BIO 111 U4 U5

(U4M1) 1. What is a virus? What are the parts of a virus?

A virus is a tiny infectious agent consisting of genetic material (DNA or RNA) enclosed in a protein coat, and sometimes surrounded by a lipid envelope. Two Parts:

1. Genetic Material (DNA or RNA)

2. Protein Capsid (surrounds genetic material) • Sometimes present: Envelope (remnants of plasma membrane of a previously infected cell which aids entry to new cells for infection)

(U4M1)2. Describe the general structure of Influenza. What is the genetic material? What are the "spikes"? What do the "spikes" do for the influenza virus? What specific spikes define influenza A?

Influenza virus has a simple structure with genetic material made of RNA enclosed in a protein coat. The "spikes" on its surface, composed of hemagglutinin (HA) and neuraminidase (NA) proteins, facilitate attachment to and entry into host cells. Influenza A is defined by specific types of HA and NA spikes.

RNA Genetic Material • Envelope Present • Glycoprotein "spikes" that determine strain • Influenza A: • H Spikes: finds receptors on host cell • N Spikes: Breaks down mucous membranes in respiratory tract to make penetrating host cell easier

(U4M1) 3. How are influenza viruses named?

1. Host (if not human)

2. Type (A or B)

3. Strain, which H/N Spikes present

4. Year of Isolation Example: A/H1N1/Michigan/2015

(U4M1) 4. Why are viruses not considered to be alive?

Viruses cannot process energy and rely on host cells to make copies of their genetic material. Exception: Giant Viruses can make their own proteins

(U4M1) 5. What are the steps in a viral life cycle? How does the lytic cycle differ from the lysogenic cycle?

1. Attachment: Virus binds to host cell surface.

2. Penetration: Virus enters host cell.

3. Biosynthesis: Virus replicates genetic material and produces viral components.

4. Maturation: Viral components assemble into new virus particles.

5. Release: New virus particles are released from host cell to infect other cells.

LYTIC CYCLE • Virus begins biosynthesis/replication immediately • Host cell is broken apart to release new virus capsids • Influenza, common cold LYSOGENIC CYCLE

• Viral DNA integrates into host genome after penetration • Virus remains inactive or latent, host cells divide with viral DNA integrated in genome • Sickness occurs long after initial infection (HIV)

(U4M1) 6. What are RNA viruses? Why do RNA viruses evolve quickly?

RNA viruses are viruses whose genetic material is composed of RNA instead of DNA. They evolve quickly due to several factors. RNA viruses have rapid evolution due to high mutation rates, short replication cycles, genetic recombination, and selective pressures.

(U4M1) 7. What are retroviruses and what enzymes do they need in order to reproduce?

Retroviruses are a type of RNA virus that can convert their RNA into DNA using an enzyme called reverse transcriptase. This DNA is then integrated into the host cell's genome, allowing the virus to replicate along with the host cell's DNA.

(U4M1) 8. What cells in your body does influenza infect?

Infects respiratory epithelial cells, replication begins immediately, leading to inflammation

(U4M1) 9. How does your body respond to influenza infection?

Body responds by sending immune cells which release cytokines, a chemical your body interprets as a warning signal of infection, leading to more inflammation

(U4M1) 10. What are the symptoms of influenza infection?

Cough, fever, chills, aches and pains, headache, loss of appetite, nausea −Mostly caused by immune response, not the Influenza virus itself

(U4M2) 1. What is the definition of evolution?

A change in allele frequencies in a population over time

(U4M2) 2. What are the observations that Charles Darwin made during his voyage on the HMS Beagle that led him to develop his theory of Evolution by Natural Selection?

1. Island species have a strong resemblance to species on nearby mainland

2. Extant (living) species have a strong resemblance to extinct species discovered as fossils

(U4M2) 3. What is the Theory of Evolution by Natural Selection?

• Similarities between island/mainland species and living/fossil species could not be coincidence • Overtime species that colonize new habitats gradually change to form new, but similar, species

(U4M2) 4. What is the difference between evolution and natural selection? Are these interchangeable terms?

Evolution is the overall process of species change over time.

Natural selection is a specific mechanism within evolution where organisms with advantageous traits are more likely to survive and reproduce.

(U4M2) 5. What are Darwin's postulates/conditions for natural selection to lead to evolution?

1. There must be variation in a trait

2. The trait must be heritable from parent to offspring

3. The trait must lead to differential reproductive success

(U4M2) 6. Be able to describe the examples of natural selection discussed in class (lab experiments, field observations, and hypothetical scenarios).

• Peppered moths: Dark moths became more common in polluted areas during the Industrial Revolution to better blend with soot-covered trees, avoiding predators.

• Antibiotic resistance in bacteria: Overuse of antibiotics has led to the selection of bacteria resistant to them, observed in various infections.

• Darwin's finches: Different beak shapes evolved in finches to match different food sources on the Galápagos Islands, showing adaptation through natural selection.

(U4M2) 7. Be able to describe the three major types of selection (directional, stabilizing, disruptive).

Directional: • Individuals with one extreme from the range of variation will have higher fitness • Ex: Farmers only allow turkeys with the biggest breasts to mate

Stabilizing: • Individuals with intermediate genotypes will have higher fitness • Ex: Baby birth weight

Disruptive: Individuals with extreme phenotypes experience the highest fitness, and those with intermediate phenotypes have the lowest Individuals with extreme phenotypes experience the highest fitness, and those with intermediate phenotypes have the lowest

(U4M2) 8. What are mutations? How can they lead to evolution? Under what circumstances will mutations spread in a population?

• Mutations: Changes in an organism's DNA sequence.

• Evolution: Mutations introduce genetic variation, which can lead to adaptations over time.

• Spread: Mutations spread in a population when they confer a survival or reproductive advantage, or if they are neutral and not harmful.

(U4M2) 9. What are the major pieces of evidence for evolution? Know the examples discussed in lecture.

1. Fossil Record: Physical record of organisms that lived in the past

2. Comparative Anatomy and Embryology: Growth, development, and body structures of major groups of organisms

3. Molecular Biology: DNA similarities

4. Laboratory and Field Experiments: Use of the scientific method to study evolutionary mechanisms

(U4M2) 10. What features of virus biology allow them to evolve quickly?

• High mutation rates: Viruses replicate rapidly with error-prone enzymes, leading to frequent mutations.

• Short generation times: Viruses have short replication cycles, allowing for rapid accumulation of mutations.

• Genetic recombination: Viruses can exchange genetic material through recombination, increasing genetic diversity.

• Selective pressures: Viruses face constant pressures from host immune systems and antiviral treatments, driving adaptation and evolution.

(U4M2) 11. What are antigens?

Spikes on virus capsid notify body that pathogen is present • Once identified, body knows exactly how to fight that virus if ever infected again in the future

(U4M2) 12. What is antigenic drift?

Small changes in surface spikes on virus makes it harder for immune system virus recognize it as a known pathogen (or make vaccines less effective) −Mutations caused by sloppy proofreading by copying enzymes

(U4M2) 13. What is antigenic shift?

Two forms of a virus infect the same cell, causing host cell to produce viral particles from both viruses, assembling a new strain with unique spikes

(U4M3) 1. What does your immune system do?

Protects your body from foreign pathogens −Viruses, bacteria, toxins, eukaryotic parasites

(U4M3) 2. What are your major immune system organs and what do they do?

• Lymph Nodes: Filter pathogens from lymph fluid

• Red Bone Marrow: Site of lymphocyte white blood cell production and (B-Cell) maturation

• Spleen: Filter blood

• Thymus: Site of T-Cell maturation

(U4M3) 3. How does your immune system recognize cells that are you vs. cells that are not you?What kind of cells are in charge of killing cells that are not you?

Correct Major Histocompatibility Complex (MHC) Glycoproteins must be present on plasma membrane of cell

• Natural Killer Cells: Kill cells not displaying correct MHC-I Glycoproteins

(U4M3) 4. Innate Immune System: a. What is the innate immune system? What are the pros and cons of this system? b. What major immune response is caused by the innate immune system? c. What are the three major branches of innate immunity and what do they do for you? d. What are the steps of the inflammatory response?

a. Innate Immune System: Definition: First line of defense against pathogens and foreign substances, non-specific and present from birth. Pros: Rapid response, always ready, initiates adaptive immunity. Cons: Lack of specificity, no long-term memory.

b. Major Immune Response: Innate Immunity's Main Action: Triggers inflammation in response to infection or tissue damage.

c. Three Major Branches of Innate Immunity: Physical Barriers: Skin, mucous membranes. Cellular Defenses: Phagocytes (e.g., macrophages, neutrophils), natural killer (NK) cells. Chemical Defenses: Antimicrobial proteins (e.g., complement system, interferons).

d. Steps of the Inflammatory Response:

Detection: Pathogens or tissue damage detected. Vasodilation and Increased Permeability: Blood vessels dilate, become leaky. Chemotaxis: Immune cells attracted to site of infection. Phagocytosis: Pathogens engulfed and destroyed. Tissue Repair: Healing process begins.

(U4M3) 5. Adaptive Immune System: a. What is the adaptive immune system? What are the pros and cons of this system? b. What are the steps in an adaptive immune response? What kinds of cells are involved? What is the role of each cell type?

a. Adaptive Immune System:

• Definition: The adaptive immune system is the body's defense mechanism that responds to specific pathogens.

• Pros: Provides long-term immunity and memory against pathogens.

• Cons: Slower response time compared to the innate immune system.

b. Steps in Adaptive Immune Response:

1. Recognition: Antigen-presenting cells (e.g., dendritic cells) recognize and present antigens to T cells.

2. Activation: T cells (helper T cells and cytotoxic T cells) become activated and coordinate the immune response.

3. Antibody Production: B cells differentiate into plasma cells, producing antibodies specific to the antigen.

4. Elimination: Antibodies and cytotoxic T cells target and eliminate pathogens.

(U4M3) 6. Vaccines: a. What is a vaccine? b. How do vaccines work at an individual level? c. How do vaccines work at the population level? d. How were modern smallpox vaccines developed? e. What are some diseases that were eradicated by vaccine programs? f. Why is the measles such a problematic disease to contract? g. What are the types of vaccines? Know an example disease for each type of vaccine. h. Why do you have to get a flu shot every year? Why are flu shots sometimes not as effective in a given year? i. How do the COVID-19 vaccines work?

a. Vaccine: A substance that stimulates the immune system to produce immunity to a specific disease, typically by introducing a weakened or killed form of the pathogen.

b. Individual level: Vaccines prompt the immune system to produce antibodies against the pathogen, providing immunity if exposed to the disease in the future.

c. Population level: Vaccination creates herd immunity, protecting individuals who cannot be vaccinated and reducing the spread of disease within communities.

d. Smallpox vaccines: Modern smallpox vaccines were developed using weakened strains of the virus, leading to immunity without causing severe illness.

e. Eradicated diseases: Diseases eradicated by vaccines include smallpox and rinderpest.

f. Measles: Measles is problematic due to its high contagiousness and potential for severe complications, especially in unvaccinated populations.

g. Types of vaccines: Examples include live attenuated (e.g., measles), inactivated (e.g., polio), subunit (e.g., hepatitis B), and mRNA vaccines (e.g., COVID-19).

h. Flu shots: Influenza viruses mutate frequently, requiring annual vaccination to match circulating strains. Effectiveness may vary due to strain changes.

i. COVID-19 vaccines: COVID-19 vaccines use mRNA technology to trigger an immune response against the virus's spike protein, preventing infection and severe illness.

(U5M1) 1. What is ecology?

The study of how organisms interact with each other and their environment

(U5M1) 2. What are the subfields of ecology and what are their major questions? Be able to remember the examples discussed in class.

ORGANISMAL ECOLOGY • The study of individual morphological, physiological, behavioral adaptations • How do individuals interact with each other and their physical environment?

ex) COMMUNICATION• Signal from one individualmodifies the behavior of arecipient individual• Sender: Individual making thesignal• Receiver: Individual respondingto signalSender ReceiverDecision/ResponseSignal (information)environment GROUND SQUIRRELS• Prey to rattlesnakes (whichcan see IR) and gophersnakes (which cannot seeIR)• Send heat to tail whenattacked by rattlesnake,but not when gophersnakes attack

POPULATION ECOLOGY • Study of the number and distribution of individual in a population over time • How and why does population size change over space and time?

ex) POPULATION • A group of interbreeding (or potentially interbreeding) individuals of same species in same area (at same time)

COMMUNITY ECOLOGY• Study of the nature of the interactions between different species in a community• How do species interact and what are the consequences?

All the populations of different species that interacting a certain area• Community Ecology: The study of how communities work−Species interactions−Community Structure−Community Dynamics

ECOSYSTEM ECOLOGY • Study of nutrient and energy movement among organisms and surrounding atmosphere/soil/water • How does energy flow and how to nutrients cycle through the local environment? ECOSYSTEM• Community of interacting species present in a region,along with the abiotic components of the soil, water,and atmosphere• Everything is linked to everything else by flow of energy and nutrients

EX) ENERGY FLOW • Energy flows through ecosystems from source (the sun) through producers then consumers

(U5M1) 3. What is climate and what characterizes it?

CLIMATE • Average weather patterns in a given area over time −Range of values does not change quickly • Characterized by temperature and precipitation

(U5M1) 4. How does the earth's axis influence climate?

Earth's axis changes sun angle by latitude, which alters amount of solar radiation per unit area

(U5M1) 5. What is weather? Are weather and climate the same thing?

• Day-to-day temperature and precipitation • Changes quickly

Weather refers to short-term atmospheric conditions, while climate refers to long-term patterns of weather in a region.

(U5M1) 6. What is the biosphere? What are biomes? What characteristics define a biome?

BIOSPHERE • The sum of the locations where life exists on earth • Location and climate heavily influence what kinds of life are present in different parts of the planet

BIOMES • A type of ecosystem found around globe with a specific range of temperature and precipitation

Characteristics defining a biome include climate, vegetation types, biodiversity, and geographical features.

(U5M1) 7. What is the greenhouse effect and what causes it?

GREENHOUSE EFFECT • Gases in atmosphere block heat energy reflected off earth's surface from going back into space −Increases earth's temperature

The greenhouse effect is primarily caused by certain gases in Earth's atmosphere, such as carbon dioxide (CO2), methane (CH4), and water vapor (H2O), which absorb and trap heat from the sun.

(U5M1) 8. What are the major greenhouse gasses?

• Carbon dioxide (CO2)

• Methane (CH4)

• Nitrous oxide (N2O)

• Water vapor (H2O)

(U5M1) 9. What has happened to atmospheric CO2 and global temperature since 1950?

• CO2 levels ↑

• Global temperature ↑

(U5M1) 10. What is global climate change and what are some pieces of evidence that show that the climate is changing? Why is climate change worse at the poles?

Warming temperatures alter normal weather patterns, leading to abnormal precipitation, droughts, floods, and, over time, changed climates

Evidence (Strongest to least)

• Heat waves -coastal flooding -extreme participation events

• severe droughts

worse at poles because of polar amplification Polar amplification refers to the phenomenon where the polar regions experience greater warming compared to the rest of the planet due to various feedback mechanisms, such as melting ice and reduced reflectivity of snow and ice (albedo effect).

(U5M1) 11. What kinds of weather and climate disasters are increasing due to climate change?

abnormal precipitation, droughts, floods, and, over time, changed climates

(U5M2) 1. Understand the structure of atoms, including the position and charge of the subatomic particles.

ATOM • Electrons −Negative charge, no mass* • Protons −Positive charge • Neutrons −Neutral charge

(U5M2) 2. Understand what an electron shell is and how electron position within those shells influences atom stability (e.g., how willing they are to make chemical bonds).

ELECTRON SHELLS • Electron shells—areas that surround the nucleus • Each shell can hold a specific number of electrons −The innermost shell can hold two electrons −Outer shells can hold eight electrons • Atoms are most stable when their outer shell is full

• Electrons move around the nucleus in electron shells • The chemical characteristics of an atom depend upon the number of electrons in its outermost shell

(U5M2) 3. Why are life forms on earth composed of carbon?

carbon has unique properties that make it highly versatile and suitable for building complex molecules essential for life, such as proteins, carbohydrates, lipids, and nucleic acids.

(U5M2) 4. Chemical Bonds: a. What is a chemical bond? What is formed by two or more atoms bonding?

CHEMICAL BONDS • Atoms are attracted to each other to find electrons to fill their outer shell • When atoms share, lose, or gain electrons a chemical bond is created • When two or more atoms are joined together by chemical bonds, the group of atoms is called a molecule

(U5M2) 5. What is the carbon cycle? How has fossil fuel use thrown the carbon cycle off balance?

• Fossil Fuels: Formed from plant/animal remains exposed to high pressures and temperatures • More carbon pumped into atmosphere than can be fixed by photosynthetic organisms

(U5M2) 6. What kind of energy is light? How is light energy packaged?

LIGHT ENERGY • Kinetic energy • Travels in waves • Made of energy packets called photons, which can carry different amounts of energy • Length of wave (wavelength) is the amount of energy the photon contains • Plant pigments absorb different wavelengths for photosynthesis

(U5M2) 7. Photosynthesis: a. What is the chemical formula? b. In what part of the chloroplast does each reaction of photosynthesis happen? c. How does energy move through chlorophyll molecules? d. Describe, in detail, the four steps of the light ("photo") reactions or photosynthesis: what happens, where it happens, what is used and produced in each step. e. Describe, in detail, the three steps of the dark ("synthesis") reactions, or Calvin Cycle: What happens, where it happens, what is used and produced in each step.

a. Chemical formula: 6CO2 + 6H2O → C6H12O6 + 6O2

b. Chloroplast parts: Light reactions occur in the thylakoid membranes, while the Calvin Cycle (dark reactions) occur in the stroma.

c. Energy transfer: Energy moves through chlorophyll molecules via absorption of photons, which excite electrons to higher energy levels, initiating the photosynthetic process.

d. Light reactions:

1. Photon Absorption: Light energy is absorbed by chlorophyll in the thylakoid membranes, exciting electrons.

2. Electron Transport: Excited electrons move through the electron transport chain, releasing energy used to pump protons across the thylakoid membrane.

3. ATP Synthesis: Protons flowing back through ATP synthase generate ATP.

4. NADPH Production: NADP+ picks up electrons and H+ ions to form NADPH, which is used in the Calvin Cycle.

e. Dark reactions (Calvin Cycle):

1. Carbon Fixation: CO2 combines with RuBP (ribulose bisphosphate) using the enzyme rubisco, forming 3-phosphoglycerate (3-PGA).

2. Reduction: ATP and NADPH from the light reactions are used to convert 3-PGA into glyceraldehyde-3-phosphate (G3P).

3. Regeneration of RuBP: Some G3P molecules are used to regenerate RuBP, while others are used to produce glucose and other organic compounds.

(U5M3) 1. How has extinction rate changed over the last 50 years?

ANTHROPOCENE MASS EXTINCTION EVENT • Currently ongoing • Cause: Human Activity • 99% of modern species extinctions are linked to human activity • Facing Extinction: −40% of amphibians −14% of birds −25% of mammals

(U5M3) 2. Disease: a. What are some causes? b. How does human activity make disease spread worse? c. How does climate change make disease spread worse?

DISEASE • Causes: −Bacteria −Fungi −Viruses −Single-celled eukaryotic organisms

• Human activity spreads diseases between wildlife populations

• As it gets warmer further north mosquitoes, sand flies, kissing bugs and other disease vectors become common

(U5M3) 3. Why are invasive species helped by climate change?

• Invasive species are better suited to unpredictable or changing environments than natives −Climate change is their ideal scenario

(U5M3) 4. What is a biome? How will biomes change with climate change? What are the consequences of biome changes for wildlife?

• Biome: Large ecological area with distinct climate and life forms.

• Climate change: Biomes expected to shift, expand, contract, or disappear.

• Consequences: Wildlife faces habitat loss, competition, and disrupted ecological relationships. Biodiversity declines.

(U5M3) 5. What are the impacts on humans of climate change?

• Droughts and extreme weather lead to agricultural losses −Fires lead to economic losses and poor air quality • Unstable ecosystems can impact human safety and quality of life • Diseases will become more common in humans and livestock

(U5M3) 6. What are ecosystem services? Know examples.

• Benefits to humans that arise from a healthily functioning ecosystem

EX) Pollination Pest Control Erosion Control

(U5M3) 7. What is an ecological footprint? What is a carbon footprint? What contributes to your ecological and carbon footprints?

• Ecological Footprint: How much land is required to support your lifestyle? −Food, Fuel, Clothes, Electronic Devices

• Carbon Footprint: How much carbon is produced to maintain your lifestyle?

(U5M3) 8. What is the single most important act a person can take to try to stop climate change?

Vote for politicians who want to stop climate change