Final Exam Bio PDF

UNIT 1 Open System: Both energy and matter is able to pass in and out of the system, meaning the energy and matter can be transferred to or from the surroundings. Ex: A lake or an ocean, this is due to the fact that heat and matter may move freely in and out the system Closed System: Matter can be...

UNIT 1 Open System: Both energy and matter is able to pass in and out of the system, meaning the energy and matter can be transferred to or from the surroundings. Ex: A lake or an ocean, this is due to the fact that heat and matter may move freely in and out the system Closed System: Matter can be transferred between the system and its surroundings, however energy may be transferred freely Ex: The Earth is an example of an closed system as energy may pass through but matter does not transfer through the atmosphere unless we force it to Biosphere: The biosphere made up of all of the parts where life is seen in Earth - all ecosystems Lithosphere: Earth’s Land -​ The lithosphere is the top layer of Earth, made of mainly soil, rocks, and minerals. Hydrosphere: Earth’s Water -​ The hydrosphere is the sum of Earth’s water Atmosphere: Earth’s Air -​ The atmosphere is the surrounding gases of Earth The Sun: Solar radiation is the primary source of energy and essential for all life on Earth. However, only half (50%) of the energy is absorbed by the Earth surface, 30% is reflected, and 20% is absorbed by the atmosphere. Albedo: Albedo is the amount of solar energy that is reflected by clouds, water, and land.  -​ An example of high albedo would be the arctic lands covered by snow, as 85-90% of the heat is reflected. -​ An example of low albedo would be the plains or grasslands, as 70% of the heat is absorbed by the surface When arctic ice melts the darker ocean which absorbs more heat, causing even more ice to melt, making the Earth warmer overall. Organization of the Biosphere -​ Biospere: The biosphere made up of all of the parts where life is seen in Earth - all ecosystems -​ Ecosystem: A community and it’s abiotic factors in an environment -​ Community: Multiple different species living together in the same area and time -​ Population: The same species living in the same area and time -​ Species: A group of organisms that can naturally breed to create fertile offspring -​ Individual Organism: A single member of a species -​ Organ Systems: Groups of organs that function similarly to produce life -​ Organ: Group of tissues that function similarly -​ Tissue: Group of cells that function similarly -​ Cells: The smallest functional unit of life Autotrophs/Producers: These are organisms that get their energy from light (phototropes) or nonorganic energy sources (chemotropes) -​ They convert nonorganic compounds into organic forms -​ As the 1st trophic level, they support all other life forms Plants are a great example of phototropes as they perform photosynthesis, turning CO2 and H2O into glucose. Abiotic: space, temperature, altitude, and amount of sunlight Biotic: food, mates, and competition with other organisms for resources DDT This was effective and reduced the mosquito population (along with other insect species), however this had lasting effects on the food web This created a domino effect on the food web, causing animals that fed on the affected insect species to also decrease The pesticides unintentionally harmed cats, causing many to die. Due to the decrease of cats, the rodent population spiked significantly. DDT reduced the calcium in birds eggs causing them to be incredibly brittle. Also decreased hormones which caused egg laying rates to decrease. These effects almost led to the extinction of the Bald Eagle. Accumulation and Amplification: -​ Bioacccumalation is when toxins such as pesticides and chemicals build up in the tissues of a single organism. -​ Bioamplification (biomagnification) is when chemicals and toxins increase across trophic levels. Intraspecific: interactions of the same species Interspecific: 2 different species relations Biogeochemical Cycles Life of earth depends on recycling of essential chemical elements Because nutrient circuits involve both biotic and abiotic components of ecosystems, they are also called biogeochemical cycles. Digestion -​ Complex, organic molecules are broken down into simpler molecules that become a part of the body structure Decay -​ Decomposers break down organic matter in dead bodies and feces, which will become a part of the living world in the future Hydrological Cycle -​ Water is a polar molecule with unique properties to make life possible Properties of water -​ Absorbs, releases, and moderates thermal energy -​ Is the medium in which metabolic reactions occur -​ A ‘universal’ solvent -​ Makes up > 60% of cells’ mass -​ Provides hydrogen to producers during photosynthesis; oxygen atoms to all organisms during cellular respiration -​ Is a reactant in some metabolic activities and a result in others Water molecules are held together by covalent bonds These bonds explain -​ High melting/boiling points -​ More energy required to break the bonds Region of “-” charge is created near O atom Region of “+” charge is created near H atom “-” end of one H2O molecule repels the “-” (negative) end of another H2O molecule but attracts the “+” (positive) end. This attraction of opposite charges creates a hydrogen bond which pulls water molecules together. Water has numerous important roles in order to maintain life, such as -​ Maintaining global heat balance -​ Acting as a solvent in reactions movement of water through environment: from atmosphere to earth -​ Volume of water remains constant, specific amounts vary in phases; water continuously cycles. This depicts:  -​ Evapotranspiration from plants -​ Precipitation over ocean -​ Movement over land by wind -​ Precipitation over land -​ Percolation through soil -​ Runoff and groundwater -​ Leaching of nutrients by percolation -​ Evaporation from ocean Transpiration: Loss of water from plant leaves. This is a naturally occurring consequence of plants ‘breathing’ through tiny pores known as stomata. Evaporation: Changing the state of matter from liquid to a gas, often in response to heat energy. Condensation: Changing the state of matter from gas to a liquid, usually in response to a decrease of temperature Precipitation: Snow or rain Percolation:Movement of a liquid through porous material (such as soil) Leaching: Removal of a solute by percolation. Ex: nutrients leach out of soil and into waterways. There are two sources of freshwater: -​ Surface water: Water from precipitation above ground -​ Groundwater: Water which has moved down through soil Percolation: -​ Water percolates faster through larger soil particles -​ Water eventually fills lower levels of soil (sand and gravel). Water table forms above a layer of relatively impermeable bedrock or clay Aquifer: A body of permeable rock which can contain or transmit groundwater Water table: The upper surface of the zone of saturation Zone of saturation: Where the pores and fractures of the ground are saturated with groundwater. Unsaturated zone: Where the pores and fractures of the ground are not saturated with groundwater. Typically above the zone of saturation. Leaching (in more detail): Seeping water carries dissolved organic matter and minerals to lower layers of soil. Plants reduce leaching by extending long branch roots deep into the soil Acid deposition: Acid rain occurs because of poisonous gases that are released when fossil fuels are burned. These gases enter the atmosphere and return to earth in the form of rain or snow. Coal-burning plants, metal smelters, and oil refineries release sulfur during combustion. Sulfur is released as a poisonous gas, sulfur dioxide (SO2). Processing of nitrogen fertilizers, combustion in automobiles, and fossil fuel-burning power plants produce various nitrogen oxides (NOx). SO2 and NOx combine with H2O droplets to form acids in the atmosphere. Pollution is SO2 Noxious Noxious: Harmful, poisonous, or unpleasant Acid precipitation kills fish, soil bacteria, and aquatic and terrestial plants Alkaline soils minimize impact by neutralizing acids before they runoff to streams and lakes SO2 and NOx can remain airborne, depending primarily on weather conditions Dry pollutants can combine with moisture and form acid on lawns, surface of lakes, and respiratory tracts of humans pH 5.5-5.9 is considered normal for water Acid precipitation leaches out heavy metals (such as mercury) from soil, which are then washed into lakes and rivers Leads to bioaccumalation and bioamplification in fish The Carbon and Oxygen Cycle Carbon is a component of all living and deceased organisms; thus it is considered organic Plants perform photosynthesis which converts carbon dioxide and energy into glucose. Both plants and animals perform cellular respiration, which converts oxygen into carbon dioxide and energy Soil organisms decompose dead organic material, returning the carbon into the soil Oxygen is a irreplaceable component of photosynthesis and cellular respiration -​ The cycling of oxygen is part of the carbon cycle as well -​ Oxygen produced by plants during photosynthesis -> atmosphere -> living organisms during cellular respiration Oxygen is also incorporated in the following -​ Ozone -​ CO2 -​ Rocks -​ Decomposition -​ Oceans (H2O) store excess CO2  -​ Gas reacts with H2O to form an inorganic compound called calcium carbonate (CaCO3) -​ Shellfish use this to create their shells -​ Carbon is stored in shells at the bottom of the Ocean -​ Therefore, we call the ocean a carbon sink Fossil fuels A biofuel created when dead organisms are compressed over long periods of time. (This is a nonrenewable energy source) Carbon is released into the atmosphere when fossil fuels are burned This additional carbon throws off the dynamic equilibrium of the cycle, disrupting natural cycling and leading to climate change The Greenhouse Effect: Carbon dioxide traps energy in the atmosphere and increases the average temperature of the Earth Inorganic carbon can be found in three main reservoirs: -​ Atmosphere -​ Ocean * -​ Earth's crust Organic carbon is held in the bodies of living things. Since living things eventually die, carbon will eventually return to the inorganic form. Bogs break rules - they store huge amounts of carbon in the inorganic form Carbon cycle: CO2 in atmosphere -> Photosynthesis-> Consumers-> Decomposition-> CO2 in the atmosphere (cellular respiration also contributes to CO2 in the atmosphere) Types of Greenhouse Gas -​ * Carbon dioxide (CO2) -​ * Methane (CH4) -​ * Nitrous Oxide (NO2) -​ Hydrofluorocarbons (HFCs) -​ Perfluorcarbons (PFCs) -​ Nitrogen trifluoride (NF3) -​ Sulfur Hexafluoride (SF6) The Nitrogen cycle consists of four key components: -​ Nitrogen fixation -​ Ammonification -​ Nitrification -​ Dentrification Nitrogen is an important component of all component of all proteins and nucleic acids (which make up our DNA: cytosine, thymine, guanine, and adenosine) Nitrogen is a whopping 78% of Earth’s atmosphere, and is an essential component of our genetic material (DNA). However, most organisms cannot actually use the atmospheric nitrogen directly The main process begins by bacteria and other organisms fixing the nitrogen and turn it into usable nitrates Animals obtain nitrogen by consuming plant life A long-term deficiency of nitrogen can lead to a large number of defects. Nitrogen fixation The process by which gaseous atmospheric nitrogen (N2( gets converted into ammonia NH3). Bacteria is responsible for 90% of nitrogen fixation, whereas lightning makes up the other 10% -​ Fertilizers provide organic nitrogen artificially -​ Lightning causes nitrogen fixation because the incredible amount of heat, breaks the bonds of atmospheric nitrogen molecules Nitrogen-fixing bacteria live in special nodules in the roots of plants called legumes. Many legumes are grains like beans, lentils, peas, and peanuts Rhizobium are a specific type of nitrogen-fixing bacteria that live in the nodules of legumes. The relationship between the two organisms is ‘endosymbiotic’. (a symbiotic relationship where one organism live inside the other) Ammonification Decomposers convert nitrogen products (from tissues) into ammonia (NH3) and ammonium (NH4). The decomposers include bacteria, soil, and fungi. Nitrification A process performed by nitrifying bacteria and fungi, in which ammonium ions convert into nitrites (NO2) and then into nitrates (NO3). The nitrates are then absorbed by plants and used to make amino acids, where they travel from trophic level to trophic level via consumption. Denitrification The process by which nitrates (NO3) convert into dinitrogen gas (N2) and return it to the atmosphere so the cycle can begin anew. This process is carried out by denitrifying bacteria and fungi Fertilizers -​ Chemical fertilizers: focus on feeding the plant in the soil using chemicals that contain (nitrogen, phosphorus, and potassium) -​ Natural fertilizers: ‘feed the soil’, contains nitrogen, phosphorus, and potassium -​ Manure: animal dung contains nitrogen which is ammonified first in soil, then nitrified to provide useful nitrates ______________________________________________ UNIT 2 Taxonomy -​ Binomial nomenclature (Genus, species) e.g. homo sapien, canis lupus The order of taxonomic ranks from least to most specific: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species (remember Dear Kevin, Please Come Over For G** S**) -​ The three domains (Bacteria, Archaea, Eukarya) Both bacteria and archaea consist of prokaryotic cells, meaning they do not have nuclei and therefore do not use mitosis to reproduce. Archaea are closer related to eukarya than it is to bacteria. Bacteria have peptitoglycan whereas archaea and eukarya do not. -​ The definition of Protista Eukaryotic cells that are neither animal, plant, or fungi. -​ The definition of Chordata Members of Chordata (aka Chordates) all possess a form of a spinal cord -​ The definition of Hominids Hominids are all a part of the family: hominidae, meaning “Great Apes” -​ The three phylum: Animalia, Plantae, Fungi (Bacteria and the others also have phyla) -​ How to use a dichotomous key to identify species -​ Intraspecific vs. interspecific competition and examples of each Intraspecific competition is competition within the same species e.g competition for mates or plants of the same species grown close together competing over nutrients (kangaroos fighting for mates) Interspecific competition is competition between different species ​ e.g. competition for habitats or prey between different species (lions and hyenas) -​ Ecotones Transitional areas between ecosystems which have higher diversity than either ecosystem because the organisms from each ecosystem move back and forth. e.g. A marshland: found in between land and aquatic ecosystems, amphibians and birds often live here. -​ Niches and how they are formed Niches are an organism's role in an ecosystem including: its habitat, breeding area, and its place in the food web. Niches are formed to create less competition between species, usually formed by species living/takingk up in different habitats. -​ The detrimental effects of exotic (or invasive) species Invasive species can carry foreign diseases which native species haven’t built an immunity to or overpopulation due to having no natural predators in the region. This overpopulation can be extremely harmful to native species as they can over hunt certain species and take up niches which are already filled by native species, essentially taking up nutrients that they need to survive. -​ Identify key abiotic factors Climate, latitude, elevation, temperature, humidity, moisture, salinity, and light Ecology -​ Biotic potential Biotic potential is the maximum amount of offspring a species could produce if faced with unlimited resources (impossible to achieve in nature due to limiting factors) -​ Carrying capacity The maximum amount of individuals that belong to one species that an ecosystem can support -​ Law of the minimum States that the nutrient in the least supply is the one that limits growth -​ Law of tolerance States that an organism can survive only within a particular range of an abiotic factor (above or below the range, it cannot survive) -​ Density-dependent factors Limit a population from growing too large e.g. food and water shortage, sexual competition, infectious disease, invasive/exotic species, increased predation -​ Density-independent factors Affects a population regardless of the population density e.g. natural disasters like floods or fires, pesticides, climate and temperature change, habitat destruction, drought Evolution Artificial selection Artificial selection is the human interference of natural selection, forcing species to evolve to their liking.  e.g. domestication of dogs into different breeds, the gradual selection for more flavorful watermelons Vestigial traits Vestigial traits are traits that lost their primary use over the course of evolution e.g. Wisdom teeth, appendixes, and a whale’s pelvis How variation occurs due to mutations Mutations are small changes in genetic code which often lead to physical changes. e.g. blonde hair and blue eyes derived from a mutation of the originally universal brown hair and brown eyes. Point mutation: When a single nucleotide base (the fundamental unit of genetic information) is changed, added or deleted. The different nucleotide bases are adenosine, thymine, guanine and cytosine. Fitness: The likelihood of an organism making it to reproductive age Natural selection: Natural selection is one mechanism by which evolution can occur. Through natural selection, traits that increase fitness are more likely to be passed to the next generation. -​ Analogous structures Structures which serve similar purposes that have evolved separately a number of different times. These do not indicate evolutionary relationships. (Similar purpose, evolved separately) -​ Homologous structures Structures which serve different purposes but are anatomically similar. Indicates evolutionary relationships. (Different purposes, evolved from same ancestor)  -​ Gradualism Gradual changes that occur steadily over time -​ Punctuated equilibrium Long periods of evolutionary equilibrium are interrupted by periods of speciation, typically following a mass extinction -​ Speciation New branching off of species from the same population ______________________________________________________________________ UNIT 3 Photosynthesis -​ 6CO2 + 6H20 + Light energy →C6H12O6 + 6O2 -​ Photons are the particles that make up light. Each photon is a small unit of energy which forms waves. Long waves have low energy(radiowaves, microwaves, infrared), short waves are high in energy (X-rays, UV rays, gamma rays). -​ Different surfaces absorb/reflect light differently. A surface may absorb all light but reflect green light, resulting in us seeing the object as green. The different types of light are ROYBGIV. -​ Chlorophyll a is the primary pigment and chlorophyll b and carotenoids are known as accessory pigments, all of which absorb different kinds of light for maximum photosynthetic efficiency -​ Eukaryotic cells have a nucleus -​ The cytoplasm is a clear liquid that fills the cell -​ Ribosomes are organelles that produce proteins -​ The cell membrane is the outermost layer of animal cells, and the cell wall is the outermost layer of of plant cells -​ Photosynthesis only occurs in plant cells & some bacteria and archaea  -​ Plant cells have the following unique organelles: -​ Vacuoles store water -​ Chloroplasts carry out photosynthesis -​ The cell wall provides support -​ Mitochondria carry out cellular respiration -​ Be able to visually distinguish between chloroplasts and mitochondria and label a basic diagram of the previous organelles -​ Structure and function of chloroplasts -​ Thylakoid membranes (where light dependent reactions take place) -​ Grana (Thylakoids are made of stacks of grana) -​ Stroma (colorless liquid which is found within chloroplasts) -​ Chloroplasts have two membranes: Inner membrane and outer membrane -​ Pro: Each stoma allows for gas exchange of carbon dioxide and oxygen with the atmosphere. Con: Evapotranspiration, meaning that the water escapes through the form of gas -​ Most chloroplasts are found in the palisade mesophyll layer Cellular respiration -​ Light dependent: generates high-energy molecules (ATP, NADPH) which is required for light independent reactions. Requires sunlight and Oxygen is a byproduct. Light independent: Converts high-energy molecules into G3P which is used to create glucose. G3P is a product of the calvin cycle -​ Anabolic pathways: Synthesize large molecules from smaller ones (endothermic). Photosynthesis is an example because it constructs glucose from particles derived from the sun’s energy. -​ Atabolic pathways: Break down large molecules into smaller ones (exothermic). Cellular respiration is an example of this because it breaks down glucose and converts it into ATP. -​ Adenosine triphosphate (ATP) and Adenosine diphosphate (ADP) + phosphate **ATP becomes ADP when it is used up -​ LEO the lion says GER -​ Steps of glycolysis -​ *Glycosis is the process by which a glucose molecule is split into two pyruvate molecules. This is done through two major stages, the first one is the investment stage, then the second is the pay off stage. -​ Glucose gets rearranged and two phosphate groups (coming from ATP) attach to it. It becomes ↓ -​ Fructose-1,6-bisphosphate (F-1,6-BP): this sugar is unstable so it won’t stay very long. This sugar then forms two phosphate-bearing three carbon sugars which become ↓. Two ATP molecules are used up in this process. -​ Glyceraldehyde-3-phosphate (G3P) (x2). In this process each G3P molecule makes two ATP molecules and one NADPH molecule. -​ Pyruvate (x2) In Pyruvate Oxidation, each pyruvate molecule is oxidized (loses electrons). These electrons are taken up by NADP+, producing NADPH. Because the NADP+ gained electrons, it was reduced to become NADPH. -​ Steps of Krebs Cycle -​ Acetyl CoA + -​ Oxaloacetate ↓ -​ Citrate returns back into oxaloacetate and the cycle restarts -​ Products of one Krebs turn: 2x CO2, 3x NADPH, 1x FADH2, 1x ATP -​ Steps of oxidative phosphorylation -​ Movement of electrons along Electron Transport Chain  -​ NADPH reduces Complex I -​ FADH2 reduces Complex II -​ Ubiquinone -​ Complex III -​ Cytochrome C -​ Complex IV -​ Purpose of ETC (Electron transport chain) is to create an H+ proton gradient from the matrix into the intermembrane space. -​ Movement of H+ protons through ATP synthase generates energy. -​ 38 ATP produced total, 34 from oxidative phosphorylation alone -​ Oxygen as the final electron acceptor, creating H2O -​ Lactate fermentation is when the body uses up its oxygen in the muscles. Ethanol fermentation is used by a number of bacteria, in ethanol fermentation, the byproduct is alcohol. -​ Anaerobic respiration happens in places where oxygen is in a short supply, so they have to create energy from food in a different way. -​ Aerobic respiration is in the presence of oxygen. ______________________________________________ UNIT 4a-b Motor system -​ Voluntary skeletal movements are movements made by muscles attached to the bone (these movements are controlled by the systemic nervous system meaning you can control them) -​ Some muscle fiber types, like cardiac or smooth muscles, are controlled by the autonomic nervous system -​ Sliding filament theory: triggered by a nerve impulse, actin and myosin overlapping with one another causes muscle contraction, relative  positioning of actin and myosin, ATP and calcium ions are required for the process. Lack of ATP (at death) is the cause of rigor mortis Circulatory system Pulmonary and systemic systems -​ pulmonary circuit is the flow of blood from the heart to the lungs and back, oxygenating the blood for system circulation -​ Systemic circuit is the flow of oxygenated blood from the heart to the body and deoxygenated blood back to the heart Label and describe the flow of oxygenated and deoxygenated blood​ -​ >the superior and inferior vena cava bring deoxygenated blood from the body to the right atrium of the heart -​ >the deoxygenated then goes down an atrioventricular valve into the right ventricle -​ >then the deoxygenated goes through the right and left pulmonary arteries into the lungs -​ >the blood becomes oxygenated and it passes through the right and left pulmonary veins into the left atrium -​ >the oxygenated blood travels through an atrioventricular valve into the left ventricle -​ >it gets passed through the semilunar valves into the aorta to leave the heart for the body  Label: -​ septum (the tissue that separates the right and left sides of the heart) -​ atrioventricular valves -​ semilunar valves -​ inferior and superior vena cava -​ Aorta -​ left and right atria -​ left and right ventricles -​ pulmonary veins and arteries ===================================================== -​ The cause of the lub-dub heartbeat sound (valves closing) and the reason why it is so pronounced (the heart valves have to be strong to prevent backflow of blood into previous chambers) Describe the flow of electrical impulses through the heart: -​ >sinoatrial node causes atria to contract -​ >triggers signal to atrioventricular node -​ >which sends a message through the Bundle of His to the Purkinje fibers ultimately causing the ventricles to contract Relative sizes and purposes of blood vessels (smallest to largest): -​ Capillaries: single cell thick, they are so thin they allow gas exchange between the capillary and tissue -​ Venules: Branching of veins -​ Veins: Carry blood towards the heart -​ Arterioles: Branching of arteries -​ Arteries: Arteries are thick and elastic to withstand blood pressure; Veins’ one-way valves and rigid structure push blood against gravity; Capillaries are one cell thick to allow gas exchange ===================================================== -​ An ECG for a healthy resting person shows consistency and is calmer with less spikes compared to the stress ECG -​ a person engaging in physical activity shows spikes which are closer together -​ a person suffering a heart attack shows irregular and/or less frequent electrical impulses -​ The buildup of cholesterol in heart valves and blood vessels can increase blood pressure -​ Relative contents of blood: plasma makes up most of the volume, then red blood cells, then white blood cells and finally platelets -​ Plasma makes up over half of blood, it is a liquid combination of gases and water. It carries nutrients, hormones, and waste products, red blood cells, white blood cells, and platelets -​ Erythrocytes (red blood cells) use an iron-containing pigment called hemoglobin which binds oxygen, their purpose is to transport oxygen -​ Leukocytes (WBCs) and erythrocytes (RBCs) mature in the bone marrow. Leukemia is cancer of the bone marrow and it is characterized by an abnormal increase in the production of immature white blood cells. Leukemia leads to a significantly weakened immune system and causes blood to clot irregularly. The steps of blood clotting: -​ >chemical messengers signal platelets to the site of injury which then rupture and release substances -​ >these released components result in thromboplastin being created. -​ >thromboplastin, calcium ions, and prothrombin (a protein secreted by the liver) create thrombin. -​ >thrombin reacts with fibrinogen (a protein located within the plasma) to create fibrin -​ >fibrin strands form a mesh, blocking red blood cells from escaping by forming clots through coagulation -​ >Hemophilia is a hereditary genetic disorder that causes an under-production of platelets. A major issue is that with hemophilia, wounds will bleed nearly endlessly without outside help. Vasodilation is blood vessels expanding and moving towards the skin to release heat. Vasoconstriction contracting and moving away from the skin, conserving heat Lymphatic (Immune) system -​ Lymphatic system consists of lymphatic vessels and lymph nodes -​ Lymph nodes are where leukocytes mature, and where macrophages and other lymphocytes are produced. Lymph nodes can swell when a person is sick due to the hyperproduction of lymphocytes First line of immune defense:​ These help prevent a pathogen from entering the system. skin, eyelashes, tears, stomach acid, nose hairs, mucous membranes, and cilia are all examples Second line of defense (inflammatory response): Phagocytes Phagocytic cells such as macrophages engulf and destroy pathogens, causing swelling and fever. They leave behind pieces of the pathogen that will be used in the third line of defense Third line of defense (antibody-mediated immunity): There are three kinds of T-cells -​ Helper T-cells: A type of lymphocyte which is tasked with analyzing the pathogen which has been broken down by phagocytosis. (they signal B-cells to assist them) -​ Killer T-cells: Another type of lymphocyte, their job is to simply kill and destroy cancer or virus infected cells. -​ Suppressor T-cells: These cells ensure the Killer T-cells do not kill healthy cells. There are two kinds of B-cells: -​ Memory B-cells: These cells remember previously dealt with pathogens, they can signal a phagocyte if a familiar pathogen has appeared. This is accomplished by using antibodies (proteins) that match antigens (proteins) displayed on the pathogen. -​ Plasma cells These cells produce antibodies that recognize and attach to the antigens of specific pathogens, essentially slowing the pathogen and marking it. Plasma cells circulate with antibodies all the time, while memory B-cells only work if a recognizable pathogen is present. Antibodies vs. Antigens -​ Antibodies are proteins in the bloodstream that recognize another type of protein called antigens. When they lock on to these foreign bodies, a  series of events is triggered in order to neutralize/kill them. Antibodies are usually Y-shaped -​ Antigens are proteins that grow off of a pathogen. Their purpose is to help the pathogen evade the immune system but it often backfires. Once a pathogen is broken down by phagocytosis, B-cells will remember the antigens and produce antibodies to identify them. -​ Vaccines work by introducing a deactivated pathogen into your body. The pathogen does not have the ability to reproduce or infect your tissues but it does carry the antigen which will allow your body to create antibodies to be able to recognize the pathogen if it is ever contracted. ​ When the body detects the presence of the deactivated pathogen, it launches a full scale immune response, although there is no actual threat which is why some may feel sick following a vaccination. -​ Antibodies and antigens are proteins and therefore deteriorate with time, which is why booster shots are often required a few years after a vaccination ===================================================== Aids is caused by HIV (human immunodeficiency virus); this virus specifically targets and kills T-cells, preventing your immune system to properly react to pathogens properly. HIV does not directly kill you, rather it cripples your immune system to the point where you are extremely susceptible to any pathogen. ABO grouping: A: People with blood type A produce A-antigens on their RBCs and they have anti-B antibodies within their plasma, ready to attack B-antigens B: produce B-antigens, their plasma contains anti-A antibodies AB: produce both B-antigens and A-antigens, they have no antibodies in their plasma, meaning they will not attack any blood antigens O: produces no antigen, their plasma contains anti-A and anti-B antibodies -​ Rh grouping: Individuals are either positive (+) and have the Rh antigen or are negative (-) and do not have the antigen The antigens of our blood are found on the RBCs, whereas the antigens of pathogens are found growing out of the pathogenic cells -​ Agglutination occurs when you receive the wrong kind of blood, your blood will agglutinate and die. Combinations of blood types which may cause it: B->A A->B AB->A AB->B Any blood type other than O->O The universal donor is O- as it doesn’t have any antigens on their RBCs The Universal recipients is AB+ as it doesn’t have any antibodies in its plasma Cause of Erythroblastosis fetalis: In subsequent pregnancies where the mother is Rh- but her first child is Rh+ The cause of allergic reactions is when the immune system recognizes harmful foreign particles as serious threats. This causes the immune system to launch in full. ______________________________________________ UNIT 4-d Respiratory System  -​ The anatomy and functions of the respiratory system: Oral cavity Gases circulate through Bronchi Bronchi are branches of the the oral cavity to inhale trachea that split into each and exhale. lung. They are mucus lined to prevent pathogens from entering the lungs. Nasal cavity Gases circulate through Pleural A thin, fluid filled membrane the nasal passage to membrane which surrounds the lungs. inhale and exhale. This allows the lungs to expand and contract without friction. pharynx The passageway to the diaphragm A muscle which works with rest of the respiratory the rib muscles to move air tract. in and out of the lungs. Larynx Contains the vocal Intercostal The rib muscles cords which contract as muscles air passes to form sound. glottis The entrance to the bronchioles Branch from the bronchi. Not trachea. rigid/no cartilage epiglottis A thin piece of cartilage alveoli Tiny clusters of air sacs that covers the glottis. found at the end of This prevents food from bronchioles. Site of gas entering the trachea. exchange Trachea Your airway where the capillaries Gas exchange occurs by lower respiratory tract diffusion between the alveoli begins. The trachea is and gases dissolved in the rigid because it is blood flowing through the supported by rings of adjacent capillaries. cartilage. -​ The right lung has 3 lobes and the left 2 due to the heart -​ The nases (nostrils) are lined with ciliated cells and secrete mucus in order to keep pathogens and foreign bodies out -​ Which sections of the tract are cartilaginous: epiglottis, trachea, bronchi -​ Inhalation: oxygen is required by cellular respiration to create ATP to fuel the body’s cells Exhalation: a byproduct of cellular respiration is CO2, which in overly high concentrations acidifies the blood With help from the intercostal muscles, the diaphragm moves air in and out of the lungs. The reason air flows into the lungs is because of a difference in pressure: when the diaphragm contracts, the lungs lose pressure and air fills the lungs. When the diaphragm relaxes, it presses against the lungs and forces air out. Gas exchange occurs by diffusion between the alveoli and gases dissolved in the blood flowing through the adjacent capillaries. The blood has a high concentration of CO2, so it diffuses into the low CO2 concentration of the alveoli. The alveoli has a high concentration of oxygen, so it diffuses into the blood and transported Carbaminohemoglobin and oxyhemoglobin are the results of hemoglobin combined with carbon dioxide and oxygen respectively Hemoglobin + CO2 -> Carbaminohemoglobin Carbonic anhydrase is an enzyme that increases the conversion of CO2 carbonic acid (H2CO3) to decrease CO2 levels for faster removal by blood. This is so the blood can continue to absorb CO2 down its concentration gradient. However, acid is bad news for blood. To fix this pH problem carbonic acid (H2CO3) dissociates into H+ (which also helps oxygen bind to hemoglobin) and bicarbonate (HCO3-) to buffer the blood. The part of the brain responsible for controlling breathing is the medulla oblongtsa. The medulla oblongsta has chemoreceptors which detect the concentration of CO2 and react by sending a nerve impulse to make the diaphragm contract/relax. Hypoxia is a state of low oxygen, during which signals are fired to increase the breathing rate. Spirometry: -​ Total lung capacity: the total amount of air the lungs can hold -​ Vital capacity: the maximum volume of air that can be expelled out of the lungs forcefully after a deep inspiration -​ inspiratory reserve volume: the volume of additional air that could be inhaled forcefully after a normal end-inspiration -​ Expiratory reserve volume: the volume of additional air that could be expired forcefully after a normal-end expiration -​ Tidal volume: the volume of air in a normal breath in and out -​ Functional residual capacity: the volume of air in the lungs after a passive expiration (normal breath rather than deep breath) -​ residual volume: the volume of air that remains in the lungs even after a forceful expiration. Normally, lungs can’t be completely emptied even after forceful expiration otherwise they would collapse Emphysema is the alveoli becoming so inflamed to the point where they can no longer stretch, this can lead to rupturing of the alveoli. Common causes are smoking and vaping Biochemistry: Carbon, hydrogen and oxygen are found in all food molecules Carbohydrates -​ Isomers are carbohydrates with the same chemical formula but arranged in different ways. Monosaccharides (glucose/fructose), disaccharides (sucrose, lactose, maltose), and polysaccharides (starch, cellulose) -​ Monosaccharides can switch between cyclic and chain forms -​ Dehydration synthesis is the loss of a hydroxide ion from one monomer and a hydrogen ion from another to create a bond between sugars. This is the process of forming disaccharides -​ Cellulose is a source of fiber, not energy Lipids - Composition: fatty acids, carboxyl group, non-polar -​ Used in cell membranes (phospholipids) -​ saturated fats: only single bonds, as single bonds are easier to pack, they are usually solid at room temp unsaturated fats: at least one double bond, tend to be liquid at room temp because it is more difficult to pack the chains -​ Triglyceride = Glycerol + 3 fatty acids formed through dehydration synthesis (it stores energy but an excess can lead to unhealthy fatty buildup in blood vessels) -​ Amphipathic nature of phospholipids, hydrophilic head and hydrophobic tail and why this causes the formation of phospholipid bilayers -​ Cholesterol’s negative and positive effects (used to make hormones like estrogen and testosterone, but also can clog arteries and lead to atherosclerosis) Proteins -​ Contain nitrogen -​ 20 amino acids in existence, 9 of which we do not synthesize -​ Amino acids form polypeptides which form proteins -​ enzymes and antibodies  -​ Enzymes decrease the activation energy of reactants. The ability of enzymes to facilitate a chemical reaction is influenced by factors such as pH, temp, and substrate concentration. Beyond 37 celsius causes denatured proteins but increased temperature increases enzyme activity to a point. -​ The higher the substrate concentration, the higher the enzyme activity, until there are no more enzymes to catalyze with. -​ Macromolecules are molecules such as proteins, lipids, and carbohydrates and monomers are the contents of them (e.g. amino acids are the monomers of proteins) Digestive System Mouth: The start of the digestion process, the mouth chews food into smaller pieces and creates a bolus salivary glands: secretes saliva which contains salivary amylase to break down starch into disaccharides Esophagus: As the bolus enters the esophagus, it is moved towards the stomach via contractions of the esophageal tissue known as peristalis stomach: Food undergoes chemical and physical digestion in the stomach. Chemical digestion by the stomac acid, physical by the churning via the stomachs muscular layers contracting small intestine: Main function is to complete digestion of macromolecules and to absorb the resulting nutrients large intestine: rectum: Main function is to concentrate and eliminate waste products through the anus anus: exit point of the waste liver: main function is to secrete bile salts which play a crucial role in digesting specifically fats Gallbladder: storage of bile from liver Pancreas: The pancreas delivers a fluid containing multiple enzymes to the small intestine. These include trypsin, chymotrypsin, pancreatic amylase and lipase. Most digestion occurs in the small intestine, however, the stomach does digest certain molecules (water, salts, alcohol, and aspirin) Peristalsis: contractions of the esophageal tissue to move bolus through Bolus: a ball of food Chyme: a substance that is created when food mixes with gastric juices -​ Increasing surface area of small intestine: segmentation, villi and microvilli Stomach absorbs water, salts, alcohol, painkillers; small intestine is where the vast majority of absorption occurs; large intestine absorbs remaining water and salts to form feces Enzymes from the pancreas and liver are secreted into the small intestine to complete chemical digestion Purposes of different enzymes: pepsin, trypsin, and chymotrypsin (proteins into polypeptides into amino acids) amylase (starches into disaccharides), lipase (lipids into fatty acids) pancreas secretes bicarbonate ions to neutralize pH Esophageal sphincter prevents stomach acid from splashing into the esophagus. In the event it fails, heartburn occurs when there is a weak point in the stomach mucus lining it leads to ulcers Emulsifying lipids with bile salts (created in the liver and held by the gallbladder) Gut bacteria breaks down undigested food, producing vitamins (B-12 and K) and aiding in the digestive breakdown process Purpose of the appendix is to store digestion-aiding bacteria, consequences of appendicitis include pain, nausea, vomiting and fever. ______________________________________________ UNIT 4e -​ The aorta feeds into the renal artery to bring blood to the kidney, which then exits the kidney through the renal veins to the vena cava (a large vein) -​ Purpose of the excretory system (to filter blood and remove wastes and excess nutrients, as well as regulate the amount of salt and water in the body) -​ Movement of blood -> filtrate -> urine through the body (Through nephrons, collecting duct, renal pelvis, ureter, bladder, urethra, exits body as urine) -​ Two kidneys and two ureters cortex: a layer of connective tissue which encircles the kidney Medulla: lies beneath, in the middle of the cortex renal pelvis: joins the kidney to the ureter  afferent and efferent arterioles glomerulus Bowman’s capsule proximal convoluted tubule proximal straight tubule descending and ascending limbs of Loop of Henle distal straight tubule distal convoluted tubule collecting duct -​ Know that capillaries surround the nephrons Filtration -​ Water, salts, glucose, amino acids, hydrogen ions and urea are filtered out of the blood through the glomerulus into the Bowman’s capsule -​ Blood components should not pass through — blood in urine likely indicates a rip or scrape somewhere in the urinary tract -​ Urea formed from excess proteins being broken down by the liver Reabsorption:  Proximal convoluted tubule begins reabsorbtion of water, salt, glucose, potassium, amino acids, and urea mostly through active transport (requires energy). Water absorbtion occurs most efficiently in the descending limb of the loop of Henle. The loop of Henle descends down into the salty medulla allowing for water to be absorbed via osmosis. The ascending limb of the loop of Henle is impermeable to water. This is where salt is reabsorbed through diffusion (in the lower part) and active transport (in the upper part) (water is attracted to salt, so it moves OUT of the nephron) Hormones control additional reabsorption of water (ADH) and salt (aldosterone) in the distal convoluted tubule -​ Aldosterone makes the distal convoluted tubule more permeable to salt, antidiuretic hormone (ADH) makes the collecting duct more permeable to water Secretion: -​ Ammonia, hydrogen ions and minerals can be secreted out of the blood and into the nephron at the proximal or distal convoluted tubules or the collecting duct -​ The secretion of hydrogen ions helps regulate pH -​ Diabetes mellitus is caused by the hyposecretion of insulin by the islet cells of the pancreas, causing the cells to not properly absorb glucose. This result in high blood sugar concentration, causing high glucose content in urine (sweet-smelling urine), high thirst and high volume of urine (peeing a lot) -​ Diabetes insipidus is caused by a defect in ADH production, making the nephron less permeable to water. Symptoms include high thirst, dehydration and high volume of urine