System: object or many objects that may be studied

• Open system: energy and matter can enter and leave (eg. open window)

• Closed system: energy can enter and leave, but matter can't (eg. closed window)

• Earth is a closed system -> no matter leaves the biosphere

Systems Organized Smallest to Largest

Ecology: study of living (biotic) factors and non-living (abiotic) factors and how they interact

Biosphere: all life on Earth (atmosphere + hydrosphere + lithosphere)

• Characterized by interdependent and interactive ecosystems

• Closed system -> Earth relies on itself for matter

• Productivity of Biosphere: determined by efficient use of incoming energy

  • Plants capture light -> converts it to organic compounds -> energy captured in molecules -> measured in energy/area/year (d/m2/yr)

• Productivity of Biomass: determined by harvested and dried plants

  • Measured as (g/m2/yr)

Lithosphere: all crust, mantle, and rocky parts of the Earth (ground)

• Dependent on interactions of biotic and abiotic sources (LOOK AT CHART)

• 3 key biotic processes for cycling matter on the earth

1. Photosynthesis

2. Cellular respiration

3. Decomposition 

Photosynthesis: process by which plants, algae, and some bacterias use the sun’s energy to convert CO2 into carbohydrates (sugar/starches) 

• Called producers

• Light energy + water + carbon dioxide -> carbohydrates + oxygen

Cellular Respiration: process by which animals, plants, and some organisms use carbohydrates (from photosynthesis) to create useable energy (ATP) 

• Called consumers

• Carbohydrates + oxygen -> carbon dioxide + water + energy

Chemosynthesis: synthesizes food from inorganic matter without light

• Atmosphere used to be a “reducing atmosphere” -> was largely hydro-based and had no cyanobacteria (ESSENTIAL FOR PHOTOSYNTHESIS) 

  • Appearance of cyanobacteria led to reactions producing oxygen -> oxygen levels in ocean and atmosphere rose

  • Today’s atmosphere is called “oxidizing atmosphere” 

• Organisms deep in the ocean have no access to sunlight -> can’t photosynthesize -> can’t produce food

• Uses chemosynthesis to produce food instead 

  • Hydrogen sulfide molecules split and capture chemical energy in bond -> produces sulfur instead of oxygen   

  • Occurs in extreme conditions (heat, cold, or acidic environments)  

• Change from reducing atmosphere to oxidizing atmosphere occurred 2.5 billion yrs ago 

  • Scientists determined this by first signs of rock layers of iron oxides -> iron + free oxygen = black band

• Biggest effect on the atmosphere is it's interaction with sunlight

  • When light enters Earth:

1. 30% of incoming energy is reflected (albedo = reflectivity of a surface) 

2. 19% is absorbed by clouds in the atmosphere

3. 51% is absorbed by land and oceans 

• ONLY 1-2% used for photosynthesis 

Producer: a self feeder (autotroph) that convert inorganic matter into organic matter using light (eg. plants)

Chemosynthesizer: form of self feeder that converts inorganic matter into other forms of inorganic matter to extract energy from chemical bonds  (eg. nitrogen fixing bacteria)

Consumer: an other-feeder (heterotroph) that consumes either autotrophs or heterotrophs for energy 

• Primary consumer: consume plants (also called herbivores or can be referred to as an omnivore) 

• Secondary consumers: consumer herbivores (also called carnivores)

• Tertiary consumers: consume the secondary consumers 

• Quaternary consumers: consume the tertiary consumers 

• Top carnivores: final consumer in the chain 

• SECONDARY, TERTIARY, QUATERNARY ALL CARNIVORES 

Decomposers: obtains nutrition from breaking down dead organic matter (aka detritus) 

**Energy transfer in ecosystems can be represented as a chain, web, pyramid 

Trophic level: feeding level where energy and matter is transferred

• Identified by number of energy transfers that have taken place from the sun (count)  

  • Eg. producer - T1, consumer 1 - T2, etc. 

• Rule of 10: only 10% of the energy from the previous trophic level is transferred to the next

  • 90% of the rest of the energy is waste material

Law of Thermodynamics: explains principles of energy transfer

1. Energy cannot be created or destroyed but it can be converted from one form to another

2. During an energy conversion some useful energy is lost as heat

• Laws apply to food chains, food webs, and food pyramids

Food Chains

• Linear depiction of energy transfer in an ecosystem 

• Grazer food chains: chains that start with a producer

  • 1 -> 2 -> 3 -> 4 -> 5

  • Grass -> grasshopper -> mouse -> snake -> hawk

  • Producer -> primary consumer -> secondary consumer -> tertiary consumer -> quaternary consumer 

Food Webs: interactions of several food chains

• Shows diversity of food sources that members of a community may rely on 

• Arrow points to where the energy is transferred

Food Pyramids / Ecological Pyramids:  depict energy transfer while moving through trophic levels and depict energy loss 

Reasons for energy loss:

• Organism dies without being eaten

• Some parts of organisms are not eaten (eg. bones, teeth, hair)

• Some parts of organisms are eaten but not digested -> goes out through bodily functions

• Lost through heat from cellular respiration

3 Types of Pyramids 

1. Pyramid of Numbers: depicts the number of organisms at one trophic level needed to support the organisms at the next trophic level

• Least accurate at depicting energy loss during transfer

2. Pyramid of Biomass: depicts the mass of the organisms at each trophic level

• Biomass: dehydrated organic tissue of the organisms at a level

• 2nd most accurate at depicting the energy loss during transfer 

3. Pyramid of Energy: depicts the energy of the biomass at each trophic level

• Energy is calculated with the use of a calorimeter which combusts tissue to determine the number of calories (J) involved in the matter 

• Most accurately depicts energy loss in matter transfer through trophic levels 

Biological Amplification / Bioaccumulation: the buildup of toxic chemicals in organisms as the chemical moves up the food chain

• The greater the number of trophic levels within a food chain = greater the amplification of the toxin

• Animals at high trophic levels are at the greatest risk

• Primary consumer eats toxins -> secondary consumer eats primary consumer and receive more of the toxins -> top carnivore consumes the most toxins at the end 

• Sources: Industrial waste (mercury, dioxins) and pesticides (DDT) 

CHAPTER 2

• Chemicals are recycled between organic matter and abiotic reservoirs 

• Sun supplies closed systems (eg. ecosystems) with energy

  • Earth’s interior supplies energy for chemosynthetic systems 

• Life depends on recycling of chemicals

  • Chemicals pass back and forth between biotic (organic matter) and abiotic (non-living) components of ecosystems

  • Routes that these chemicals take through biotic and abiotic components of the biosphere  -> called biogeochemical cycles

Biogeochemical Cycles: show the flow of an element through living tissue and the physical environment of an ecosystem 

• Cycles are crucial -> only way that materials can be recycled once organisms die

• Substances temporarily stored in nutrient reservoirs 

  • Nutrient Reservoir: A component of the biosphere in which nutrients temporarily accumulate. 

  • eg.) an organism, soil, water, the air, rocks, or fossil fuels. 

  • It is anywhere beneficial chemicals are stored for a length of time

  • eg.) plants take carbon from the air and build chemicals such as cellulose and starch where the carbon is “stored” until the plant is decomposed or eaten

  • eg.) Nutrient Reservoir Chart -> 

Rapid Cycling: carbon (or element) stored for a short time

• Rapid Cycling (of nutrients): quick movement of nutrients through nutrient reservoirs, such as organisms, soil, air, and water

• eg.) Carbon stored in a plant for a short period of time b/c it dies quickly or is eaten

Slow Cycling: carbons (or element) stored for long periods

• Slow cycling (of matter/nutrients): when nutrients stay in nutrient reservoirs and are unavailable to organisms for long periods of time (eg. fossil fuels in deposits)

• Ancient cedar can live for hundreds of years

• Plants can become fossil fuels -> carbon can be stored in the ground for millions of years

Water: a polar molecule with one positive molecule (hydrogen end) and one negative molecule (oxygen end)

• Water moves through the biosphere in a global cycle carrying w/ it essential nutrients

• Vital to all life -> unique substance w/ unique properties

  • Absorbs and releases thermal energy and moderate temp fluctuations 

  • Makes up 70% of human tissue and 80+% of a cell’s mass

  • Supplies hydrogen atoms to producers during photosynthesis and oxygen atoms during cellular respiration

  • Reactant in some metabolic activities and a product in others

Unique Properties of Water:

1. Universal Solvent: water is polar so it can dissolve some molecular and ionic compounds

• Necessary chemical compounds required by living cells are absorbed through diffusion from water

• eg.) oxygen, CO2, and electrolytes in blood

2. High boiling and freezing points: Water exists in all three states in the biosphere

• Can remain as a liquid over fairly large temp range (0-100 C) -> allows transport to happen over great temp range

3. Liquid water more dense than solid water: Water expands when frozen causing it to be less dense and float on liquid water

• Water is at its most dense at 4 degrees celsius

• Allows for aquatic ecosystems to exist in cold climates and allows for the replenishing of nutrients in lakes during spring and fall “turnover”

4. Hydrogen Bonding: Opposite charges of water molecules attract to one another causing a weak type of bonding called cohesion or adhesion

• Cohesion: attraction of one water molecule to another 

  • Causes surface tension

• Adhesion: attraction of water molecules to other molecules

  • eg.) water molecules attracted to xylem cells -> water climbs up against gravity -> brings water from roots to leaves

5. High heat capacity: stores large amount of heat energy

• Hard to get molecules to move apart due to hydrogen bond

• Large amount of energy needed to make water molecules gain kinetic energy

  • Lets water absorb and hold large amounts of energy w/o dramatically changing temp 

• eg.) hot day -> sandy beach heats up more and faster than the ocean 

• Water moderates the temp of the land around it

  • Absorbs heat when it's hot

  • Releases heat when it's cooler

2 Major Functions Performed by the Water Cycle

• Limited amount of water in the biosphere -> water must cycle

1. Distribution: water is distributed by weather patterns and other processes to all parts of the biosphere

• As water is distributed -> energy (heat) and other nutrients dissolved in the water are also redistributed

2. Cleaning: evaporation cleans the water by the process of distillation

Global water cycle is driven by heat from the sun

• 3 Major Processes Driven by Heat from the Sun: 

  • Precipitation

  • Transpiration

  • Evaporation

• Processes continuously move water between land, oceans, and the atmosphere

Hydrological Cycle: how water moves through the biosphere 

• Water reaches the Earth as precipitation -> can remain on the surface as standing water (lakes) or form rivers which lead to oceans

• Water enters the soil to form groundwater -> seeps to the surface forming springs or entering lakes

• Water off of the surface evaporates after absorbing energy from the sun -> condenses to form water droplets suspended in clouds

  • Temp drops -> clouds release water as precipitation -> cycle continues

• Plants and animals return water into the cycle through cellular respiration, decay, and transpiration

  • Transpiration: loss of water through plant leaves

Acid Deposition: occurs when rain, snow, or sleet becomes acidified

• Fossil fuels and metal ores are burned (or when combustion occurs) -> sulfur dioxide and nitrous oxides are produced and enter the atmosphere

• Gasses combine w/ water to form acids which returns to the surface in the form of either:

  • Snow and rain (WET DEPOSITION)

  • Falls to the surface in a dry state and only form acids when combining w/ surface moisture (DRY DEPOSITION)

Effects of Acid Deposition:

• Increases the acidity of surface water affecting aquatic plants and animals

• Leaching into ground water

• Destroys terrestrial vegetation and erodes statues, monuments, etc. 

Solutions

• Installs scrubbers which remove harmful emissions

• Add lime to lakes to help neutralize the water (AB lakes are naturally basic)

• Improves smelters which release the oxides 

Carbon and Oxygen Cycle

• Carbon key element of living things

• Organic carbon is stored in the bodies of living organisms

Rapid Cycling of Carbon: Plants take in CO2 from the air and during photosynthesis they convert the carbon into useable plant products (eg. starch, cellulose, sugar)

• During process of cellular respiration -> carbon products are used up for energy and growth -> carbon is returned back into the atmosphere as CO2

• Oxygen is used in cellular respiration -> combines w/ carbon to form CO2 gas -> which returns carbon to the environment 

• Organisms die -> decomposition returns the carbon stored in tissues back into the cycle in an inorganic form

  • eg.) Fall -> plants release carbon in form of discarded leaves, rotting wood releases carbon, decaying carcass releases carbon into air and soil

Slow Cycling of Carbon: majority of inorganic carbon is stored in the ocean as dissolved CO2 in the Earth’s crust as sedimentary rock or in the atmosphere

• Limestone (calcium carbonate) stores billions of tons of carbon

• 48% of CO2 generated is absorbed by oceans

• eg.) Phytoplanktons photosynthesize -> they store carbon like any other plant

  • They die -> fall to the bottom of the ocean -> carbon contained in their tissues becomes part of the ocean sediment -> gets trapped for millions of years as limestone or fossil fuels

  • Only gets released when rock weathers or fossil fuels are burned

Summary of Rapid Cycling and Slow Cycling of Carbon

Summary of the Carbon Cycle

Carbon Sinks: anything with the ability to absorb CO2 from the atmosphere

• eg.) Carbon can be stored in large trees and is only released when the tree dies or is burned

• eg.) Forests, oceans

• Don't store carbon for as long nutrient reservoirs 

Global Warming and the Greenhouse Effect: the change in the net radiation budget caused by an increase in human generated greenhouse gasses

• Net Radiation Budget: difference between incoming and outgoing solar radiation

• Greenhouse effect is necessary -> adds 33 degrees celcius to our average temp

• Human activities enhance the effect -> causing it to be bad / harmful

  • Rate of climate change is concerning -> since last ice age average global temp has risen by 4.5 degrees celsius

• CO2 contributes to the green house effect -> leads to global climate change

  • Burning forests and fossil fuels -> humans release much of the carbon that would be held in carbon sinks and otherwise slowly released 

Effects on Global Warming

• Predicted that if temps rise by the same amount over the next 5 decades -> trees, shrubs, crops, and wildlife may be unable to adapt in such a short period of time

• Rapid climate change places stress on a cities natural resources such as air, water, cultivated land, and forest

• eg.) climate change thawing permafrost and melting icecaps -> buildings collapse and flood coastal cities

The Sulfur Cycle

• Sulfur is used by living things in production of proteins, amino acids, and vitamins

• Used by bacteria in chemosynthesis

• Plants need sulfur in the form of SULFATE for proper growth

Rapid Cycling of Sulfur

• Sulfates from atmosphere are deposited in the soil -> bacteria changes the sulfates to various forms that are usable by dif organisms

• Plants take up various sulfur compounds and incorporate them into their tissue

  • Plants die -> decomposing bacteria releases the sulfur back into the atmosphere

Slow Cycling of Sulfur

• Sulfur is changed to inorganic forms -> get stored in rock sediments (gypsum) and fossil fuel reserves (coal and sour gas)

• Sulfur can be trapped for years -> until it's released by weathering, hot springs, volcanic activity, or the burning of fossil fuels

• Sulfur released in the form of sulfur dioxide gas -> reacts with water in atmosphere to form sulfurous acid (H2SO3)

Nitrogen Cycle - BACTERIA BASED

• Life depends on the cycling of nitrogen

• Nitrogen is necessary to make proteins and DNA

• Atmospheric nitrogen is abundant -> Nitrogen gas is useless to living organisms

  • Nitrogen gas must be converted into nitrate ion before being used by plants

Nitrogen fixation: converts atmospheric nitrogen into nitrate ions by:

1. Lighting: causes nitrogen gas to react w/ oxygen in atmosphere to form nitrates

• Nitrates dissolve in water -> enter soil -> move into plants

• Plants use the nitrates to make DNA and amino acids 

• Plants are consumed by animals who then use the amino acids to make proteins they need

2. Bacteria located in nodules of legumes: (clovers, peas, soybeans, alfalfa)

• Convert nitrogen into nitrate ions

• Plant produces more nitrate than needed -> releases excess into soil

3. Farmers take advantage of the bacteria: incorporates one of these crops into the crop rotation

• Ensures there is a constant supply of nitrogen in the soil

• Certain crops needs certain nutrients -> cycling ensures crops aren't overusing specific nutrients in a certain area

Ammonification: decomposers break down nitrogen containing chemicals in waste and dead organisms into ammonia in the presence of oxygen 

• Ammonia can be converted into nitrites and then into nitrates by nitrogen fixing bacteria  

• WASTE -> AMMONIA -> NITRITE -> NITRATE -> ABSORBED BY PLANTS

Denitrification: When no oxygen is present bacteria can convert nitrates that are unused into atmospheric nitrogen

• Opposite of nitrification

• EXCESS NITRATES -> NITROGEN GAS

Phosphorus Cycle

• Key element in cell membranes, energy storage molecules (ATP) and in mammalian bone as calcium phosphate 

Slow Cycle: Involves the Earth’s Crust

• Phosphate ions in bedrock are soluble in water -> can be dissolved out of rock -> absorbed by plants and enter the food chain

• Phosphates eroded from rock can be carried from land to oceans -> absorbed by algae and enter the food chain

• Marine animals use phosphate to create bone and shell

  • Organisms die -> remains are deposited on the ocean floor -> phosphorus is returned -> marine cycle complete

Rapid Cycle: Involves living organisms

• Waste from living organisms (bone, teeth, cell membranes, etc.) containing phosphorus are broken down

  • Releases phosphorus into soil to be taken in by plants

  • Cycle repeats

Human Impact on Nitrogen and Phosphorus Cycles

• Nitrogen and phosphorus both essential plant nutrients -> serve as limiting factors for plant growth 

• Humans impact the nitrogen and phosphorus cycle -> add nutrients to ecosystems through:

  • Overuse of synthetic fertilizers

  • Large cattle operations -> deliver tonnes of nitrogenous wastes via urine

    • Phosphate and nitrogen rich cattle waste runoff into stream/lakes

  • Use of Phosphate containing chemicals like detergent  and soaps

Algae Blooms: mass amounts of algae

• Caused by extra nutrients added to ecosystems

• Nutrients leech into nearby water bodies -> promotes uncontrolled growth of aquatic plants and algae

•  Eutrophication: accumulation of nutrients in lakes or other bodies of water

  • Algal Blooms are dangerous to aquatic ecosystems 

  • Ecosystem uses up all the nutrients -> algae that grew dies -> decomposers use up oxygen as they decompose dead plants -> use up all oxygen in body of water

  • Leads to death of aquatic animals such as fish / insects

Other Effects of Using Fertilizers

• Soil converts nitrogen in fertilizer into nitrates -> increases the amount nitric acid in the soil -> increases soil acidity -> affects food production

• Accumulation of nitrates in water -> convert into nitrites which is a competitive inhibitor w/ oxygen for hemoglobin

  • Esp dangerous for infant who don't have high stomach acidity needed to destroy the bacteria that do the conversion

Biosphere: open system

• Constantly has energy coming in (sunlight) and energy leaving (heat)

• Humans can shoot things (matter) out into space

  • Meteorites can enter Earth

Productivity: the rate at which organisms produce new biomass

• Rate at which an ecosystems producers capture and store energy within organic compounds over a certain length of time

• Measured in energy per area, per year (J/m2/a) 

  • OR biomass of vegetation added to an ecosystem per area, per year (g/m2/a)

• Most productive ecosystem on Earth: algal beds and reefs

• Least productive ecosystems on Earth: extreme desert, rock, sand, or ice

Factors influencing productivity in ecosystems

1. Amount of solar radiation (light and heat)

2. Number of producers present in the ecosystem

3. Amount of rainfall the system receives

Gaia Hypothesis: the biosphere acts as a self regulating organism, maintaining a balance of environmental conditions

• Life itself helps maintain these conditions

• Without life, CO2 and oxygen levels would be different

  • Early life influenced Earth's atmosphere by contributing to creation of oxygen -> w/o it there wouldn't be any oxygen, just high levels of CO2 

Stromatolites: Fossilized sedimentary structure formed from ancient bacteria

• Iron bands present in stromatolites provides evidence of oxygen formation in Earth’s past

  • Earth used to not have oxygen

UNIT C: PHOTOSYNTHESIS AND CELLULAR RESPIRATION

CHAPTER 5.1 

Energy Activities in cells involve:

• Photosynthesis in plant cells

• Cellular respiration in the cells of all living things 

• One form of energy is converted to another in both processes 

Cellular Respiration: Food is “oxidized” in mitochondria of the cells to release energy

• C6H12O6(aq) + 6 O2(g) -> 6 CO2(g) + 6 H2O(l) + energy

• Energy released used to produce ATP (adenosine triphosphate)

ATP Provides Energy for all Cellular Activities:

• Active transport

• Biochemical synthesis

• 5 Cytoplasmic streaming

• Movement of chromosomes

• Phagocytosis

• Cell motility

• Muscle contraction

• Heat production

Energy Storage and Transformation:

• ATP: cells basic unit of energy storage and usage 

  • It's a form of chemical potential energy

• ADP (adenosine diphosphate): lower form of chemical potential energy than ATP

• ADENINE + RIBOSE = ADENOSINE

Phosphorylation: addition of one or more phosphates to a molecule

• Requires energy input

• ADP + P + energy -> ATP 

  • P = Phosphate ion

De-phosphorylation: removal of one or more phosphate from a molecule

• Energy is released 

• ATP -> ADP + P + energy

• Energy is now available for cellular activity

Relation Between Phosphorylation and Dephosphorylation

1. ATP and ADP cycled through the cell

2. ADP is phosphorylated during cellular respiration -> produces ATP

3. ATP used in the cell to do work

4. Work releases ADP to go back to mitochondria to be phosphorylated again

Electron Transport: process of which production of ATP by phosphorylation occurs through

• Purpose of cellular respiration in cells -> to make electrons available from food molecules for electron transport

• Electrons are passed between series of acceptor molecules in mitochondria 

  • Generates the energy to produce ATP

  • Acceptor: a molecule that receives or accepts electrons from another molecule

Photosynthesis: plants use sunlight to synthesize sugar from CO2 and water

• 6 CO2(g) + 6 H2O(l) + energy -> C6H12O6(aq) + 6 O2(g) 

• Glucose produced -> used by plants for energy to produce molecules for growth, etc.

  • Plant may be eaten by animal

• Occurs within chloroplasts of plant cells

  • Chlorophyll: green pigment in chloroplasts that trap sunlight energy

Metabolic Pathways: sequence of reactions sped up by enzymes in living cells to support and sustain life functions

• Simplified equations of photosynthesis and cellular respiration -> show only the overall reactions

  • They are summaries of more complex sequences of reactions that are linked tgt

  • Sequences = metabolic pathways

• In metabolic pathway -> product of one step becomes starting material for next step

  • Each step catalyzed by an enzyme

  • Catalyst: a substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change

• Metabolism: refers to all chemical reactions that take place in an organism

Two Types of Metabolic Pathways:

1. Catabolic Pathways: breakdown complex substances into simpler substances 

• Releasing energy

• Complex -> simple + simple

2. Anabolic Pathways: synthesize complex molecules from simple starting material 

• Require energy

• Simple + simple -> complex

Oxidation and Reduction

• Compound is oxidized in chemical reaction -> it loses electrons (becomes more positive)

• Compound is reduced in chemical reaction -> it gains electrons (becomes more negative)

• COMPOUNDS CONTAIN MORE CHEMICAL ENERGY IN REDUCED FORM THAN IN OXIDIZED FORM 

• O.I.L R.I.G

  • Oxidation Is Loss (of electron)

  • Reduction Is Gain (of electron)

Reducing Power: the chemical potential energy available in molecules that are in their reduced form

Relation Between Photosynthesis and Cellular Respiration

• Both are related reactions in the biosphere -> need one to have the other

• Photosynthesis produces energy rich compounds and oxygen required for cellular respiration

• Cellular respiration provides energy for all life processes and releases raw materials for photosynthesis (eg. CO2) 

• Sun provides energy to operate both processes

CHAPTER 5.2 PHOTOSYNTHESIS

Mechanism of Photosynthesis 

• Takes place in 2 distinct phases in the chloroplasts of plant leaf cells:

1. Light dependent reactions: involves chemical reactions that NEED light energy to occur

2. Light independent reactions (carbon fixation): chemical reactions don't directly use light energy but need the products of light dependant reactions

• Structure of chloroplast and role of chlorophyll -> play vital role

Chloroplast

• Has a double membrane structure enclosing stacks of membranous discs

• Two parts inside chloroplast:

1. Stroma: a solution containing enzymes and other chemicals used to manufacture carbohydrate

2. Thylakoid Disks: a membrane network studded with chlorophyll molecules, surrounded by the stroma

• Grana: stacks that thylakoids are arranged in (singular stack: granum)

  • Inside each thylakoid disk is the thylakoid space

  • Membranes of thylakoids -> have chlorophyll pigments and other molecules attached to them to gather sunlight 

Chlorophyll: mixture of pigments

• Absorbs light of many wavelengths (esp. Blue and red) -> but transmit / reflect green

  • Causes chlorophyll to appear green

• Plants need warm temp and sunlight to produce chlorophyll -> summer is warm -> lots of chlorophyll -> leaves appear green

• Autumn gets colder - > chlorophyll gets broken down / leaves stop making chlorophyll -> less green pigment reveals the red and orange pigments THAT WERE ALWAYS THERE

• Green covers other colors

Chromatography

• Show us what pigments are in leaves by separating them

• Rf value calculated shows pigments found in plant

• Solvent carries dissolved pigments as it moves up the paper

• Pigments carried at dif rates b/c they aren't equally soluble

• Distance pigment travels is used to identify the pigment in plant

Light Dependent Reactions: 

• Occur within thylakoid disks

• Require light energy and chlorophyll pigments

• Light energy converted to chemical potential energy

• Chlorophyll is energized and water molecules are split (photolysis) into hydrogen and oxygen 

  • Oxygen from split water molecules are released into the atmosphere

  • Hydrogen is split into hydrogen ions (protons) and electrons

  • Electrons and protons used to generate ATP through electron transport

  • Hydrogen ions and electrons attach to a carrier molecule called NADP+ to become NADPH

    • H -> extra hydrogen 

    • Loses positive charge due to electron

  • ATP and NADPH then used in Light Independent Reactions

• Process by which light energy is trapped and harnessed:

  • Chlorophyll molecules and carotenoids are arranged in clusters on thylakoid membranes

  • Photosystems: name of clusters^

  • Two types of photosystem:

1. Photosystem II (PSII)

2. Photosystem I (PSI)

• Light absorbed by photosystem -> electrons are excited and emitted from a specialized “chlorophyll a molecule”

• Electrons passed to an electron acceptor in the photosystem and down electron transport system

• Excited electrons used to generate energy through electron transport  -> energy used for phosphorylation (independent light reaction)

SUMMARY OF STEPS:

1. Photolysis -> provides electrons from H2O

2. Electrons begin at lowest energy level PSII

3. Photon of light excites PSII -> electron is removed and picked up by electron acceptor molecule

4. Electron then passed via electron transport chain to PSI

5. Light energy hits PSI excited electrons there -> electrons are emitted and picked up by another electron acceptor 

6. Electrons from PSII fill up the “holes” left by electrons being emitted from PSI

7. “Holes” left in PSII when electrons are emitted -> filled by electrons from water molecules

8. Electrons from PSI -> passed onto special molecule called NADP+

• Each NADP+ molecule receives 2 electrons and a proton -> becomes NADPH

  • 2 electrons and proton -> from hydrogen ions left over from photolysis of water

  • NADPH IS A REDUCED FORM -> has reducing power

    • Ability to give electrons to another molecule 

Photolysis: splitting of water molecules during photosynthesis 

• Key to process of light dependent reactions

• Oxygen from water molecules released into atmosphere -> available for all organisms in biosphere

• Electrons released from the hydrogen atoms let the light reactions to occur

• Electrons from PSII lose energy as they pass through electron transport system

• Loss energy used to pump hydrogen ions released during photolysis from stroma into thylakoid space

  • Called PROTON PUMP

• Build up of protons inside thylakoid space -> produces concentration gradient between inside and outer stroma

• Protons rush down gradient through specialized protein molecule (called ATP SYNTHASE) in thylakoid membrane 

  • Energy used to phosphorylate ADP by adding terminal phosphate to become ATP

• Chemiosmosis: use of proton channel in thylakoid membrane to utilize energy of protons  

• Photophosphorylation: production of ATP in photosynthesis

  • Due to process using light energy as fuel

Light Independent Reactions / Calvin Benson Cycle

• Also referred to as ”dark reactions” or “carbon fixation”

• DOESN’T require direct light energy -> needs products of light dependent reactions

  • ATP from light reactions -> provides energy needed

  • NADPH provides hydrogen -> raw material needed for dark reactions

• Occur in stroma of chloroplast

Calvin/Benson Cycle: complex sequence of events that occur in the stroma

• Starting pt of cycle is 5-carbon compound -> called Ribulose bisphosphate (RuBP for short)

• During cycle energy -> ATP adds hydrogen (from NADPH) and carbon dioxide to RuBP -> forms glucose molecules C6H12O6

• Sugar (glucose) -> converted into materials that plants need OR eaten by animal to provide it food

• At other pts in cycle -> intermediate compounds used to form compounds such as proteins or fats

Calvin and Benson

• Melvin Calvin and Andrew Benson -> figured out sequence of events involved in carbon fixation (1940s)

• Used radioactively labeled CO2 to trace movement of carbon -> through complex cycle of chemical reactions in stroma of chloroplast 

• Process of turning carbon dioxide into glucose is complex

Three Major Stages of Calvin/Benson Cycle

1. Fixing Carbon Dioxide / Carbon fixation

• CO2 molecule is added to a molecule of 5-carbon compound -> w/ help of enzyme called Rubisco

• Ribulose bisphosphate (RuBP): 5-Carbon compound

• Adding one more carbon atom to 5-C compound -> forms unstable six-carbon compound -> immediately splits into 2 molecules of 3-carbon compound ( called PGA)

2. Reduction

• ATP (generated in light reactions) -> used to modify 3-carbon compounds 

• NADPH (from light reactions) -> used to reduce 3-carbon compounds

• Produces 12 molecules called glyceraldehyde-3-phosphate (G3P/PGAL)

  • Molecules apart of the major intermediate in the cycle

3. Replacing RUBP / Regeneration

• 2 PGAL molecules used to form 1 glucose molecule

  • 2 x 3-Carbon = 6-carbon

• Other 10 PGAL used to regenerate 6 RuBP molecules to continue cycle

  • Requires more ATP (from light dependent reaction) to be used

• SUMMARY: 6 CO2 molecules + 6 RuBP molecules = 1 glucose molecule

USE TO UNDERSTAND SPLITTING OF PGA (6-C -> 2 3-C)

CHAPTER 5.3 CELLULAR RESPIRATION

• Only couple of life forms need photosynthesis -> ALL life forms need cellular respiration to stay alive

  • ALL LIFE PROCESSES REQUIRE ENERGY

• Chemical bonds of high energy molecules (glucose) break -> new bonds formed -> releases energy for us to use

  • 36% of released energy from glucose used to make ATP -> rest is lost as heat/waste energy

• During cellular respiration -> glucose molecules OXIDIZED to release hydrogen ions and electrons

  • Hydrogen ions and electrons passed through electron acceptors (Electron Transport Chain) -> energy is released -> forms ATP

Anaerobic Cellular Respiration: cellular respiration that occurs without oxygen

• Involves 2 major stages:

1. Glycolysis: series of reactions that cause glucose (6-carbon) to be broken down into 2 pyruvic acid (3-carbon) molecules 

• ALL CELLULAR RESPIRATION BEGINS W/ GLYCOLYSIS 

• Occurs in cytoplasm of cell (outside of mitochondria) -> doesn't need oxygen (anaerobic)

• Needs ATP to occur -> ATP added -> activates the glucose

  • Small amount of energy released -> more ATP formed later in glycolysis 

• Hydrogen acceptor (NAD+) -> reduced to NADH

• Glucose (6C) -> 2 pyruvic acid molecules (3C)

2. Fermentation: occurs when pyruvic acid (from glycolysis) is under anaerobic conditions

• Regenerates NAD+ needed to keep glycolysis running

• Bacteria and yeast cells -> alcohol(s) formed

• Animal cells (muscle cells) -> lactic acid formed

Fermentation in Yeast and Bacteria: pyruvic acid -> ethanol + CO2

• Pyruvic acid (from glycolysis) -> no oxygen -> undergoes decarboxylation (removal of 1 CO2) 

  • Forms ethanol (C2H5OH(aq))

  • Process is basis for bread, beer, wine making

  • Used to make food and alcohol products

• Reducing power of NADH -> provides power for process -> NAD+ also regenerated

• Small amounts of ATP formed -> keeps yeast alive

Lactic Acid Fermentation: pyruvic acid -> lactic acid

• Pyruvic acid (from glycolysis) + reducing power of NADH -> lactic acid (C2H5OCOOH(aq))

  • NAD+ also regenerated (required to keep glycolysis going)

• Muscle cells continue to breathe aerobically for long periods of time

  • Lactic acid fermentation -> muscle fatigue and cramps

  • Muscle fatigue -> more complicated than js lactic acid accumulation

  • Oxygen reconverts lactic acid back into pyruvate when available

    • Leaves muscles in oxygen debt -> debt must be repaid

  • Hella long periods under anaerobic conditions -> animal cells stop working

Bacteria uses lactic acid fermentation

• Lets us make dairy products

• Controlled fermentation of milk spoiling -> buttermilk, cheese, yogurt, sour cream

• Pickles, sauerkraut, kimchi

Aerobic Cellular Respiration: cellular respiration that occurs in the presence of oxygen

• Occurs within mitochondria -> oxygen required

• SUMMARY: Pyruvic acid (from glycolysis) -> moves into mitochondria -> goes thru Kreb’s cycle -> releases hydrogen for electron transport  

• Involves 4 major stages:

1. Glycolysis: series of reactions that cause glucose (6-carbon) to be broken down into 2 pyruvic acid (3-carbon) molecules 

• ALL CELLULAR RESPIRATION BEGINS W/ GLYCOLYSIS 

• Occurs in cytoplasm of cell (outside of mitochondria) -> doesn't need oxygen (anaerobic)

• Needs ATP to occur -> ATP added -> activates the glucose

• Small amount of energy released -> more ATP formed later in glycolysis 

• Hydrogen acceptor (NAD+) -> reduced to NADH

• 1 glucose (6C) -> 2 pyruvic acid molecules (3C)

2. Kreb’s Cycle Preparation ASK WHAT THE FUCK THIS IS

• Pyruvic acid enters mitochondria -> molecule called co-enzyme A (CoA) added = 2 carbon acetyl-CoA + CO2 released

• NAD+ reduced at this stage to NADH

Structure of Mitochondria

• Double membrane oval shaped organelle -> found in plant and animal cells

• Required for aerobic respiration

• Inner membrane -> folded to form cristae

  • Electron transport -> occurs through cristae membranes

• Inner chamber -> filled with fluid -> called matrix

  • Kreb’s cycle -> occurs in matrix

3. Kreb’s cycle

• CO2 lost to atmosphere as waste -> ATP energy for cell -> high energy electron carriers move into electron transport chain

1. Acetyl-CoA (2C) added to 4C compound -> begins complex sequence of chemical reactions

• Reactions remove hydrogen from molecules in cycle

2. More CO2 produced

3. Hydrogen removed from molecules -> reduce NAD+ -> NADH

• Also reduce FAD+ -> FADH2

4. NAD and FAD carry hydrogen to electron transport system (attached to cristae membranes)

• Hydrogen splits into ions and electrons 

5. Ions and electrons go through electron transport system

4. Electron Transport

• Energy of electrons -> powers proton pump that pumps hydrogen ions into space between 2 mitochondrial membranes

• Proton gradient created -> allows hydrogen ions to flow back through ATP synthase molecules in membrane (chemiosmosis)

  • ATP also generated by phosphorylation of ADP w/ P (photophosphorylation)

• End of electron transport system -> hydrogen added to oxygen (final electron acceptor) = water

  • REASON WHY oxygen required for Kreb’s cycle -> no oxygen = no water = NAD+ can't regenerate -> cycle shuts down

Energy Production as ATP

1. Glycolysis: net gain of 2 ATP

• 2 ATP needed for activation of 1 glucose molecule

• 4 ATP directly produced

• 2 NAD+ reduced to 2 NADH

2. Kreb’s Cycle

• Each pyruvic acid molecule entering cycle -> reduced to 4 NAD+ molecules

  • Gives total of 8 NADH (2 pyruvic acid from 1 glucose molecule)

• 1 NADH molecule -> generates 3 ATP

  • 10 NADH = 30 ATP

• FAD+ reduced to FADH2 (instead of NAD+)

• FADH2 generates 2 ATP

  • Gives 4 ATP (2 per pyruvic acid molecule)

• 1 ATP phosphorylated into cycle per pyruvic acid entering cycle

  • 1 glucose = 2 pyruvic acid = 2 ATP

• Oxidation of 1 glucose molecule = 38 ATP

  • EXCEPTION: NADH from glycolysis transported through mitochondrial membrane -> less ATP may be phosphorylated

  • LOSS OF 2 ATP MAY OCCUR -> complete oxidation of 1 glucose molecule = 36 ATP

• Cellular Respiration Formula: C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O + 36 ATP

• Conditions of cell at particular time -> determined if 36 or 38 ATP produced

UNIT B: ECOSYSTEMS AND POPULATION CHANGE

CHAPTER 3.1

Biosphere: the earth

• All areas on Earth inhabited and/or support life

• Largest level of biological organization

• Includes all life and all parts of Earth containing living things

Environment: everything that affects an organism throughout its life; and everything that an organism has an effect on

• Includes biotic and abiotic factors

Biotic Factors: living (factors)

• eg.) insects, bacteria, fungi, animals, grasses, other plants, etc.

Abiotic Factors: non-living (factors)

• eg.) water supply, light, soil quality, climate/temp

Organism: living being

• Individual animal, plant, or single-celled life form

Species: organisms capable of interbreeding (fucking) and producing fertile offspring

Ecologists: scientists who study individual organisms

• Want to learn how the abiotic environment in which an individual lives affects its behavior or physical features

• eg.) investigates physical features of a species of alpine plant that allows it to live in a dry, cold, windy environment

Interactions between organisms and their environment divided into 4 levels

1. Individual organism: only one organism

• eg.) single clownfish

• Study includes effect of abiotic elements of its environment on physical features and behavior

2. Population: all of the same type of organism living in the same area  at the same time

• eg.) all clownfish in a reef

• Info abt a population obtained by studying individual’s:

  • Life span

  • Food preferences

  • Reproductive cycle

3. Community: all populations interacting with each other that live in the same area at the same time

• eg.) coral reef

• NOTE

  • Study of a COMMUNITY includes only living organisms

  • Study of an ECOSYSTEM includes both biotic and abiotic factors

4. Ecosystems: a community plus all the abiotic factors

• eg.) coral reef including light levels and water conditions

• Study of ecosystem -> includes all biotic and abiotic factors and their interactions

• “Eco” refers to environment

• “System: describes situation where exchange of energy and/or matter with the surroundings occur

Studying Organisms

• Ecologists specialize and focus on one lvl of environment

• Spend time studying individual studies or interactions between dif species within ecosystem

Environmental Changes overtime

• Communities are dynamic -> change over time b/c abiotic factors change over time

  • Changing abiotic elements -> affects organisms and their interactions on all levels

  • Population lvl on 1 organism fluctuates -> affects the population lvls of other organisms that consume or are consumed by the organism

    • Predator-prey relationships

  • Populations in community interact with one another -> modifies environment so that it becomes suitable for other species 

Biosphere: made up of all the ecosystems in the world and their interactions 

• Living things inhabiting environments and the abiotic components that they interact with -> apart of biosphere

• Populations aren’t randomly scattered throughout biosphere -> species have their own “place” in biosphere

• Distribution of species -> related to ways biotic and abiotic components of environment affect individual organisms + their ability to survive

CHAPTER 3.2

Taxonomy: language classifying living things

• Language is international -> understood worldwide

• Work in progress -> ways of classifying organisms always changing 

In the Past

• Early classification systems -> simplistic

• Developed for ease of identification

• Until 1950 -> all life classified as plant or animal

Modern system 

• Show evolutionary relationships -> displayed in tree of life diagrams

• Organisms sorted into hierarchical system -> starts w/ broadest (most general) categories 

• King Phillip Came Over for Good Spaghetti

Classification System

• All living things have a name that can follow classification system

• System also capable of naming newly discovered species -> living and extinct

• 3 domains and 6 kingdoms

• Modern classification -> shows degrees of evolutionary relatedness between dif organisms

EXAMPLE: Are humans related to sharks or dolphins more?

1. Phylum:

• Humans = Chordata

• Dolphins = Chordata

• Sharks = Chordata

2. Class:

• Humans = mammalia

• Dolphins = Mammalia

• Sharks = Chondrichthyes 

• MORE IN COMMON W/ DOLPHINS -> GO DOWN KPCOFGS HIERARCHY

Binomial Nomenclature: two part system used to name all organisms

• Uses latin words

• Includes an organism’s genus and species

• NOTE: 

  • Domain name through Genus name is CAPITALIZED

  • Species is NOT capitalized 

  • Genus and species both italicized 

  • eg.) Humans classified as Homo sapiens

Dichotomous Key: branched or stepped process created to help identify organisms

• Identify species by binomial nomenclature

• STEPS:

1. Use physical feature / observable traits as guide 

2. Follow specific series of questions

3. One question answered -> key directs to what question to ask next

CHAPTER 3.3

Studying Organisms in Ecosystems

• Organisms are distributed evenly across Earth

• Patterns of distribution largely determined by abiotic factors 

  • eg.) climate, latitude, elevation

• Ability of organisms to tolerate ranges of temperature, humidity, salinity, moisture, and light also play major role  

• Graph shows how temp and precipitation is used to classify biomes

Climate: the weather conditions prevailing in an area in general or over a long period

• Earth heats unevenly

• Affects surface temps and movement of ocean and atmospheric currents

• Latitude and altitude/elevation have similar effects on the distribution of living things

  • Two factors + factors like topography and temp -> determine types and abundance of plants and other photosynthetic organisms that can survive

• Determined by temp and rainfall -> results from unequal heating of Earth and other factors (local geography, snow and ice cover, proximity of large bodies of water)

• Unequal heating of atmosphere -> sets up conditions that produce global air and water movements (trade winds and ocean currents)

  • Produces patterns of rainfall -> causes some areas in the world to be v dry and others v wet

Biomes: distinct biological communities that have formed in response to a shared physical climate

• Community of plants and animals that have common characteristics for environment they exist in

• Identified based on their mean annual temperatures and precipitation lvls

• If temp and precipitation increase -> abundance of organisms increase

• DO NOT HAVE SET FIXED BARRIERS -> blends into other nearby biomes

Types of Biomes: 

1. Tundra

• Northern Canada

• Cold, treeless, lowland area of far northern regions

• Lower layer of soil permanently frozen

  • Summer -> top layer of soil thaws and supports low-growing mosses, lichens, grasses, small shrubs

2. Taiga (Boreal Forest)

• Roughly Northern Alberta

• Forest located in Earth’s far northern regions

• Consists of cone-bearing evergreens (firs, pines, spruces) and some deciduous trees (larches, birches, aspens)

• Found SOUTH of Tundra

3. Temperate Grassland

• Southern Alberta

• Area dominated by grass / grass-like vegetation

• Moderately dry climatic conditions and seasonal disturbances

  • Floods and fires help growth of grasses -> prohibit growth of trees and shrubs 

Habitat: specific area where an organism grows and thrives

• Organisms ideal habitat -> perf combination of biotic and abiotic factors that best meets it's need

  • More suited to habitat = better chance of survival and reproduction for organism

• Organisms habitat determined by:

1. It's own personal needs

2. Needs of the species

Range (of species): refers to the geographical area in which the species can be found

• Related to species habitat 

• Not all places within range will have suitable habitat for those organisms

  • Causes organisms to NOT live throughout their range -> live in particular habitat within that range instead

  • Range of a particular species -> changes as humans interfere / modify environment 

Ecological Niche (of a population): role that it’s members play in an ecosystem

• Describes how an organism or population responds to distribution of resources and competitors -> and it's response in altering those same factors

• Variety of niches and habitats within ecosystem -> allows it to support diversity of organisms

• Many species share same range -> don't share same niches

  • Issue when one organism occupies another organism's niche / destroys it's niche 

  • eg.) mountain pine beetle destroying pine trees

• SUMMARY: live in same area -> eat dif parts -> have dif roles 

Niches in Terrestrial Environments

• Great amount of diversity among terrestrial ecosystems

• Biodiversity in these ecosystems depend on biotic and abiotic factors present

• Greater the number and variety of organisms in ecosystem = greater number of niches

Niches in Aquatic Environments

• Niches determined by available biotic and abiotic factors -> amount of available light in aquatic environment -> determining factor in available niches 

• Causes each zone of lake to have distinct group of organisms    

Limiting factors: factor that controls the growth of a population 

1. Abiotic Limiting Factors 

• Known as density-independent limiting factors

• Affect all populations in similar ways -> regardless of population size and density

• eg.) Soil, relative humidity, moisture, ambient temp, sunlight, nutrients, oxygen, fires, droughts, hurricanes

2. Biotic Limiting Factors

• Known as density-dependent limiting factors

• Operates strongly only when population density reaches certain level

• Factors DON'T affect small scattered populations as much

• eg.) Competition, predation, herbivory, parasitism, disease, stress from overcrowding, humans as predators 

Competition 

• Populations become crowded -> individuals compete for food, water, space, sunlight, other essentials 

• Some individuals obtain enough essentials to survive and reproduce

  • Others obtain js enough to live -> not enough to raise offspring 

  • Others starve to death / die from lack of shelter

• Lowers birth rates, increase death rates, or both

Intraspecific Competition

• Number of resources required by all individuals of the same species/population

• But there aren’t enough resources to ensure survival of all individuals

Interspecific Competition

• Competition between species occurs when two dif species occupy the same niche

• Same niche -> stronger species become dominant -> weaker species disappear (thru extinction or migration) 

Invasive Species

• Human introduces new species to ecosystem -> disrupts niche of another native species -> causes extinction

• Lack natural population controls

• Can out-compete native species

• Change natural ecosystems

• Expensive and difficult to control

Predation

• Naturally limits population of prey species

• Change in numbers of prey -> affects trophic lvls beneath prey species

• Predators feed on multiple prey types -> affect numerous food chain relationships

Parasitism and Disease

• Parasites and disease-causing organisms feed at expense of their hosts -> weakens host and causes disease or death

  • eg.) ticks feeding on blood of hedgehog -> transmits bacteria that cause disease

• Density-dependent effect -> denser the host population -> parasites spread more easily from one host to another

• Parasitism differs from predation -> parasite doesn't kill it's host when feed

• Parasitic infestations limit reproductive and survival ability of host

Population Sampling

• Often used to determine population sizes  

• Sampling an area -> transects / quadrats used to divide study area into smaller areas

Estimating Population Densities

• Density of organisms -> determined by calculating average number of individuals per unit of area

  • Assumption applied to larger area to determine total population of area (we assume the data)

• When sampling samples should be RANDOM -> avoids groupings of organisms that occur in small areas

CHAPTER 4.1 

Environmental Limiting Factors: environmental conditions that kill organisms

• Includes: 

1. Biotic Environmental Limiting Factors

• eg.) competition (for food and space), disease, parasites, predators

2. Abiotic Environmental Limiting Factors

• eg.) availability of water, oxygen, light

• Populations need adaptations -> overcome factors to survive

  • Factors make sure only strong / most well adjusted organisms of population survive 

  • Organisms survive long enough to reproduce -> pass genetic info that helped them survive onto offspring

Adaptations: physical features, behaviors, or physiological processes that help organisms survive and reproduce in a particular environment

• Result of gradual change in characteristics of members of a population over time

• eg.) camouflage, night vision, deep roots, nesting, hibernation, herding

Structural Adaptations: physical features and special body parts

• eg.) fur or hair structure, shape of ears, camouflage or warning colouration, leaf shape, large paws on wolf to help it run in snow

Behavioral Adaptations: how organisms act (a behavior or instinct)   

• eg.) hibernation, diurnal vs nocturnal, migration, mating rituals, pack hunting, burrows / nest building

Physiological Adaptations: systems present in an organism that allow it to perform certain biochemical reactions or physical/chemical events

• eg.) bioluminescence, slime production, poison production, maintaining a constant body temperature

Variation: visible or invisible differences between one individual and other members of its population  

• All members of population have some differences -> some populations have more variation than others

• Variation within population + environment where organism lives -> situation where natural selection occurs

  • Through generation of survivors -> variation becomes more common -> too common -> variation becomes characteristic / trait of population

• Can be beneficial, harmful, or neutral:

1. Advantageous / beneficial traits: likely to survive and increase in future generations

2. Disadvantageous / harmful traits: likely to be eliminated

3. Neutral traits: persist until change increases or eliminates them, or until change in environment alters their value

How Variation Occurs

1. Reproduction: SEX !

• Offspring have combination of genetic material (DNA) passed down from both parents

• # of possible combinations of genes that offsprings can inherit from parents -> great genetic variation among individuals within a population 

• Population Variation: a variation that becomes more common in a population b/c it helps/helped individuals survive and reproduce throughout generations 

2. Mutation: a permanent change in the genetic material of an organism

• Mutations can occur in 2 places:

1. Somatic cells: cells that make up body tissue

• Mutation disappears when organism dies

2. Germ Line cells: cells that produce sperm / eggs

• Mutation is passed onto next gen

• Happens continuously and spontaneously in DNA of any living organism

• Occurs from either:

1. Errors in copying DNA

2. Damage from radiation or mutagens

• Can be beneficial, harmful, or neutral:

1. Beneficial Mutations: create trait that helps organism survive it's environment better

• Organism w/ mutation will survive and reproduce more successfully and pass mutation onto offspring -> compared to individual w/o mutation

• Situation common when organisms’ environment is changing

2. Harmful Mutations: kill or cripple organism, preventing it from surviving

3. Neutral Mutations (or disadvantage): can become favorable in new environment

• Mutation provides selective advantage in new environment in this situation

• Eventually population variations develop into adaptations (when it becomes the norm)

  • Adaptations develop in populations slowly and gradually (over long period of time)

  • Enough different adaptations develop -> separate populations -> form into new species

SUMMARY OF VARIATION

• Variation in population -> caused by mutations or sexual reproduction 

• Harmful variation -> organism dies and doesn’t pass it on

• Beneficial variation -> helps organism and is passed on

• Variation becomes more common -> becomes adaptation 

CASE STUDY #1 OF VARIATION: Venom-Resistant Squirrels

• Ground squirrels in California developed mutation -> makes them resistant to rattlesnake venom

• Therefore ground squirrels w/ mutation have greater chance at survival -> will pass traits onto next gen

• Cause majority of squirrel population to have this beneficial adaptation b/c they’re more likely to survive and reproduce 

CASE STUDY #2 OF VARIATION: Superbugs

• Sir Alexander Fleming discovered penicillin could kill bacteria (1928)

• Penicillin first used as medicine (1941)

• Reports of penicillin-resistant strains of bacteria (1945)

• There are now bacterial strains that are resistant to all antibiotics

Natural Selection: process that results when the characteristics of a population of organisms change because individuals with certain inherited traits survive specific local environment conditions, and through reproduction, pass on their traits to their offspring 

• In population -> individuals selected for their traits by environment (not them as a person)

  • Specific individuals chance of survival to point of reproduction -> determined by their entire set of genes + random chance

• Individuals don't change over time -> populations change over time

• Environmental limiting factors exert selective pressure -> limits populations

  • Selective pressures cause sudden chance

  • Variety in population is crucial -> traits that were once successful can become unsuccessful when selective pressure changes 

  • eg.) White and black peppered moths

    • White ones blended in better w/ birch trees -> black ones had less chance of survival

    • Volcanic eruption occurred -> trees became black -> black peppered moths blended in better -> white peppered now have less chance of survival

• eg.) Population of grass

  • Some grasses better adapted to survive drought conditions

  • Drought occurs -> exerts selective pressure -> favors plants that are drought resistant

  • Causes change in makeup of population (population now consists of majorly drought resistant grass -> non-drought resistant grasses died) 

• Doesn't anticipate changes in environment -> random chances occur -> produce traits that may be beneficial in future

  • Beneficial variation: Environment changes -> variations/traits produced increase survival ability of some organisms 

  • Neutral variation: Variations not beneficial in certain environments may not be harmful -> just useless

  • Harmful variation: Detrimental variation -> won't be passed on until environment changes to select for that variation

Foundation for Evolution by Natural Selection 

• Individuals in populations have physical, biochemical, and behavioral differences (variation)

  • Variation controlled by inheritable genes

• Individuals have set of characteristics allowing them to survive and reproduce -> makes them well suited to their environment 

• More individuals born than number that can survive to reproduce

• Competition ensures most well adapted individuals are more likely to reproduce and pass their characteristics / adaptations to next gen

Artificial selection: humans selecting organisms for particular traits, rather than the environment 

• Modern corn vs teosinte

• Breeding domestic dogs for specific traits

  • Snout size, hypoallergenic fur, hunting/tracking ability

• Wild mustard

  • Where kale, kohlrabi, cabbage, brussel sprouts, cauliflower, and broccoli originate from

CHAPTER 4.2: Developing a Theory to Explain Change

Theory: set of ideas based on scientific evidence

• May be changed/discarded if new info or research contradicts original theory

• Developed through observations, analysis of data, and formulation of hypotheses 

Ancient Greeks

• Plato and Aristotle (most important Greek philosophers) -> believed organisms are immutable

  • Immutable organisms: organisms born in a perfected, unchangeable form

  • No changes from generation to generation

Georges-Louis Leclerc, Comte De Buffon

• One of first ppl to challenge idea that life forms don't change -> his ideas revolutionary for his time

• Noticed similarities between human and apes (1749) -> speculated they have common ancestor 

• Believed organisms could change over time

Georges Cuvier

• Credited for developing science of paleontology

  • Paleontology: study of ancient life through examination of fossils

  • Found each stratum characterized by unique group of fossil species

    • Stratum: layer of rock

  • Deeper (older) the stratum -> more dif the species are compared to modern life

• Worked from stratum to stratum -> discovered evidence that new species appeared and others disappeared over time

  • Evidence proves species could become extinct 

• Observations led him to believe Earth experienced many destructive natural events (floods and volcanic eruptions) in the past, killing many species each time

  • Called events “Revolutions”

Charles Lyell

• Rejected idea of revolution

  • Suggested geographical process that occur on Earth take long time (same rates in the past as today -> not quick natural events -> opposes Curvier’s belief)

  • If geological changes are slow and continuous -> not catastrophic -> Earth over 6000 years old

• Believed slow and subtle processes happen over long period of time -> results in substantial changes

  • eg.) forced that build and erode mountains

  • eg.) person loses weight 

    • Someone who sees person constantly -> won't notice

    • Someone who hasn't seen them in a while -> notices change 

Jean-Baptiste Lamarck

• First to attempt to explain how species change over long periods of time

• Suggested Species change /  increase in complexity over time -> till reaching lvl of perfection

  • Environment provides pressure for changes to occur

Lamarckism: Jean-Baptiste Lamark’s beliefs (broken into 3 theories)

1. Theory of need: organisms need or want to change 

2. Theory of use and disuse: life is not fixed (is changeable) 

• Organs remain active and strong when used

• If not used -> organs weaken and disappear

• **NOT TRUE b/c of appendix, tailbone

3. Theory that acquired traits can be passed to offspring

• Inheritance of acquired characteristics (eg. large muscles)

  • NOT TRUE -> babies aren't born with large muscles -> have to work out

• **NOT TRUE b/c we can acquire nose ring -> baby won't be born w/ one

• Ideas never became popular -> never got respect of colleagues 

• Too much proof showing Lamarckism was invalid/wrong

• eg.) chop off tails of mice in one gen -> mice still born w/ tails in next gen

• His views controversial -> went against the Church / popular scientific beliefs at the time -> forced him to live in poverty

Charles Darwin

• First to develop concept of natural selection

• Traveled aboard the HMS Beagle on voyage to survey coast of South America (Galapagos Islands) -> made observations abt organisms he saw along the way

• Noted environment exerts certain forces on organisms within it

  • Forces include: light intensity, availability/location of food and water, shelter, amount and kinds of predators, parasites/diseases

• Saw Finch-like birds on dif islands w/ dif shaped beaks -> beaks well suited for type of food birds had available on each of the dif islands

  • Hypothesized all the dif birds descended from original common ancestor

Darwin’s Theory of Natural Selection

1. Overproduction (overpopulation)

• Although all individuals born within a species -> not all will survive, reproduce, or live to maturity

2. Struggle for existence (competition)

• Presence of many within a species + limited resources -> organisms compete for limiting resources

3. Variation

• Although organisms belong to a common species -> aren’t identical to each other b/c there’s variety in the inherited traits

4. Survival of the fittest (natural selection)

• Individuals within a population w/ most advantageous variations -> better able to compete, survive, and reproduce

• Survivor (in Darwin's terms) means one’s traits get passed onto next gen

5. Origin of a new species (speciation)

• Many generations of passing only advantageous adaptations -> populations accumulate variations (structural, physiological, or behavioral) -> cause population to appear significantly dif than it's ancestor

  • Cause it to be referred to as new species

Darwin’s influential book

• Called “On the Origin of Species” (1859)

• Filled w/ his theories -> proposed 2 main ideas based off of observation:

1. Present forms of life have descended from ancestral species

2. Mechanism for modification is natural selection -> takes place over long period of time

Alfred Russel Wallace (DARWIN'S SHADOW)

• Studied organisms in South America and Malaysia 

  • Same time as Darwin studying observations made on HMS Beagle

• Reached similar conclusions as Darwin's -> published his theories in an essay (same time Darwin published book)

  • Allowed Darwin to take credit for the ideas -> Darwin's ideas backed up by hella research and evidence -> his was theoretical 

Evidence for Theory of Evolution by Natural Selection

1. Fossil Evidence

• Fossils: preserved remains of once living organisms 

  • Most direct evidence that evolution occurred

  • Fossils discovered provide detailed info on course of evolution through time

• Fossils arrayed according to age (oldest to youngest) -> provide evidence of evolutionary change

  • Law of superposition: deeper layers of rock contain older fossils, while rock layers closer to the surface contain younger fossils 

  • Fossils of organisms found in newer rock layers -> appear more closely related to modern species than fossils found in older layers

• Not all organisms appear in fossil record at same time -> indicates dif species evolved at dif times

• Paleontologists look for transitional fossils

  • Transitional fossils: fossil remains that seem to show some characteristic from organisms of both lower and higher strata

  • Show relationship and sequence of change to more recent organisms

2. Biogeography: study of the distribution of organisms on Earth

• Earth's land masses undergo change over time 

  • Fossils of same species found in dif continents -> suggest continents were once joined tgt

  • Fossils younger than 150 mil years old arent found on dif continents -> suggest they evolved after breakup of continents

• Examples proving hypothesis of continents being all connected:

  • Geographically close environments (desert and first habitats in South America) more likely to be populated by related species -> compared to locations geographically separate but environmentally similar (desert in Africa and desert in Australia)

    • Dif environments + close together = related species

    • Same environments + far apart = species aren't as related

  • Animals found on islands -> closely resemble animals found on closest continent

    • Suggest animals on islands evolved from mainland migrants -> populations adapted over time by adjusting to environmental conditions of new home

  • Fossils of same species found on coastline of neighboring continents

  • Closely related species never found in exactly same location or habitat

3. Comparative Anatomy: allows scientists to compare how related organisms are based on their anatomy

1. Homologous structures: those with similar structures but not necessarily the same function

• Similar structure -> dif function

• Anatomy is similar -> makes organisms more related

2. Analogous structures: those with different structures but similar (or the same) functions

• Dif structure -> same/similar function

• Have evolved separately from each other

• Anatomy is dif -> organisms less related 

3. Vestigial Structures: serve no useful function in a modern organism

• Show evidence of common ancestor

• eg.) appendix, coccyx (tail bone) in humans, pelvic and hip bones in snakes and whales

4. Embryology: study of the changes that an embryo goes through as it develops

• Similar patterns of development are seen -> indication organisms more closely related

5. Biochemistry: study of the organic molecules that make up an organism 

• If molecules (eg. proteins, DNA, chromosome numbers) are common between organisms -> indicate that organisms more closely related

    CHAPTER 4.3: How Species Form

Speciation: the formation of a new species

• Species consist of a reproductively compatible population

• Occurs when two populations of same species are isolated/separated from each other in some manner -> prevents them from interbreeding/reproducing/mating 

  • Must be separated for a LONG period of time

• Reproductive isolation: when members of two populations cannot interbreed and produce fertile offspring 

Speciation can happen due to 4 Types of Reproductive Isolation:

1. Geographical Isolation: two populations separated by geographic barriers (eg. rivers, mountains, bodies of water)

• eg.) Abert and Kaibab Squirrel

  • 10 000 yrs ago -> Colorado River split Abert species into 2 dif populations

  • Both sides of river had dif environmental limiting factors -> natural selection worked separately on each group -> formation of distinct species called Kaibab squirrel

2. Behavioral Isolation: two populations capable of interbreeding, but have differences in courtship rituals or other reproductive strategies that involve behavior 

• eg.) Eastern and Western Meadowlarks

  • Members of two species won't mate w. each other -> use dif songs to attract mates

  • Eastern meadowlarks won't respond to Western meadowlark songs -> vice versa

3. Temporal Isolation: form of reproductive isolation in which two populations reproduce at dif times

• eg.) spotted skunks 

  • Eastern spotted skunks mate late winter

  • Western spotted skunks mate early fall

  • IMPOSSIBLE for two species to interbreed

4. Mechanical Isolation: species have reproductive structures that are physically incompatible 

• eg.) snails 

  • Snails of same species have reproductive organs that align

  • Snails of dif species can't reach each others reproductive organs

  • IMPOSSIBLE FOR SNAILS TO FUCK

Forming a New Species

• 2 pathways that lead to formation of new species of speciation

1. Transformation: when 1 species changes into dif species over time, as a result of accumulated changes that occurred in the population

• Mutations and adaptations made to the changing environment -> alter the population -> old species gradually replaced

• If this pathway was the only way to create new species -> total # and diversity of species in existence wouldn't change 

• eg.) Mammoths

  • Ancestral mammoth lived 2.6 mil-700 000 yrs ago

  • Slowly evolved into steppe mammoth that lived 700 000-500 000 yrs ago

  • Finally evolved into wooly mammoth that lived 350 000 - 10 000 yrs ago

2. Divergence: when one species becomes 2 (or more) species over time; those two or more related species then become more dif over time

• Population isolated for long enough -> mutations accumulate -> natural selection occurs

  • Causes population to form into new species -> increasing biological diversity 

• eg.) Vertebrate limbs

  • Limb in dif species have common origin -> diverged somewhat in overall structure and function

Adaptive Radiation: diversification of a common ancestral species into a variety of species, all of which are differently adapted due to dif environments and selective pressures

• eg.) Fruit fly genus Drosophila of Hawaiian islands

  • Descendents of ancestral Drosophila -> increased rapidly in numbers on first island they inhabited 

  • Individuals began to disperse to other islands -> islands ecologically dif enough to have dif environmental situations acting on individuals

  • Selective pressures -> resulted in dif feeding and mating habitats and morphological (physical) differences -> hundreds of types of fruit flies now inhabit the islands 

Evolution

• Two models scientists have proposed for pace of evolution 

1. Gradualism: model of evolution in which slow, gradual, steady changes happen over long periods of time, which leads to biological diversity

• Big changes (such as evolution of new species) occur as a result of many smaller, subtle changes

• Popular model in Darwins time -> but fossil record doesn't support this

• **says og species doesn't exist anymore but they do

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2. Punctuated Equilibrium: model of evolution in which short periods of drastic change in species, including mass extinctions and rapid speciation, are separated by long periods of no change (equilibrium)

• Species undergo most of their morphological (physical) changes when they first diverge from parent species

• eg.) population colonizes new area -> species will change relatively little even as they give rise to other species

• THE ACCEPTED MODEL OF EVOLUTION TODAY

UNIT D: Human Systems - Respiratory and Muscular

CHAPTER 7.1: Respiratory System

Lungs and Breathing

• Average human breathes:

  • 12-20x per min

  • ~20 000 times a day

  • ~600 mil times in a lifetime

• Avrg total lung capacity -> 4-6 L

• Total surface area of lungs -> size of tennis court

Functions of the Respiratory System

• Primary function: obtain oxygen for use by the body cells and eliminate CO2 that's produced as waste

• Mitochondria in cells use oxygen for aerobic cellular respiration (NEEDS AIR)

  • Muscles have largest # of mitochondria -> biggest consumer of oxygen in body

Requirements for Respiration

• 2 main requirements:

1. Surface area / respiratory surface must be large enough for exchange of oxygen and CO2 to occur at fast enough rates to meet the body’s needs

2. Respiration must take place in a moist environment -> oxygen and CO2 dissolved in water

Stages of Respiration

• Breathing: taking air into lungs (inhaling) and expelling air from lungs (exhaling)

• External Respiration: gas exchange (O2 and CO2) between air and blood in lungs

• Internal Respiration: gas exchange (O2 and CO2) between body’s tissue cells and blood

• Cellular Respiration: in mitochondria of cells (final stage of respiration and important in homeostasis)

  • Homeostasis: any self-regulating process by which an organism tends to maintain stability while adjusting to conditions that are best for its survival

    • Balance in the body

Gas Exchange

• Respiration: a large, moist surface is exposed to air and:

  • O2 diffuses into blood

  • CO2 diffuses out of blood

• Transport: O2 attaches to hemoglobin molecules on erythrocytes (red blood cells) -> transported to body’s tissues -> while CO2 taken away

• Tissue Exchange: O2 enters the cell and CO2 exits the cell -> each according to their concentration gradients 

Respiratory Tract

• Lungs are principal organ of respiration

  • Located deep within the body -> protected by bone and muscular structure of thoracic (chest) cavity

  • Since location is deep -> passage has to exist to allow air to move from environment into lungs

    • Passageway referred to as the “Respiratory Tract” and is divided into:

1. Upper respiratory tract

2. Lower respiratory tract

Upper Respiratory Tract

1. Sinus and Nasal Passages

• Air enters through nasal passages -> moves to hollow spaces in head called sinuses

• Turbinate bones: very thin bones in nasal passages

• Bones are covered in cilia (hair-like cells) and mucus -> increase surface area of nasal passages

  • Cilia and mucus trap and remove particles from air -> effectively clean air (natural version of a mask)

2. Pharynx and Epiglottis

• Pharynx: a cavity at the back of the throat that branches into the trachea and the esophagus

• Epiglottis: a flap like piece of cartilage that separates the trachea and the esophagus

  • Closes off the trachea during swallowing -> keeps food out of respiratory tract

3. Larynx and Glottis

• Larynx: the voice box consisting of cartilage and vocal cords

  • Air passes over larynx

• Glottis: vocal cords made of thin sheets of ligaments

  • Air passing through causes cords to vibrate -> produces sound

  • Muscles contract -> glottis change cord length -> changes pitch and tone of voice

4. Trachea

• Trachea (windpipe): a thick, muscular tube containing C-shaped rings made from cartilage

• Connects upper airways w/ lower airways

• Lined w/ ciliated mucus-producing cells

  • These cells further trap and remove debris

Lower Respiratory Tract

1. Bronchi: carry air to right and left lungs

• Singular: bronchus

• Contain C-shaped cartilaginous rings (like trachea)

2. Lungs: organs in which the diffusion of gasses take place in

• Each lung divided into lobes

  • Right lung: 3 lobes

  • Left lung: 2 lobes (to make room for the heart)

• Pleural Membrane: a thin, 2 layered membrane with a space containing fluid in between layers

  • Surrounds each lung

  • Helps reduce friction between lungs and chest cavity during breathing -> connecting them

  • Maintains vacuum that allows air pressure in lungs to change during breathing

3. Bronchioles: smallest air tubes

• Subdivide again and again -> become progressively smaller as they branch thru lung tissue

• DON'T have cartilaginous rings (that are found in trachea and bronchi)

  • Made of smooth muscle instead

4. Alveoli: inflatable clusters of air sacs in which most gas exchange takes place

• Singular: alveolus

• Lungs filled w/ 600 millions microscopic air sacs (alveoli)

  • Having many small sacs rather than 2 large ones -> increases surface area available for gas exchange

• Alveolar wall is 1 cell thick -> same w/ surrounding capillaries -> provides easy passage for gasses 

  • Oxygen diffuses INTO blood through surrounding capillaries

  • CO2 diffuses OUT of blood and enters alveoli

5. Diaphragm: a band of smooth muscle that separates the chest cavity from the digestive cavity

• Used to change the volume of the pleural cavity during breathing

CHAPTER 7.2: Breathing and Respiration

Pressure

• Air doesn't js flow into and out of lungs on it's own

  • 2 muscular structures (diaphragm and rib muscles) control air pressure inside lungs -> cause air to move into and out of lungs

• Pressure difference between atmosphere and lungs -> determine movement of gases into and out of lungs

• Gas moves from area of high pressure to area of low pressure

  • Atmospheric pressure remains relatively constant

  • Pressure in chest cavity (pleural pressure) varies

Inhalation 

• Diaphragm contracts -> it flattens -> pulling downwards 

• This increases volume of lungs -> decreases pleural cavity pressure

• Air enters lungs b/c atmospheric pressure is higher than pleural cavity pressure

Exhalation

• Diaphragm relaxes -> returns to dome shape

• This decreases volume of lungs -> increases pleural cavity pressure

• Air leaves lungs b/c pleural cavity pressure is higher than atmospheric pressure

Pneumothorax: a hole in the pleural cavity

• Makes it impossible for pleural cavity to establish pressure difference -> results in collapsed lung

Intercostal Muscles: found between the ribs

• Antagonistic pair: work in opposition of each other

  • Internal intercostal muscles: pull rib cage downward

    • Used when exhaling

  • External intercostal muscles: pull rib cage upward

    • Used when inhaling

Regulation of Breathing: depends on respiratory control centers located in medulla oblongata and pons of the brain stem

• Breathing is regulated -> so lvls of oxygen, CO2, and acid are kept within normal limits (homeostasis)

• Diaphragm and other muscles of respiration -> voluntary in sense that they can be regulated by messages from higher brain centers (eg. holding your breath)

Chemoreceptors: specialized nerve receptors that are sensitive to specific chemicals 

• 2 dif types of chemoreceptors used to regulate breathing: 

1. CO2 (acid) Chemoreceptors

• CO2 dissolves in blood -> forms weak acid (carbonic acid)

• Acid lvls in blood too high -> receptors trigger increased breathing rates

2. Oxygen Chemoreceptors

• Located in aorta -> detects lvls of dissolved oxygen in blood

• Oxygen lvls too low -> receptors trigger increased breathing rates

Chemoreceptors in Action

1. High Altitude

• CO2 lvls in body remain constant

• Lower O2 lvls initiate increased breathing

2. Carbon Monoxide (CO) Poisoning

• Occurs when CO outcompetes oxygen for binding sites on hemoglobin

• Low O2 in tissue -> medulla increases breathing rates -> further increasing CO concentrations

3. Holding your breath

• CO2 lvls rise -> O2 lvls drop -> triggers increase in breathing

Gas Exchange

• Combo of 2 major processes:

1. External Exchange

• Gases are exchanged b/w the alveoli and capillaries 

• Takes place in the lungs

2. Internal Exchange

• Oxygen rich blood travels from lungs to body tissues 

  • Oxygen diffuses from blood into body cells 

  • CO2 travels from body cells into blood

• Blood now returns to lungs where CO2 is expelled and more oxygen can be picked up

• 30% of O2 transfer occurs thru facilitate diffusion to increase rate of exchange

  • Protein based molecules in wall of alveoli facilitate diffusion by “carrying” oxygen across cell membrane 

  • Process DOESN'T require extra energy -> oxygen moving along concentration gradient from area of high concentration to low concentration

  • Facilitated diffusion js SPEEDS UP gas exchange

Oxygen

• Is carried in blood

• 99% of all oxygen in blood is carried bound to hemoglobin 

  • Oxygen + hemoglobin = oxyhemoglobin

• 1% dissolved in plasma

Carbon Dioxide

• CO2 transported from body cells back to lungs in 3 dif ways:

1. Carbaminohemoglobin - 20%

• Formed when CO2 combines w/ hemoglobin (that gave up their oxygen)

2. Dissolved in the plasma - 10%

3. Bicarbonate ions (HCO3) - 70%

Spirometer: used to measure lung volumes

• Assist w/ diagnosis of lung disorders

Respiratory Volume

• Under normal circumstances -> reg breathing doesn't use full capacity of lungs

• Body needs more oxygen -> volume of air drawn into lungs can increase

• Sipograph: represents amount of air that moves into and out of lungs w/ each breath 

Lung Volume and Spirograph Terminology

• Tidal Volume: amount of air that is inhaled and exhaled in a normal breathing movement

  • 250 - 500 ml

• Inspiratory Reserve Volume: additional air that can be taken into lungs beyond tidal breathing

  •  2500 ml

• Expiratory Reserve Volume: additional air that can be found out of the lungs beyond regular tidal breathing

  • 1500 ml

• Vital Capacity: total of all gas that can be moved into or out of the lungs

  • Tidal volume + inspiratory reserve volume + expiratory reserve volume

  • 3000 - 5000 ml

• Residual Volume: amount of air left in lungs after full exhalation

  • Residual air keeps respiratory system from collapsing on itself

  • 1500 ml

CHAPTER 7.3: Respiratory Health

Respiratory Tract Disorders

1. Tonsillitis: an infection of the tonsils

• Location: pharynx (tonsils located in pharynx)

• Cause: 

  • Common: a viral infection

  • Rare: bacterial infection 

• Treatment: tonsils get removed surgically (if infection is frequent / breathing impaired)

• Symptoms: impaired breathing 

• Benefits of tonsils: 

  • Prevent bacteria / foreign pathogens from entering body

    • Removing tonsils = increase in # of infections ltr in life

2. Laryngitis: inflammation of larynx causing the vocal cords to not vibrate normally 

• Location: larynx

• Causes: 

  • Viral infection

  • Allergies

  • Over straining of voice 

• Treatments: 

  • Medication to clear up suspected infection

  • Voice Therapy (resting your voice, improving your voice)

  • Avoidance of irritation (tobacco products)

• Symptoms: 

  • hard to/can’t speak

  • Sore throat

  • Hoarseness 

3. Bronchitis: inflammation of the bronchi causing it to be filled with mucus, which is expelled by coughing 

• Location: bronchi

• Acute Bronchitis: short term disorder

  • Cause: bacterial infection 

  • Treatment: antibiotics 

• Chronic Bronchitis: long term disorder 

  • Cause: regular exposure to irritants and foreign bodies (cigarettes)

    • Long period exposure to irritants -> cilia destroyed -> cleansing properties (mask filter) stops working -> bronchi becomes more inflamed + higher chance of infection

  • Treatment: 

    • No cure

    • Medication and exercise (reduces symptoms and complications)

    • Quit smoking

  • Symptoms:

    • Cough (aka smokers cough)

    • Chest soreness

    • Coughing up mucus

    • Chest discomfort / wheezing

    • Runny nose, tired and achy, headache, chills, fever, sore throat 

4. Pneumonia: disease that occurs when alveoli in lungs become inflamed and fill w/ liquids

• Interferes w/ gas exchange -> body starved of oxygen

• Location: alveoli / lungs

• Lobular Pneumonia: affects lobe of lung 

• Bronchial Pneumonia: affects patches thru both lungs

• Causes: bacterial and viral infections 

  • Streptococcus pneumonia (bacterial pneumonia): bacterial infection that spreads out of lungs (via bloodstream) and affects other tissues

    • Causes lobular pneumonia

    • Treatment (preventative): Pneumococcal vaccine -> provides long term protection from bacterium

    • Ppl w/ AIDS get rare type of bacterial pneumonia

  • Viral pneumonia: less severe than bacterial pneumonia 

    • Treatment: anti-viral medications

    • Second infection can follow -> needs to be treated w/ separately w/ antibiotics / preparations w/ antibiotic properties

• Symptoms: 

  • Cough

  • Fever, sweating, chills

  • Rapid, shallow breathing

  • Sharp or stabbing chest pain

  • Loss of appetite, low energy, fatigue  

5. Pleurisy: lung disorder caused by swelling and irritation of pleura (membranes that surround lungs)

• Causes: 

  • Viral or bacterial infections

  • Blood clot in lung

  • Cancer

• Symptoms: 

  • Sharp stabbing pain chest (localized in 1 area)

• Treatment: target treating cause of swelling and infection 

  • Anti-inflammatory medication

  • Antibiotics

  • Medication 

6. Emphysema: obstructive respiratory disorder where walls of alveoli break down and lose elasticity 

• Reduces surface area for gas exchange -> causes oxygen shortages in tissue

• Location: alveoli / lungs

• Causes: smoking

• Symptoms

  • Shortness of breath

  • Coughing with mucus

  • Wheezing

  • Chest tightness

• Treatments: permanent and incurable but medications help open up bronchioles to help improve breathing

  • Inhaler

  • Low-flow oxygen tank: provides concentration of oxygen that vary w/ individuals rate of breathing (variable performance system) 

  • Lung volume reduction surgery (effectiveness uncertain)

7. Cystic Fibrosis: serious genetic condition that affects the lungs

• Mucus in lungs get thick -> trap pathogens -> can't cough out

• Location: lungs

• Cause: abnormal gene disrupts function of cells lining passageways of lungs

• Treatments:

  • Medication (thin out mucus)

  • Antibiotics (treat lung infections)

  • Gene therapy (inhaler)

  • High-frequency chest wall oscillation: inflatable vest that is attached to a machine -> machine mechanically performs chest physical therapy by vibrating at a high frequency to loosen and thin mucus.

• Symptoms:

  • Mucus trapped in lungs

  • Infected lungs

  • Trouble breathing

8. Asthma: chronic obstructive lung disease that affects bronchi and bronchioles, making breathing hard / impossible b/c of reduced air flow

• Location: bronchi and bronchioles

• Cause: N/A (genetics?) -> can develop at any age

• Treatments: incurable

  • Inhaler

    • Metered dose inhalers

    • Dry powder inhalers

  • Nebulizer: mask contains medicine suspended in mist

  • Asthma medication reduces inflammation in airways and relax bronchioles -> opens airways

  • Peak flow: measures lung volume -> shows when lung volume decreasing -> warns early asthma attacks

• Symptoms:

  • Asthma attacks: bronchi and bronchioles swell, bronchial muscles tighten, mucus production increases -> causing obstructed airway and difficulty breathing

  • Constant inflammation in airway = sensitive to pollen, dust, cigarette smoke, other air pollutants

  • Difficulty breathing

9. Lung Cancer: uncontrolled invasive growth of abnormal cells in the lungs

• Location: lungs

• Abnormal cells multiply -> form malignant tumors / carcinomas

  • Tumors reduce surface available for gas exchange / stop air from entering bronchioles

  • Tumor grows -> damages tissue -> produces toxins harmful to lung cells

• Causes:

  • Smoking: carcinogens / cancer-causing agents

  • Exposure to Radon: heavy gaseous radioactive element that's colorless and odorless

  • Exposure to asbestos: fibrous mineral resistant to heat and fire 

• Treatments:

  • Surgery

  • Chemotherapy

  • Radiation therapy

  • Targeted therapy

• Symptoms: 

  • Coughing / w/ blood or phlegm

  • Chest pain 

  • Shortness of breath / hoarseness

  • Tired / weak

Technologies for Detecting and Treating Lung Disorders

1. CT Scan (helical low-dose): specialized X-ray that detect lung cancer when tumors are very small

• Tumor gets diagnosed -> past stage for treatment / can't be stopped

• Metastasis: spread of a tumor throughout the body

• Metastatic cells: cancerous cells that are spread

2. DNA analysis: looks for genetic changes that warn the cell may become cancerous 

• Goal: detect lung cancer before tumors grow too large to treat

3. Liposomes: artificial microscopic vesicles that consist of a liquid center surrounded by phospholipid layers

• Manufactured in lab -> filled w/ cancer fighting drugs -> releases into bloodstream

• Tiny size allows them to follow spread of cancerous cells -> attacks cells before cells start uncontrolled growth at new location 

CHAPTER 10.1: Movement and Muscle Tissue

Smooth Muscle

• Cell: long, arranged in parallel lines in flat sheets, tapered at the ends

• 1 nucleus per cell

• Contracts involuntarily -> isn’t under conscious control

• Found in many parts of the body:

  • Bronchioles: made of smooth muscle 

    • dilate or contract to increase or decrease airflow

  • Digestive system: forms sheets of muscles in the walls 

    • moves food along by peristalsis 

  • Blood vessels: in the walls 

    • regulates blood pressure and directs blood flow by vasoconstriction and vasodilation  

  • Sphincters: made of smooth muscle

    • Circular muscles control movement of fluids and control amnt of light that enters eyes 

  • Walls of most internal organs

Cardiac Muscle

• Cell: Striated (alternating bands of light and dark color) cylindrical tube 

  • Branched -> form net like shape

• 1 nucleus per cell

• Contract involuntary -> arent under conscious control

• Found in:

  • Walls of heart: allow heart to continuously pump blood

Skeletal Muscle: “meat” of animal bodies

• Cell: Long, striated (marked with long, thin parallel streaks), cylindrical (tubular) 

• Multiple nuclei -> maintain normal functions of cells

  • Length of skeletal muscle cell -> need for energy and materials -> too much for 1 nucleus to control

• Contract voluntarily -> controlled by nervous system 

• Found: 

  • Attached and anchored to bones of skeleton 

• Structural organization + presence of many nuclei -> cells called fibers 

Functions of Skeletal Muscles:

1. Allow joints to move -> pull on bones they are anchored to

2. Support body and enable us to stand upright

3. Provide protection to organs (kidneys and abdominal organs)

4. Stabilize joints by their attachment thru tendons

5. Maintain body temp by generating heat

Organization of Skeletal Muscles

• Tendons: bands of connective tissue attaching skeletal muscles to bones

  • Assist w/ movement and stability of muscles

  • Withstands certain amnts of tension -> can snap from movements that contradict typical muscle action or overuse

• Ligaments: bind bone to bone

• Muscle fiber bundles (fascicles): muscle fibers that are organized into bundles of many long muscle cells

  • Skeletal muscles made of long muscle cells (muscle fibers)

  • Connective tissue wraps around multiple fascicles and whole muscle itself 

• Blood vessels and nerve fibers

  • Pass b/w bundles of muscle fibers

  • Provide blood supply needed to bring nutrients and oxygen to muscle

  • Are the msgs that trigger and control muscle contractions

• Myofibrils: hundreds of thousands of units within the cytoplasm of each muscle cell (called sarcoplasm) 

• Myofilaments: make up myofibrils (finer/smaller)

  • Types of myofilaments:

    • Actin

    • Myosin

  • Contain proteins responsible/required for muscle contraction

i

Flow Chart Summary of Skeletal Muscle Structure (biggest to smallest)

1. Muscle

2. Muscle fiber bundles (fascicles)

3. Muscle fibers

4. Myofibrils 

5. Myofilaments

6. Actin and Myosins

the best of both of their respective countries uyyyyyyyy hi uuuuuuuuyyy

Actions of Skeletal Muscles

• Muscles can only contract (shorten) -> can only pull -> can't push

• Can't stretch or lengthen past normal state

• A force must stretch a muscle after it's contracted -> muscles work in pairs opposition to each other (antagonistically)

  • Pairs of muscles oppose each other -> produce opposite movements

  • 1 muscle contracts (active state) -> other relaxes (passive state) 

• Muscle contraction occurs from coordinated actions of 2 types of myofilaments:

1. Actin: thin, consisting of 2 protein strands wrapped around each other

• Acts like a rope

2. Myosin: thick, w/ bulbous head attached to rod like tail

• To make muscle fibre contract -> heads have to be attached to binding regions of actin

Sliding Filament Model

• Contraction of muscle fiber -> begins by heads of myosin molecules flexing backwards 

  • Heads attached to actin molecules -> pull actin fibers along

  • Actin slides past myosin in step by step fashion as more heads flex backwards

• Z line: where actin myofilaments are anchored at each end of the muscle

• Movement of actin sliding along -> pulls Z lines towards center of fiber -> shortens muscle

• Takes energy (ATP) for myosin heads to release from actin proteins

ATP: adenosine triphosphate made in cellular respiration

• Aerobic respiration (in presence of oxygen) -> more efficient than anaerobic respiration (in absence of oxygen)

• Anaerobic respiration (fermentation) -> makes little ATP and hella lactic acid -> causes muscle fatigue and cramping

• Respiratory system delivers oxygen to muscles -> helps get rid of built up lactic acid

• Cellular respiration makes hella CO2 and heat -> needs to be taken away from muscles

  • Circulatory and respiratory systems important in transporting heat away -> maintains homeostatic equilibrium

Initiation and Control of Muscle Contraction

• In relaxed state -> myosin heads can't bind to actin molecules

  • Binding sites are blocked by tropomyosin (protein) -> is wrapped around actin

• Muscle needs to contract -> calcium ions bind w/ troponin (protein) -> moves tropomyosin out of the way -> exposes myosin binding sites on actin filaments

CHAPTER 10.2: Muscle, Health, Homeostasis

Muscle tone: muscles contracting at some lvl, even at rest 

• Rely on proper muscle tone to maintain posture and keep us upright

Muscular System Complications

• Muscles vulnerable to injuries -> result of sudden stress on muscles

• Muscles (one of few organ groups) whose activity is impaired thru lack of use

Muscular Atrophy: reduction in size, tone, and power of a muscle

• Results from lack of movement of muscle

• Skeletal muscle experiences reduced stimulation -> fibers decrease in size and become weaker

  • Temp reduction in muscle use can lead to muscular atrophy

• Ppl who experience damage to nervous system / become paralyzed by spinal cord injury -> gradually lose muscle tone and size in affected (injured) areas

  • Atrophy is reversible -> but dead or dying muscle fibers arent replaced

    • Extreme atrophy occurs -> loss of muscle function is permanent 

  • Reason why physical therapy important for ppl who have temp loss of mobility due to injury or surgery

Hypertrophy: muscle fibers get thicker through exercise 

• Muscles grow in size cus each fiber grows larger -> not b/c there are more fibers

• Exercise causes more mitochondria produced in muscles -> increase ATP production

  • Can contract muscles for longer periods of time -> lots of ATP available

Muscle Conditions 

1. Muscular Dystrophy: a collective term for several hereditary conditions in which the skeletal muscles degenerate, lose strength, and are gradually replaced by fatty and fibrous tissue that impedes blood circulation

• Accelerates muscle degeneration in fatal spiral of positive feedback

2. Botulism: potentially fatal muscular paralysis caused by toxin produced by bacterium Clostridium botulinum 

• Toxin prevents release of muscle-stimulating compound (acetylcholine) by muscle-related cells of the nervous system -> leads to paralysis

3. Cramps: painful muscle spasms triggered by strenuous exercise, extreme cold, dehydration, salt (electrolyte) imbalance, low blood glucose, or reduced blood flow

4. Contracture: abnormal muscle shortening NOT caused by nerve stimulation

• Results from inability to remove calcium ions from sarcoplasm or from contraction of scar tissue (ppl w/ severe burns)

5. Fibromyalgia: chronic muscular pain and tenderness associated w/ fatigue and sleep disturbances

• Caused by infectious diseases, physical or emotional trauma, or medications

6. Crush syndrome: shock-like state following massive crushing of the muscles

• eg.) aftermath of earthquake, collapse of building following an explosion, or traffic accident 

• Associated w/: 

  • High fever

  • Heart irregularities caused by potassium ions released from muscles

  • Kidney failure caused by blockage of renal tubules w/ myoglobin released by traumatized muscles 

7. Delayed Onset Muscle Soreness: pain, stiffness, and tenderness felt from several hrs to a day after strenuous exercise 

• Associated w/: 

  • Trauma to muscles

  • Disruptions in myofibrils and sarcolemma

  • Increased lvls of myoglobin and muscle fiber enzymes in blood

8. Myositis: muscle inflammation and weakness resulting from infection or autoimmune disease

Muscle Twitch: a muscle contracting quickly (for a fraction of a sec) when stimulated to a sufficient degree

• Isolated skeletal muscles -> studied by stimulating them artificially w/ electrolytes

  • Attaching muscle to moveable lever and stimulating it -> muscle twitch recorded on myogram

Myogram: a graph recording muscle twitch as a visual pattern

• Shows 3 periods:

1. Latent Period: period of time b/w stimulation and initiation of contraction 

2. Contraction Period: when the muscle shortens

3. Relaxation Period: when muscle returns to it's former length

• Stimulation of individuals muscle fiber w/i muscle -> results in maximal, all or none contraction

  • Contraction of whole muscle varies in strength -> depends on number of muscle fibers contracting

• Summation: when a muscle is given rapid series of threshold stimuli and responds to next stimulus w/o relaxing completely

  • Tetanus: maximal sustained contraction (achieved from summation)

    • Continues until muscle fatigues due to depletion of energy reserves

Slow Twitch Fibers (Type I): muscle fibers contract slowly, but resist fatigue

• Fibers produce energy aerobically -> have large amnt of myoglobin and mitochondria (makes them look darker in color)

• Surrounded by dense capillary beds -> draw more blood and oxygen than fast twitch fibers

• Most helpful in activities like biking, jogging, swimming, long distance running

Fast Twitch Fibers (Type II): muscle fibers adapted for rapid generation of power, but fatigue quickly 

• Fibers depend on anaerobically produced energy

• Most helpful in activities like sprinting, weight lifting, swinging hockey stick, swinging baseball bat

Intermediate Fibers (Type III): fast twitch but have high oxidative capacity (more resistant to fatigue) 

Homeostasis: muscular system allows us to maintain balance/equilibrium