive isolation and genetic divergence to occur.

true

Allopatric speciation

• appearance of a new species.  reproductive isolation and are caused by a geological feature

Sympatric-

• no geographic feature…

Ecological Species Concept- and pros and cons

•  two organism that have exactly the same habitat and niche required belong to the same species.

  • Pro- accommodates for organisms that don't really fit into the Biological species concept.

  • Con- Artificial increase in diversity *everything has a conservation status.

Phylogenetic Species Concept

• organisms with similar gene sequences are the same species.

  • Pro- same as Ecological Species Concept

  • Con- how much genetic difference is required to justify naming a new species

• Mass Extinction and Adaptive Radiation

AR- a period of rapid diversification that follows a mass extinction- as survivors move into the vacant niches.

Virus structure

• - Capsid- a protein “shell” made up of capsomeres (ind. proteins)

• Nucleus Acid- DNA or RNA- inside the capsid

• Capsides may be:

• Losahedral- many sided polygon

• Helical (filamentous) a hollow tube

• Complex- both

  • Only found in bacteriophages. (virus that target bacteria)

• Every organism on the planet, and every tissue in every multicellular organism, has at least _____ virus that targets it.

• one

• Viruses have ______ they don't move to different tissues and it's unusual for them to jump to a new species.

• high specificity

Animal viruses have an ____ outside the capsid. The envelope is derived from the host cell membrane. There are viral proteins embedded in the envelope called spike proteins.

envelope

• The spike protein enables a virus to infect another ___.

• The spike proteins are the only viral component “visible” to the _____ system.

Cell and immune

• Viruses are considered “non living” because

• Only carry out one metabolic process- reproduction. Even then, they can only carry it out inside a host cell. 

• They are called, “obligate parasites”.

Life cycle-

Lytic and Lysogenic

• Lytic- 5 stages

• 1) Infection- virus inserts its nucleic acid into the host cell

• 2) Circulization- the viral NA forms a circle to mimic the bacterial chromosome.

• 3) Hostile ta keover- viral NA takes over the host cell’s enzymes respiration for transcription and translation. The bacterial chromosomes is destroyed.

• 4) Synthesis- new viruses are assembled

• 5) Lysis- host cell breaks open and new viruses are released.

Lysogenic- 7 stages

• 1) Infection

• 2) Integration- the viral NA inserts itself into the host cell’s chromosome. (prophage). It can sit there indefinitely. *Every time the host cell divides, it produces daughter cell carrying the prophage,

• 3) Excision- an environmental cue causes the prophage to remove itself from the host cell’s chromosomes and resume the lytic life cycle

• 4) Circulization

• 5) Hostile takeover

• 6) Synthesis

• 7) Lysis

• Animal Viruses- 5 types

Virulent, Persistent, Latent, Oncavirusus

Virulent-

•  the classical lytic virus. 

  • Ex- common cold, flu

Persistent

• the chronic replication without killing the host cell. Like lysogenic. Viral NA integrates itself into the host's chromosomes. (Provirus)

• Chronic low levels of viral production without harming the host cell.

• Ex- aids, hepatitis

Latent

• virus lies dormant for many years. “Hiding” inside a host cell. Environmental cue (stressor) causes the viruses to become active, causing a “flare up”.

  • Ex- varicella zoster and herpes simplex

Oncavirusus

• may cause cancer- retroviruses.

  • If the enzyme that integrates the viral NA cuts the DNA at a sequence that falls within a gene that regulates cell division, then that virus could contribute to cancer.

  • Ex- papillomavirus

Vaccination does what

• Prepares the immune system for a certain pathogen.

  • Decreases severity of illness and shortens duration of illness.

 Live/attenuated-

• exposes the immune system to either 

  • Live- a close relative to a pathogen that causes a milder form of disease.

  • Attenuated- a weakened strain of a pathogen

Inactivated

•  expose immune system to a chemically inactivated pathogen.

Subunit

• expose the immune system to a pathogen’s recognition factor.

  • Viruses- the spike protein

  • Bacteria- a membrane protein

  • *mRNA vaccines- cheaper, and more accurate.

Toxoid

• vaccine targets a toxin made by a pathogen instead of the pathogens itself. (bacteria)

The Singularity

• all the matter in the universe compressed into a unit of a dime.

The Big Bang

• B.7 bya- the matter expands outward

• Things that came directly out of the Bang: 8 things

• Photons- particles of light has characteristics of both energy and matter

• Quarks- adhere to each other in groups of 3: Hachron

  • Displays more properties of matter

  • Protons- 2 up quarks and 1 down quark

  • Neutrons- 2 down quarks and 1 up quark

• Electrons- not Hadrons, not Quarks (not in same class)

  • Leptons

• Protons, Neutrons, E- can naturally and spontaneously form the smallest elements: Hydrogen, Helium, and Lithium.

• Clouds of hydrogen “collapse” to form stars

• Stars exist for billions of years

• When they die, they collapse and explose– the violence forms the rest of the elements

• These elements for planets

Evidence of big bang theories

• 1) Hubble expansion- the galaxies are moving apart

• 2) The abundance of H, He, Li, in the observable universe.

• 3) Cosmic Microwave Radiation- energy from the original BB itself.

Formation of the earth-

• 4.6 billion years ago- Pre cambrian Era- 500 million years ago

Early Earth atmosphere-

•  may have formed due to volcanic outgassing

• The gasses contain MOST of the elements associated with life.

• Can these elements spontaneously and abiotically recombine to form biological precursor molecules? (glucose, amino acids, nucleotides)

  • Scientists look and meteorites they formed under the same conditions as earth but have remained unchanged

  • They see amino acids and other hydrocarbons.

Synthesis of organic compounds

Miller experimnets

What did miller do

• Miller was able to produce amino acids and other organic compounds (amines, carbs) under “early earth” conditions

• Further experiments produced glucose, ribose, deoxyribose, other sugars, and adenine.

  • Miller experiments- simulate Early earth conditions

  • Shows that many biological precursor molecules could form in early earth conditions.

Amino acids -> protein

Glucose → starch

Nuclieotides → nucleoic acids

YES! Lab research stimulating early earth conditions supports the hypothesis.

Which came first; RNA or DNA?

RNA

RNA can

• Can duplicate itself (DNA can too)

• Are enzymes– carry out a task (like having a niche)

• Can be favored by selection

• Probably, RNA would have been the earliest molecule of inheritance

• Also, biological membranes spontaneously/ abiotically form

• Membrane + RNA + other biological molecules may = precursor to cells (protobiont)

• Three Domains of Life:

• 1) Eukarya- Eukaryotic cell type: has a nucleus and internal membrane system. Included single and multicell organisms.

• 2) Bacteria- Prokaryotic cell type: no nucleus; no internal membrane system, single celled organisms only “germs”- pathogenic bateria

• 3) Archaeans- Prokaryotic; Extremophiles- have adaptations to survice in extreme environments.

  • Single celled only; no pathogenic at this time

  • Genetically moot similar to Eukarya

• Earliest trace of life:

• In rocks- 3.8 bya

• Isoprenoid Residue- A cell membrane component produced ONLY by Archaeans

• This suggests that the earliest life was similar to the Archaeons

• Early Earth oceans were probably like the areas around hydro thermal Vents today; Archea- like ancestors would be suited for this environment.

• Earliest fossils of cells:

• In rock from 3.8 bya

• Cyanobacteria- (domain bacteria)

• Photosynthetic- produces 02 gas; we credit cyanobacteria with converting the earth atoms to the 02-rich atoms as we know it today.

• Stromatolites- Fossilized layers of Cyanobacteria

True or false 02 is a terrible, corrosive gas and has huge consequences for like on Earth

True

• *Bonder Iron Formations-

• Rocks that contain iron show cyclical saturation and finally, maintained saturation of the atmosphere with 02.  

Oxygen is a corrosive gas. Saturation of the ocean and atoms with O2 has major effects on the Earth: 3 things

• 1 No more Spontaneous and Abiotic formations of biological mols.

• 2) Mass Extinction of anaerobic organisms- orgs that have no way to remove/change O2. The surviving anaerobes are restricted to environments with very specific conditions. Followed by an Adaptive Radiation- of aerobic organisms.

• 3) Formation of the Ozone Layer- protects the Earth from UV radiation. Life can move out of the ocean onto land.

Origin of Cells are

 Eukaryotic

Earliest Fossil of Eukaryotic Cells- in rocks– 1.9 billion years old. Defined by organelles and nucleus “protistan”

Snowball Earth Event = –700 million years old. what happened

• Global Glaciation. Mass Extinction. - survivors can live in “warm” regions near volcanoes.

  • Followed by Adaptive Radiation of multicellular Eukaryotic organisms. 

• The earliest of these organisms are unrecognizable. We don’t know what these are– 

• THEN- the Cambrian Explosion-

• Cambrian Explosion- 500 Million years ago - what about it

• The sudden appearance of many recognizable multi-cellular eukaryotic organisms. 

• This marks the end of the Pre-Cambrian

Paleozoic

ancient animals

• Paleozoic- ancient animals- Name everything that happened…… appearances and ages

• Starts- 500 mya without cambrian explosion

• Warm, humid climate.

• Earliest plant fossil= moss

• Appearance (earliest fossil) and Diversification (many species) of Ferns

• Age of Giant Ferns

• Earliest terrestrial animal fossil- looks like a giant millipede. 

• Earliest terrestrial predator- giant salamander

• Appearance and diversification of Amphibians- Age of Giant Salamanders

• Appearance and diversification of fish: Age of fishes

• Appearance of Gynmosperm-  cone-bearing plants

• Appearance of the ancestor of Reptiles and Mammals

  • Appearance of Reptile Lineage

  • Appearance of the Mammalian Lineage. Looks like Reptiles but have distinctly mammalian skeletal structures. 

• End with Permian Mass Extinction- 250 mya.

  • The largest mass extinction- 90%+ all life destroyed

  • Associated with formation of pangaea 

Mesozoic starts - 250 mya with permian mass extinction.- name everything… ages and appearances

• Hot and dry climate

• Ferns and salamanders- only the small survive

• Diversification of reptiles and dinosaurs

  • Age of reptiles, age of dinosaurs

  • Appearance and 1st diversification of birds

• Mammals present- oppressed by dinosaurs

  • Appearance of true mammals.

• Diversification of Gymnosperms

  • Age of Gymnos

• Appearance of Angiosperms (flower-bearing plants)