Module 1 Notes

Precambrian

• 4.6 billion–590 million years ago

• Origin of prokaryotes and eukaryotes

• Mostly marine life

• No complex multicellular organisms for most of this period

Paleozoic

• 590–248 million years ago

• Fish and amphibians

• First vascular plants

Mesozoic

• 248–65 million years ago

• Dinosaurs dominated

Cenozoic

• 65 million years ago–present

• Mammals became dominant

• Modern humans eventually appeared

Cambrian Explosion

Approximately 540 million years ago

• Rapid appearance/diversification of many major animal groups.

Spontaneous Generation

The old idea that life could arise from nonliving matter.

It was disproven through experiments, including work by Louis Pasteur.

Biogenesis

Life comes from pre-existing life.

But this creates the question:

Where did the first life come from?

Oparin

Alexander Oparin proposed that early Earth had a very different atmosphere, including:

• Methane

• Water vapor

• Ammonia

• Little/no free oxygen

He proposed that conditions on early Earth could have allowed increasingly complex molecules to form.

Miller-Urey Experiment

Stanley Miller attempted to simulate early Earth conditions.

The experiment produced organic molecules, including:

• Amino acids

• Some sugars

⭐ Important distinction:

The experiment did NOT create life.

It showed that some organic molecules could form from simpler inorganic materials under certain conditions.

Coacervates

• Droplet-like structures formed from organic molecules

• Possible precursors to cells

Microspheres

• Protein-based spherical structures

• Another possible early cell-like structure

A major idea is that:

Simple molecules → organic molecules → larger molecules → membranes → primitive cells

RNA and proteins are proposed to have played important roles before DNA became the primary genetic material.

Endosymbiotic Theory

The endosymbiotic theory explains the origin of some eukaryotic organelles.

The basic idea:

An early cell engulfed free-living bacteria, and instead of digesting them, the bacteria lived inside the cell and eventually became organelles.

Most importantly:

• Mitochondria originated from bacteria

• Chloroplasts originated from bacteria

Basic Virus Structure

A virus contains:

Genome + Capsid

• Genome: DNA or RNA

• Capsid: protein coat surrounding the genome

• viruses also have an envelope

• The envelope is a lipid membrane obtained from the host cell.

• Glycoproteins help viruses attach to host cells.

A virus has…

either DNA OR RNA, not both.

Viruses Are Not Considered Cellular Life

They:

• Are extremely small

• Cannot reproduce independently

• Require a host cell to replicate

Virus Discovery

Dmitri Ivanovsky studied Tobacco Mosaic Virus.

He discovered that the infectious agent could pass through filters designed to trap bacteria.

This helped demonstrate that there were infectious agents smaller than bacteria.

Tobacco Mosaic Virus

• RNA virus

• Infects plants

studied Tobacco Mosaic Virus.

Dmitri Ivanovsky

Lytic Cycle

Infect → Replicate → Burst

• Virus enters host

• Viral components are produced

• New viruses are assembled

• Host cell is destroyed/lysed

• New viruses are released

Lysogenic Cycle

Hide → Copy with host → Activate later

• Viral DNA integrates into the host's DNA

• Host cell reproduces

• Viral DNA gets copied along with the host DNA

• Virus can later become active

• It can then enter the lytic cycle

Retroviruses & HIV

RNA

HIV is a retrovirus.

Important characteristics:

• RNA virus

• contracted via bodily fluids

• destroys t - helper cells, cells that create anti bodies which causes aids

• Has an envelope

• Uses reverse transcriptase

• Causes AIDS

Reverse Transcriptase

RNA → DNA

This is important because most of the time we learn the central dogma as:

DNA → RNA → Protein

Retroviruses use the unusual direction:

RNA → DNA

HPV

Human papillomavirus

• Can cause warts

• Some types can increase cancer risk

• Can be sexually transmitted

• Vaccine available: Gardasil

• DNA

Herpes Simplex Virus

DNA

HSV-1

• Typically associated with oral/cold sores

HSV-2

• Typically associated with genital herpes

Important:

• DNA virus

• Can remain in the body

• Immune system can suppress it

• Antiviral medications can help manage it

• No currently available vaccine

Chickenpox / Varicella-Zoster Virus

• Member of the herpesvirus family

• Highly contagious

• Spread through respiratory droplets/direct contact

• Causes characteristic itchy, blister-like rash

• Vaccine available

After infection, the virus can remain dormant in the body.

Later, it can reactivate as:

Chickenpox → dormant virus → shingles

DNA

The classification hierarchy is:

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

Father of Modern Taxonomy

Linnaeus

• Developed binomial nomenclature

binomial nomenclature

• Linnaeus

  • Developed

  • Genus — capitalized

• species — lowercase

• Both are italicized or underlined.

• Example: Homo sapiens

Domains of Life

• Bacteria

• Archaea — includes many extremophiles

• Eukarya — animals, plants, fungi, and protists

Prokaryotic cells

no nucleus; bacteria and archaea

Eukaryotic cells

have a nucleus and membrane-bound organelles

Charles Darwin's natural selection

explains how populations change over generations.

The basic idea:

1. Organisms can produce more offspring than the environment can support.

2. Resources are limited, creating competition.

3. Individuals within a population have variation.

4. Individuals with advantageous characteristics are more likely to survive.

5. Those individuals are more likely to reproduce and pass those traits to offspring.

Evidence of Evolution

• Fossil record

• Biogeography — geographic distribution of organisms

• Comparative anatomy

• Homologous structures — same evolutionary origin, different functions

• Analogous structures — similar function, different evolutionary origin

• Vestigial structures

• Comparative embryology

• Molecular biology/genetics — DNA, RNA, and proteins

⭐ Important: Molecular evidence is especially important in modern taxonomy because scientists can compare DNA, RNA, and protein sequences to determine evolutionary relationships.

Artificial selection

• Humans intentionally select traits to reproduce.

• Example: breeding dogs for certain characteristics.Artificial selection = the human-directed selection process

Domestication

• A long-term process where humans bring a wild species under their control.

• Can change an organism's behavior, physiology, and reproduction.

• Artificial selection can be part of domestication.

Domestication = the long-term transformation of a species

Cladistics

groups organisms based on shared characteristics and common ancestry.

A clade contains:

• A common ancestor

• All of its descendants

phylogenetic tree/cladogram

characteristics can help determine which organisms are more closely related.

Modern phylogenetic trees often use:

• DNA sequences

• RNA sequences

• Amino acid/protein sequences

⭐ Key idea: The more similar the molecular sequences, the more closely related the organisms are likely to be.

Earth forms

4.5 billion years ago

First life

4.0–3.0 billion years ago

Earliest prokaryotes

3.5 billion years ago

Earliest eukaryotes

1.5 billion years ago

Earliest animals

~0.5–0.6 billion years ago

Sall Pox Virus

• Type: DNA virus

• Transmission: Mainly airborne/respiratory droplets and direct contact with infected sores/scabs.

• Mortality: About 25%.

• Survivors could have permanent pockmarks/scars.

• Historically spread to new populations by European travelers, causing devastating outbreaks.

• Worldwide vaccination eventually eradicated smallpox.

Variolation

Early method of protection—infecting someone with material from smallpox sores to cause a milder infection.

• About 5% died from variolation.

Vaccination

Developed from cowpox observations.

• People exposed to cowpox were protected against smallpox.

Monkeypox (Mpox)

• Type: DNA virus

• Transmission: Direct contact, contact with sores/fluids, respiratory exposure, and sometimes sexual/intimate contact.

• Symptoms: Similar to smallpox—fever, rash, and lesions.

• Vaccination: Smallpox vaccines can provide protection against mpox.

• Severe disease/death is more likely in people with certain pre-existing conditions.

Parvovirus

• Type: DNA virus

• Transmission: Primarily direct contact/respiratory droplets depending on the specific parvovirus.

• Key point: Highly contagious.

• Prevention: Some important parvoviruses have effective vaccines, particularly canine parvovirus in dogs.

RNA Viruses

RNA viruses generally mutate rapidly, which can make prevention and treatment more difficult.

Polio

• Type: RNA virus

• Transmission: Mainly fecal-oral transmission, often through contaminated food/water.

• Can attack motor neurons, causing paralysis.

• Symptoms: Fever, headache, vomiting, neck stiffness, and limb pain.

Iron Lung

Historically used to help patients breathe when respiratory muscles were paralyzed.

Jonas Salk

• eveloped the first widely used polio vaccine.

• Vaccination has brought polio close to eradication in many parts of the world.

Measles

• Type: RNA virus

• Transmission: Airborne/respiratory droplets and direct contact.

• Very contagious.

• Causes fever and a widespread rash.

• Prevented by the MMR vaccine.

Rubella (German Measles)

• Type: RNA virus

• Transmission: Mainly respiratory droplets.

• Usually mild in children/adults.

• Major danger: Infection during pregnancy can seriously harm the developing fetus.

• Prevented by the MMR vaccine.

Mumps

• Type: RNA virus

• Transmission: Respiratory droplets, saliva, and close/direct contact.

• Symptoms:

  • Swollen salivary glands

  • Very sore throat

  • Fever

  • Fatigue

• Most cases are not fatal, but serious complications can occur.

• Prevented by the MMR vaccine.

Yellow Fever

• Type: RNA virus

• Transmission: Mosquito bites.

• Common in tropical regions.

• Cannot normally spread directly from person to person.

• Causes jaundice (yellowing of the skin/eyes) because the liver is affected.

• Vaccine: Highly effective.

Rabies

• Type: RNA virus

• Transmission: Usually through the bite/saliva of an infected animal.

  • Bats

  • Foxes

  • Raccoons

  • Unvaccinated dogs

• Virus travels through the nervous system toward the brain.

• Once symptoms appear, rabies is almost always fatal.

• Symptoms: Abnormal behavior, spasms, difficulty swallowing, and foaming/drooling.

• Prevention after exposure: Rabies vaccine + rabies immune globulin (antibodies) can prevent disease if given promptly.

Influenza (Flu)

• Type: RNA virus

• Transmission: Airborne/respiratory droplets and aerosols, especially through:

  • Coughing

  • Sneezing

  • Close person-to-person contact

• Can mutate/change frequently.

• 1918 Influenza Pandemic: One of the deadliest pandemics in modern history, causing an estimated 50 million deaths worldwide.

Ebola

• Type: RNA virus

• Transmission: Direct contact with infected body fluids.

• Considered an emerging disease—animal viruses can cross into humans.

• Natural reservoir is thought to involve fruit bats.

• Can cause extremely high mortality in severe outbreaks.

• Symptoms:

  • High fever

  • Diarrhea

  • Vomiting

  • Severe illness

  • Sometimes bleeding

Zika

• Type: RNA virus

• Transmission:

  • Mosquitoes

  • Sexual transmission

  • Mother-to-fetus transmission

• Originated in Africa and later spread to South America and other regions.

• Many infected people have no symptoms.

• Major concern: Infection during pregnancy can cause serious fetal developmental problems, including microcephaly.

Coronavirus / COVID-19

• Type: RNA virus

• Transmission: Primarily respiratory aerosols/droplets.

• Coronaviruses can affect different body systems depending on the virus and route of infection.

• -

Prions

infectious proteins that do not contain a nuclear genome (DNA or RNA).

unusually resistant to heat and standard sterilization methods.

abnormal proteins accumulate and damage brain tissue, eventually causing severe neurological problems and death.

myelin sheath

Normal prion proteins are found near nerve cells and are believed to help maintain

Prions

An abnormal ____ can cause normal proteins to change shape and become abnormal as well.

This creates a chain reaction in which more and more proteins become misfolded.

prions affect

Brain tissue eventually develops many tiny holes, giving it a sponge-like appearance.

Kuru

• Found historically among people in New Guinea.

• Associated with ritual cannibalism, through which abnormal prion proteins could be transmitted.

• Symptoms included:

  • Loss of muscle control

  • Weight loss

  • Rapid neurological decline

• Once symptoms appeared, the disease was essentially 100% fatal.

Bovine Spongiform Encephalopathy (BSE)

"Mad Cow Disease."

• developed symptoms similar to those seen in human prion diseases.

• Examination of infected cow brains showed thousands of holes, giving the brain a sponge-like appearance.

• The disease was associated with cattle consuming feed containing infected animal by-products.

Creutzfeldt-Jakob Disease (CJD)

• A human prion disease with similarities to BSE.

• Causes progressive neurological damage and is fatal.

Chronic Wasting Disease (CWD)

A prion disease found in deer, elk, and related animals.

Prion Transmission

diseases can occur when abnormal prion proteins enter the body, including through:

• Consumption of contaminated tissues

• Exposure to contaminated biological material

General Characteristics of Bacteria

• are prokaryotic organisms.

• They do not have a membrane-bound nucleus.

• Their DNA is located in a region called the nucleoid.

• They can live in environments that are too hot, cold, acidic, or alkaline for many eukaryotic organisms.

Cocci

spherical — bacteria

Bacilli

rod-shaped — bacteria

Spirilla

spiral/helical — bacteria

Pili

• hair-like structures on the surface of some bacteria.

• They can help bacteria attach to surfaces.

• Specialized pili can also be involved in DNA transfer between bacteria.

binary fission

Bacteria reproduce asexually through ____

One bacterial cell copies its DNA and divides into two genetically similar cells.

This is somewhat comparable to mitosis, but bacteria do not have a nucleus or undergo mitosis.

Conjugation

Bacteria reproduce sexually through ____

DNA, often in the form of plasmids, is transferred directly from one bacterium to another.

Usually occurs through a specialized pilus.

Transformation

Bacteria reproduce sexually through ____

A bacterium takes up DNA from its surrounding environment.

Transduction

Bacteria reproduce sexually through ____

DNA is transferred between bacteria by a virus (bacteriophage/phage).

Autotrophic Bacteria

Make their own food.

Cyanobacteria are important examples.

Heterotrophic Bacteria

Obtain nutrients from other organisms or organic material.

Many types of true bacteria are heterotrophic.

Archaea

• Prokaryotic

• No membrane-bound nucleus

• Cell walls lack peptidoglycan

• Have unique cell membranes

• Many live in extreme environments

Halophiles

Live in environments with very high salt concentrations.

Domain Archaea.

Thermophiles

Live in very hot environments.

Domain Archaea.

Methanogens

• Produce methane.

• Found in places such as marshes and the digestive systems of some animals.

Domain Archaea.

Cyanobacteria

• Often called blue-green bacteria.

• They are photosynthetic autotrophs.

• Examples:

  • Nostoc

  • Anabaena

• They were among the earliest organisms capable of photosynthesis and played an important role in Earth's early oxygen production.

Cyanobacteria can cause:

• Algal blooms

• Eutrophication

• Production of toxins that can harm animals and ecosystems

Beneficial Uses of Bacteria

Decomposers

• Break down dead organic material.

• Help recycle nutrients in ecosystems.

Nitrogen Fixation

Nitrogen-fixing bacteria convert atmospheric N₂ into forms such as ammonium (NH₄⁺) that plants can use.

Beneficial Uses of Bacteria

Nitrification

Nitrifying bacteria convert nitrogen compounds into nitrite (NO₂⁻) and nitrate (NO₃⁻).

Beneficial Uses of Bacteria

Denitrification

Denitrifying bacteria convert nitrogen compounds back into N₂ gas, returning nitrogen to the atmosphere.

Beneficial Uses of Bacteria

Bacteria are used to produce:

• Vinegar

• Yogurt

• Alcohol and other fermented products

can look funglu like

produces some anti-biotics

Pneumonia

• Infection that can cause fluid to accumulate in the lungs.

• Can be caused by:

  • Bacteria

  • Viruses

  • Fungi

  • Other physiological or metabolic problems

• Treatment depends on the cause.

Typhus

Cause

• Rickettsia prowazekii

Characteristics

• Caused by very small bacteria.

• These bacteria are obligate intracellular parasites, meaning they must live inside host cells.

• Symptoms may include:

  • Severe headache

  • Rash

  • Chills

  • High fever

  • Lesions at the site of infection

Transmission

• Primarily spread by body lice.

• Other biting insects can transmit related Rickettsia species

Typhoid Mary"

• Mary Mallon was a famous asymptomatic carrier of Salmonella Typhi.

• She was associated with multiple infections and deaths due to the spread of the bacteria through food handling.

Tuberculosis

Cause

• Mycobacterium tuberculosis

Characteristics

• Mycobacterium has a protective outer envelope that makes the bacteria difficult to treat.

• It is primarily transmitted through the air.

• The immune system may surround the bacteria in structures called tubercles.

• Can cause:

  • Severe coughing

  • Bloody sputum

  • Lung damage

• TB can spread from the lungs to other parts of the body.

• Antibiotics can treat TB, but treatment must be continued for a long period

Leprosy

Causes

• Mycobacterium leprae

• Mycobacterium lepromatosis

Characteristics

• Has existed for thousands of years and is mentioned in historical and religious texts.

• Causes inflammation and damage to the:

  • Skin

  • Peripheral nerves

• Can produce nodules and tissue damage.

• Historically, infected individuals were often isolated or quarantined.

• Still exists today but responds well to appropriate antibiotic treatment.

Bubonic Plague

Cause

• Yersinia pestis

Characteristics

• Caused massive outbreaks throughout history, including the Black Death, which killed a large portion of Europe's population.

• Causes swollen lymph nodes called buboes.

• The disease can progress rapidly and become fatal without treatment.

Transmission

• Primarily transmitted by infected fleas, often associated with rodents.

Clostridium Diseases

Tetanus, Gangrene, Botulism

Tetanus

Cause: Clostridium tetani

• Often enters the body through contaminated wounds, such as puncture wounds.

• Causes severe muscle contractions and rigidity.

• Can result in lockjaw.

• Causes rigid paralysis.

Gangrene

Cause: Commonly Clostridium perfringens

• Occurs when tissue loses adequate blood supply and oxygen.

• Risk factors can include:

  • Severe wounds

  • Diabetes

  • Frostbite

  • Poor circulation

• Bacteria thrive in damaged, oxygen-poor tissue.

• Can cause severe tissue death (necrosis).

Botulism

Cause: Clostridium botulinum

• A potentially deadly form of food poisoning.

• The bacterial toxin causes flaccid paralysis.

• Muscles become unable to contract.

• Particularly dangerous if respiratory muscles are affected.

• Can occur in improperly prepared or preserved foods.

• Botox uses a purified form of botulinum toxin in controlled medical/cosmetic applications.