Midyear Study Guide 1 2023 PDF

Table of Contents ​ Life Processes/Scientific Method ​ Ecology ​ Human Impact ​ Biochem ​ Cells ​ Tools ​ Digestion Life Processes/Scientific Method Scientific Method ​ Observation ○​ Flashlight doesn’t work ​ Question ○​ Why doesn’t it work? ​ Hy...

Table of Contents ​ Life Processes/Scientific Method ​ Ecology ​ Human Impact ​ Biochem ​ Cells ​ Tools ​ Digestion Life Processes/Scientific Method Scientific Method ​ Observation ○​ Flashlight doesn’t work ​ Question ○​ Why doesn’t it work? ​ Hypothesis (if IV, then DV) ​ Responding variable = dependent variable ○​ Batteries are dead ○​ Bulb is broken ○​ Batteries are in wrong ○​ No batteries ​ If the batteries are put in the flashlight, the light will go on ​ Variable being manipulated ○​ Batteries ​ Independent variable ​ Variables that can affect plant growth ○​ Sunlight exposure ○​ Temperature ○​ Water needed ○​ Fertilizer ​ Negative control ○​ Doesn’t receive the IV ○​ Eliminates false positives ​ Source of comparison ​ Positive control ○​ Eliminates false negatives ​ Ex. measuring DNA in something ​ Positive control ○​ Sample known to contain DNA ​ Control ​ Experimental  ○​ All variables are the same between the control and experimental groups except the independent variable ​ Constants ○​ Same type of plant ○​ Temperature ○​ Water provided ○​ Sunlight exposure ○​ Amount of soil ○​ Type of soil Experiment ​ Fertilizer ○​ Control group ​ 5 plants ​ 1 control group ​ 5 plants ○​ Experimental group ​ 5 plants ​ 4 experimental groups with different amounts of fertilizer ​ DV needs to be operationally defined ​ Hypothesis can only be supported; not proved ○​ Hypothesis must be testable ○​ Hypothesis can be disproven ​ Line graph ○​ Continuous ​ Bar graph ○​ Categorical ​ Problem ○​ How does dissolving CaCl2 affect the temperature of the water? ​ Hypothesis ○​ If CaCl2 is added to H2O, then the temperature will increase ​ 76 mL of H2O ○​ 1 tbsp of CaCl2 ​ Original temperature ​ 23°C ​ After temperature ​ 32°C ○​ 2 tbsp of CaCl2 ​ Original temperature ​ 23°C ​ After temperature ​ 42°C ○​ 3 tbsp of CaCl2 ​ Original temperature​ ​ 23°C  ​ After temperature ​ 52°C ○​ 4 tbsp of CaCl2 ​ Original temperature ​ 23°C ​ After temperature ​ 61°C ​ Exothermic reaction between the CaCl2 and H2O Grouping ​ Living ○​ Plant ​ Cellular respiration ​ Capable of reproduction ​ Obtain nutrients ​ Non-living ○​ Leaf ○​ Cocklebur ○​ Rock ○​ Twig ○​ Robot ○​ Soil ​ Dormant ○​ Seed ○​ Acorn ​ Biotic ○​ Leaf ○​ Twig ○​ Soil ○​ Seeds ○​ Plant ​ Abiotic ○​ Soil Life Processes ​ Characteristics of Life (* means life processes) ○​ *Growth and development ​ Cells increase in size and number ○​ Highly organized ○​ Made up of cells ○​ Homeostasis ​ Maintain a stable internal environment ○​ *Nutrition ​ Ingestion ​ Taking in raw materials ​ Digestion  ​ Breaking down raw materials into form usable by body ​ Egestion ​ Removal of undigested waste ○​ Carry on complex chemical reactions ​ Metabolism ​ Autotrophs ​ Make their own food ○​ Photosynthesis ​ Heterotrophs ​ Search for our food ​ Don’t make their food ○​ *Cellular respiration ​ A series of chemical reactions that occur in cells ​ Aerobic respiration ○​ Requires O2 ​ Anaerobic respiration ○​ No O2 ○​ *Transport ​ Circulatory system ​ Consists of tubes and a pump to move materials throughout an organism ​ Materials must move across cell membrane ○​ Materials must be small enough to move across cell membrane ​ Active transport ○​ Requires energy ​ ATP ○​ Moves materials from low to high concentration ​ Cyclosis or cytoplasmic streaming ○​ Internal transport within cell ○​ *Synthesis ​ Organism makes complex molecules from simple molecules ​ Ex. glucose + galactose = lactose ○​ *Assimilation ​ Incorporation of nutrients into the organism ○​ *Excretion ​ Waste products from metabolism are removed from the organism due to their toxicity ○​ *Reproduction ​ Important for continuation of the species ​ Sexual reproduction ○​ Involves male and female ​ Asexual reproduction ○​ One individual  ​ Clones ○​ Organisms evolve ​ Change over time ○​ *Regulation ​ Involves a # of coordinated activities that serve to maintain a constant internal environment. ​ For us, it involves nervous + endocrine system Ecology Grouping ​ Plants ○​ Need sunlight for photosynthesis ○​ Sunlight determines how many and what kind of plants will grow ○​ Need rainfall ○​ Temperature affects plant growth ○​ Need CO2 for photosynthesis ○​ Provides O2 to atmosphere ○​ Plants also obtain energy via cellular respiration ​ Biotic ○​ Living things ○​ Parts of living things ○​ Wastes of living things ○​ Soil ​ Abiotic ○​ Minerals ○​ Include physical and chemical factors that affect living organisms ○​ Oxygen, CO2, (gasses) ○​ Moisture (H2O) ○​ Temperature ○​ Sunlight ○​ Soil ​ Animals eat plants ○​ Types of plants in an area determine the type of animals found in a location ○​ Herbivores eat plants ○​ Animals (carnivores) eat other animals ​ Predator -> prey ○​ Animals need to eat plants or other animals in order to survive to obtain the energy stored in the bonds of molecules ​ Cellular respiration ​ Scavengers eat dead animals ​ Predators hunt and kill animals for consumption  ​ Decomposers break down the remains of dead plants, animals, and the waste products of other animals ○​ Ex. fungi and some bacteria ​ Scavengers are detritivores ​ Decomposers are detritivores ○​ Decomposers eat dead and dying animals ​ Scavengers are ingestive heterotrophs ​ Decomposers are absorptive heterotrophs ​ Fungi secrete enzymes ○​ The enzymes digest food outside the body of the organism and then digested food absorbed by the organism ​ During process of breaking down food, decomposers release substances that can be reused by other members of the ecosystem Food Chain ​ Grass -> grasshopper -> frog -> snake -> hawk ​ Grass ○​ Producer ​ Grasshopper ○​ Primary consumer ​ Frog ○​ Secondary consumer ​ Snake ○​ Tertiary consumer ​ Hawk ○​ Quaternary consumer ​ 6CO2 + 6H2O -> C6H12O6 + 6O2 ○​ Energy from the sun is incorporated into the bonds of glucose via mitosis ​ Omnivores ○​ Eat plants and animals ​ Energy flows through the ecosystem ○​ Energy is not recycled ​ This is why an input of energy is required ​ A population is made up of organisms that are the same species living in a particular area ​ A community is composed of all living things living in an area ​ An ecosystem is a community of organisms and their abiotic factors ​ Conservation of energy ○​ Energy can neither be created nor destroyed ​ Energy used for life processes and released as heat ○​ Available energy decreases as move up pyramid ​ Not mainly predators because not enough available energy ○​ Top predators are usually large because biomass is concentrated in fewer predators ​ Inverted pyramid = impossible  ○​ Not enough energy ​ Lichens ○​ Algae ​ photosynthesis ○​ Fungus ​ Hyphae of the fungus reach into algae to get nutrients ​ Fungus provides protection for algae and needed elements ​ Fungus is a decomposer and recycles needed materials for other organisms to use ​ Mutualistic relationship ​ Fungus secretes enzymes that break down rock ​ When lichens die and decompose, the decayed lichens mix with particles of rock, forming a thin layer of soil ​ Now moss (blown in by the wind) can grow in soil ​ Moss shade lichens ​ Lichens die and decompose ​ When moss dies, so it gets deeper and richer in nutrients ​ Cycle of life ○​ Born -> live/offspring -> die ​ Soil becomes deeper and richer than before ​ Eventually, short plants and grasses will invade area ​ Soil is deep enough to support a root system ○​ 100 years later ​ Tall plants ​ Trees ​ Shrubs ○​ Competition for sunlight is why trees remain and grass and plants eventually die ○​ Eventually trees will all be beech-maple ​ Climax community ​ Stable until disaster strikes ○​ Lichens are pioneers because it’s the first organism of the ecosystem that leads to its development ○​ Physical factors (climate, soil type) determine the climax community in an area Ecological Succession ​ Primary ecological succession ○​ Lichen -> moss -> shrubs -> trees ​ Soil gets deeper and richer ​ More diversity in animal population in the climax community than the previous communities due to the increased diversity in plants ​ Ex. more food ​ More shelter ​ No prior soil ​ Pioneer ​ Lichen  ​ Nearly lifeless ​ Primary succession can take hundreds of hundreds of years ​ Ex. of primary succession ○​ Receding glacier ○​ Lava ​ Secondary ecological succession ○​ Soil already present ​ With nutrients ○​ Herbaceous (non-woody) plants ​ Pioneer ○​ Occurs in a community that was destroyed by fire or other disaster ○​ As the soil rises, the fish are eliminated and its secondary succession ​ Carbon based ○​ To build new molecules ○​ To obtain molecules from bonds of molecules via cellular respiration Characteristics ​ Plants are autotrophs ○​ They make their own food ​ Photosynthesis ○​ 6CO2 + 6H2O + sunlight = C6H12O6 + 6O2 ○​ Herbivore eats plants and uses glucose for cellular respiration ○​ ATP ​ ATP is energy that can be used for life processes ○​ Use carbon skeletons from breaking down glucose to build new molecules ​ Synthesis + assimilation ​ Cellular respiration ○​ C6H12O6 + 6O2 -> 6CO2 + 6H2O + Energy (ATP) ○​ Both plants and animals perform cellular respiration ○​ Decomposers feed upon the waste products and remains of animals and plants ​ They also release CO2 and use O2 during cellular respiration ​ Drink H2O to prevent dehydration ​ Drink H2O when you’re thirsty ○​ Water is recycled ​ Evaporation ○​ L-G ​ Condensation ○​ G-L ​ Precipitation ​ Runoff and percolation soil ​ Plants use some H2O for photosynthesis and H2O leaves the leaves vis transpiration Evapotranspiration ○​ Phosphorus cycle ​ Major constituent of nucleic acids, phospholipids and ATP ​ PO43- = phosphate  ○​ Dissolved in oceans ○​ Weathering of rocks adds PO43- to soil ​ Taken up by producers and incorporated into biomolecules ​ Distributed via food webs ​ Returned to soil of H2O by decomposers or excretion ​ No phosphorus present as gas (in the atmosphere) ​ Plants absorb PO43- from soil ​ We need Nitrogen (N2) ○​ To make proteins and nucleic acids ​ Digest ​ Cellular respiration ​ To make new proteins ​ Make nucleic acids ○​ DNA and RNA ​ Animals get N2 from eating plants and other animals ​ Eat proteins from plants or other animals ​ Neither plants nor animals can use N2(g) from atmosphere ​ Goal ○​ Convert N2(g) ito a usable form by plants ​ Nitrogen fixing bacteria ○​ Found in soil and in the modules of a legume ​ Mutualistic relationship between nitrogen fixing bacteria and legumes ​ NH4+ ○​ Ammonium ion ​ Other H is picked up from acidic soil ​ NO2 ○​ Nitrite ion ​ NO3 ○​ Nitrate ion ​ Plants take up NO3- to use to synthesize proteins and nucleic acids Commensalism ○​ + ​ Benefit ​ Remora ○​ Free ride and leftover food ○​ O ​ No impact ​ Shark ○​ Doesn’t benefit Climate ○​ General weather conditions in an area ​ Related to distance from equator  ○​ Temperature ○​ Precipitation ○​ Wind ○​ Adaptation = characteristic ○​ Cacti have adaptations that minimize water loss and store H2O ​ Swollen stem ​ Thin, spiky leaves ○​ Soil type also affects plants that grow in a particular area ​ Plants have different requirements for H2O ​ Some need a lot, but some don’t ○​ Plants are adapted to their environments ○​ Plants have characteristics that enable them to survive and reproduce in particular environments ○​ Camel/desert ​ Adaptations to store H2O and minimize loss Biomes ​ Biome ○​ Region of the world with similar climate, animals and plants ​ Cold at the top of a mountain due to low pressure and higher UV radiation ​ Damaging to plants ○​ Tropical Rainforest ​ Many species of broad leaves ​ Snakes ​ Jaguars ​ Monkeys ○​ Arctic tundra ​ Permanently frozen subsoil ​ Permafrost ​ Ponds and bogs ​ Caribou ​ Snowy owls ○​ Savanna ​ Grass ​ Scattered trees ​ Zebras ​ Lions ​ Cheetahs ​ Giraffes ​ Antelopes ○​ Chaparral ​ Shrubs ​ Deer ​ Fruit eating birds ​ Rodents  ​ Snakes ​ Lizards ○​ Temperate grasslands ​ Bison ​ Wild horses ○​ Taiga ​ Moose ​ Elk ​ Horses ​ Bears ​ Wolves ​ Coniferous trees Aquatic biomes ○​ Intertidal ​ Along the shoreline ​ Lots of wave action ​ High tide, low tide ​ High level of sunlight ​ Crabs, seaweed, mussels, seagulls, snails ​ Adaptations ○​ Anchoring to rocks ​ Ex. mussels have thin thread like anchors ○​ Protective shell ○​ Can burrow into moist sand ○​ Ocean/lake (differences) ​ Depth of water ​ Salinity ​ Water temp ​ Amount of O2 ​ Currents ○​ NaCl ​ Marine ​ 10% salt ​ 90% water ​ Fresh water ​ 0.05% salt ​ 99.95% water ○​ Aphotic zone ​ No photosynthesis ​ Hydrothermal vents ​ Chemoautotrophs ​ Provide O2 ○​ O2 gas ​ Non-polar  ○​ H2O ​ Polar ○​ Neritic zone ​ (continental shelf) ​ Lots of light ​ Productive ​ Algae ​ Many heterotrophs ​ Fish ​ Clams ​ Oysters ​ Phytoplankton ​ Photosynthesis ○​ Producers ​ Zooplankton ○​ Primary consumers ​ Herring ○​ Secondary consumers ​ Sardines ○​ Tertiary consumers ​ Neritic zone is completely in the photic zone ​ Different water depths affect light penetration ○​ Coral reefs ​ Biologically diverse ​ Rainforest of the ocean ​ Photosynthetic dinoflagellates live within corals Human Impact ​ Exponential growth ○​ # of individuals in each succeeding generation is a multiple of the previous generation ​ Carrying capacity ○​ Maximum population size that a particular environment can support at a particular time ​ Ecological niche ○​ Organism’s role in the environment ​ Sum total of a species use biotic and abiotic resources Density Factors ​ Density dependent ○​ Limiting factor depends on size of population​ ○​ Ex: food, predators, disease ​ Density independent  ○​ Limiting factor does not depend on size of population ○​ Ex: Temp, habitat destruction, natural disaster ​ Both dependent and independent ○​ There can be a middle ground where it’s both. ○​ For example, O2 in the environment can change from size of tree population but in an ocean ecosystem the O2 levels at a certain depth may be considered density independent. ○​ Other ex: H20, Sunlight Competition ​ Intraspecific competition ○​ Between members of the same species ​ Interspecific competition ○​ Between different species ​ Competitive exclusion principle ○​ Species compete with each other (interspecific) and the one that was better at competing would survive and the species that was worse would be eliminated from the niche. Eliminated species die out, move someplace else, or try to occupy a closely related niche ○​ This means two species cannot occupy the same niche. ​ Resource partitioning ○​ The resources of the niche are divided up between the species ​ Spatial partitioning - different habitats ​ Trophic partitioning - different food sources ​ Temporal partitioning - different times Population ​ Habitat ○​ Where species lives ​ Niche ○​ How species use biotic and abiotic factors (Role in the ecosystem) ​ Population ecology ○​ The study of population in relation to environments ​ Factors ecologists study about population ○​ Effect of climate and natural disasters ○​ Study their habitat and niche ○​ Age of population ○​ Total # of population ○​ How often they reproduce ○​ Effects on humans ​ Dispersion patterns ○​ Clumping ​ Lots of resources ​ Safety in numbers ○​ Uniform ​ Severe competition  ​ Territorial ○​ Random ​ Wind blows seeds ​ Wind blows birds ​ Resources not evenly spaced Reproduction ​ Reproductive potential ○​ Age ○​ Gender (male + female) ​ Males are less needed than females because females cannot get impregnated again once pregnant but the males can impregnate as many females as they want 1.​ Individuals live a long time (High individuals to % of max life span ratio) a.​ Humans b.​ Large mammals c.​ Tortoises 2.​ Equal chance of death at each age (Even individuals to % of max life span ratio) a.​ Squirrels b.​ Birds 3.​ Very few organisms survive. If they do, they live for a long time i.​ Many offspring b.​ Semelparity i.​ Single reproductive event. Small offspring. Low investment of energy ​ Iteroparity ○​ Repeated reproduction ○​ Large offspring ○​ Few individuals ○​ High investment of energy Resources ​ Resources ○​ Renewable ​ Given sufficient time, it can be replaced by natural, ecological cycles. ​ Even though a resource may be renewable, the resource should be used carefully ○​ Non renewable ​ Once used, cannot be replaced for millions of years Protection of Biodiversity ​ Preserving species ○​ Maintain valuable resources from plants ○​ Helps maintain food chain and webs ○​ Make use of population growth curves to establish when good to hunt ​ 3 R’s  ○​ Reduce ​ Public transportation ​ Carpool ​ Bike ○​ Reuse ​ Dishes (not paper plates) ○​ Recycle ​ Paper ​ Metal ​ Plastic ​ Glass ​ Destruction of habitat ○​ Build a dam ​ Positive ​ Control flooding ​ Provide electricity ​ Negative ​ Destroys habitat of fish ​ Breeding ground - poor drainage for insects ​ Creates lake that can flood ​ Deforestation ○​ Affects biodiversity ○​ Flooding ○​ Destroys habitats ○​ Increases CO2 levels (trees use CO2 for photosynthesis) ○​ Erosion ○​ Nitrate concentration in soil increases ​ Causation ○​ IV has an effect on DV ​ Correlation ○​ Shows a relationship between variables ​ Biodiversity ○​ Species diversity ​ # of different species in the biosphere ○​ Genetic biodiversity ​ # of different genes in species ○​ Ecosystem biodiversity ​ Variety of ecosystems in the biosphere Eutrophication ○​ Build a house by a lake ○​ Use fertilizer ​ Contains nitrates, phosphorus ○​ It rains ○​ Fertilizer flows into the lake  ○​ Algal Bloom: Algae multiply to cover top of lake ○​ Not enough sunlight for plants underneath ○​ Plants decompose. Decomposers utilize O2 ○​ O2 decreases, which results in fish dying ○​ Animals decompose further and decrease O2 levels ○​ Eventually aerobic decomposers die ○​ Anaerobic decomposers excrete lots of toxic materials ○​ Eventually, plants at the top (algae) die ​ Invasive species ○​ Organisms that become established outside their native range ○​ May not have predators ○​ Can enter accidentally or be introduced by humans ○​ Decrease biodiversity by outcompeting native species, causing native species to decrease in # or die out ​ Ex: Zebra mussel ​ Great lakes ​ Cut into food supply of clams and native mussels ​ Cluster on pipes and clog ​ Ex: Australian Rabbits ​ No native predators ​ Care about biodiversity ○​ Depend on species for food, clothing, soil fertility ○​ 25% of prescription medication contains substances derived from plants ​ Rosy Periwinkle ​ Hodgkin's disease ​ Foxglove plant ​ Heart medicine Causes of Extinction ​ Habitat fragmentation ○​ Habitats become biological islande ​ Fewer species, smaller populations, and now more vulnerable to climate change ​ Overhunting ○​ Species may become extinct or endangered ○​ Disrupt food chains, webs, and the ecosystem ​ Decreased biodiversity ○​ Hunting season ​ Time you can hunt and the amount you can ​ pH ○​ 7 = basic ○​ 7 = neutral ​ Acid rain  ○​ Damages buildings, plants, and animals ​ Greenhouse effect ○​ Greenhouse gas ​ A greenhouse gas is a molecule that can absorb infrared radiation and slows it’s escape from Earth therefore causing warming ○​ Burning of fossil fuels, deforestation = increase in greenhouse gasses - global warming ​ Global warming ○​ Polar ice caps can melt, raising sea levels, which can result in coastal flooding ○​ Change in wind patterns ○​ Alter patterns of global rainfall ​ Drought in certain areas ​ Affects farming ○​ Some species can’t tolerate warmer temperatures ○​ Acidification of ocean ​ CO2 + H2O = H2CO3 (carbonic acid) ​ H2CO3 = H++HCO3- ​ Structures made of CaCO3 (calcium carbonate) dissolve ○​ (Coral reefs start to dissolve) Preservation ​ Alternative energy sources ○​ Conserving non-renewable resources ○​ Reduces the use of fossil fuels (coal, gas, oil) ​ Reduces global warming ​ Reduces burning of fossil fuels ​ Reduce air pollution ○​ Burning fossil fuels produces sulfur oxides and nitrogen oxides. These oxides in water vapor and air produce HNO3 (nitric acid) and H2SO4 (sulfuric acid). Results in acid rain ​ Alternative energy sources ○​ Solar ​ Advantages ​ Renewable ​ Reduces burning of fossil fuels ​ Disadvantages ​ Costly ​ Not always sunny ○​ Hydro power ​ Extract energy from from moving water ​ Ex: dam, wave tidal ​ Advantages ​ Reduces burning of fossil fuels ​ Disadvantages ​ Destroys habitats  ○​ Turbines can kill fish ○​ Nuclear ​ Advantages ​ Produces a large amount of energy ​ No greenhouse gasses released ​ Disadvantages ​ Nuclear waste ​ Thermal pollution ○​ Need to dispose of hot H2O that they released into our H2O. Warm H2O cannot hold as much O2 ​ Species die or leave ○​ Wind ​ Advantages ​ Renewable ​ Reduces burning of fossil fuels ​ Disadvantages ​ Costly ​ Not always windy ​ Birds fly into them ​ They explode ○​ Geothermal ​ Power from the Earth’s intense heat ​ rAdvantages ​ Doesn’t use fossil fuels ​ Disadvantages ​ Expensive Ozone layer ○​ Layer of ozone gas (O3) that protects the Earth from the sun’s radiation ○​ CFC’s (chlorofluorocarbon) ​ CFCs used as coolants in refrigerators and air conditioners and also as propellants in aerosol cans ​ CFC causes thinning of the ozone layer ​ Thinning layer of ozone results in: ○​ Increase in skin cancer ○​ Increase of cataracts ○​ Increase of genetic mutations Pesticides ​ Kills insects that eat crops ​ Mosquitoes ​ Malaria ​ West Nile virus ​ Kill insects = increase crop yield ​ Control disease ​ 1950s - DDT - caused cancer  ​ Found high concentration in fat of birds and mammals and marine animals ​ Eagles - thinning of the egg shell ​ Biomagnification ○​ Chemical becomes concentrated as it moves through the food chain. At each higher trophic level, there is less biomass than the level before. Higher trophic levels ingest much more concentrated toxin in biomes ​ Solutions ○​ GMO ​ Genetically modified crops to synthesize insecticide ​ Ex: BT Corn (Monsanto) ○​ Problem: ​ Seeds spread by wind and become invasive species ○​ Plants that naturally make pesticides and surround crops with them ○​ Release native predator of pests ​ Possible problem: ​ Can be an invasive species ○​ Increase traps that use chemical scent to attract insects and sterilize the males Ecological Necessities ​ Keystone species ○​ Pivotal ecological role (niche) ○​ Large impact for small abundance ○​ Remove keystone species: ​ Ecosystem collapse ​ Decrease biodiversity ​ Farming ○​ Sustainable agriculture ​ System embracing a variety of farming methods that are conservation minded and environmentally safe and profitable ​ Use H2O efficiently ​ Contour farming ​ Reduces runoff of the topsoil ​ Fertilizer ​ Manure ​ Compost ○​ Needs to decompose (releasing materials slowly) Pollution ○​ Air ​ Burning fossil fuels ​ Smoke ○​ Smog ○​ Noise ○​ Light  ○​ Water ​ Dumping chemical waste ​ Harms food webs ○​ Land ​ Dumps trash on street ​ Attract vermin ○​ Thermal ​ Dumping hot water into the waterways ​ Bioremediation ○​ Bacteria or microorganisms added to toxic waste to stabilize ​ Oil spill ○​ Genetically engineered bacteria that metabolizes oil Biochem CHEMISTRY ​ Matter ○​ Has mass ○​ Takes up space ​ Uniform throughout ○​ Yes ​ Homogenous mixture: a mixture in which the components are uniformly distributed, meaning you cannot easily distinguish the individual substances. Ex: salt water ​ Does it have variable composition? ○​ Yes ​ Solution ○​ No ​ Pure substance (constant composition) ​ Element ​ Compound ○​ No ​ Heterogeneous mixture: a mixture where the components are not uniformly distributed, and you can see or separate the individual substances. Ex: trail mix, salad. ​ 2H2O -> 2H2+O2 ○​ H2O can only be separated by chemical means ○​ Atoms are the smallest unit of matter that cannot be broken down by chemical means ​ Compound ○​ Composed of two or more different elements ​ Element ○​ Many of the same type of atom  ​ H2O ○​ Liquid ○​ Compound ○​ Molecule ○​ High specific heat ○​ Made up of hydrogen and oxygen ​ NaCl ○​ Compound ○​ Not a molecule ○​ Made up of sodium and chloride ​ Carbon ○​ Atomic mass = 12.0111 ○​ Mass = 12 ○​ Atomic # = 6 ○​ Electron configuration = 2-4 ​ Electrons are negatively charged (-) ​ Protons are positively charged (+) Neutrons have no charge (n) ​ Atoms are neutral ○​ They have no charge ​ # of electrons = # of protons in a neutral atom because protons are positively charged and electrons are negatively charged ​ Atomic # = # of protons in an atom ​ Atoms ○​ Made up with electrons, which have a negative charge, protons, which have a positive charge, and neutrons, which have no charge ○​ Protons and neutrons are found in the nucleus ○​ Electrons are found outside the nucleus in orbital ○​ Electrons, protons, and neutrons are all subatomic particles ​ Mass # = atomic # + # of neutrons ​ Group 18 = inert/noble gasses ​ Stable octet ○​ They have a complete energy level in terms of electrons ​ Helium is a stable duet ​ Positive ions = cations ​ Negative ions = anions ​ Ionic bond ○​ Involves transfer of electrons ​ NaCl is an ionic compound because it contains ionic bonds ○​ It’s not a molecule, because molecules do not contain ionic bonds ​ Electron configuration ○​ Determines the chemical properties of an atom ○​ Valence electrons are the electrons involved in bonding ​ Ex. 7e- in chlorine and 2e- in Calcium  ○​ CaCl2 = ionic compound ​ High boiling/melting point ​ Composed of ions ​ Contains ionic bonds ○​ Ionic compounds, when dissolved in water, conduct electricity ​ Covalent bond ○​ Sharing of electrons ​ Electronegativity ○​ Attraction of an atom for electron in a bond ​ Fluorine is the most electronegative atom ​ HF ○​ Covalent bonds ○​ Compound ○​ Molecule ​ NaCl ○​ Ionic bonds ○​ Compound ○​ Not a molecule ​ H2 ○​ Not a compound ○​ Molecule ​ NaOH ○​ OH ​ Polyatomic ion ​ CH4 (methane) ○​ Non polar molecule ​ Symmetrical distribution of charge ​ Asymmetrical distribution of charge -> polar molecule ​ Hydrogen bonds ○​ Intermolecular: ​ Between molecules ○​ Intramolecular: ​ Between atoms within the molecule ○​ Hydrogen bonds can also be intramolecular in very long biomolecules ○​ Hydrogen bonds are formed from the attraction between the hydrogen atom in a polar bond and the unshared pair of electrons on a nearby, small, electronegative atom. ​ Electronegative atoms are fluorine, oxygen, or nitrogen ​ Isotopes ○​ Same atom with different number of neutrons ​ H2O ○​ Universal solvent ○​ High specific heat ○​ Polar  ○​ High boiling point ○​ Liquid at room temperature ○​ Water expands when it is frozen ​ Most substances contract when frozen ○​ When H2O goes from liquid to solid, it becomes less dense ​ Because ice floats, it covers the top of water when a lake freezes in cold weather, thereby insulating the water below. ​ If ice was denser than water, the lake would freeze solid, affecting the survival of organisms ​ To break bonds, energy is required ​ When bonds are formed, energy is released ​ Energy used to break bonds (and there are lots of hydrogen bonds to break) so temperature doesn’t increase that much. ​ Eventually, enough hydrogen bonds are broken, and the water molecules move faster, thus increasing water temperature ○​ H2O resistance to cooling ​ Hydrogen bonds are formed and energy is released. ​ That energy released counteracts cooling which results in lowering of water temperature ​ Water molecules moving slowly ​ Water has a high surface tension ​ At surface, there is a net inward force ​ In the interior, it is attracted in all directions ​ Hydrogen bonding ​ High specific heat ○​ More resistant to temperature change ​ Temperature ○​ Measure of average kinetic energy ​ Capillary action ○​ The movement of water within the spaces of a porous material due to the forces of adhesion, cohesion, and surface tension ​ Due to hydrogen bonding: ○​ Adhesion ​ Water is attracted to a surface ○​ Cohesion ​ Water attracted to other water molecules ​ These forces cause water to rise up a tube ​ Water ○​ Universal solvent ○​ Polar and ionic substances dissolve in water ○​ Non-polar substances do not dissolve in water ​ Water separates the sodium and chloride ions ○​ Known as dissociation ​ Action of water to produce ions throughout the solution  ○​ Ionic compound is dissociating ​ Autoionization is the property of water responsible for pH ​ Autoionization ○​ Important for the development of the pH scale ​ H3O+=OH- ​ pH=7 ​ H2O+H2O -> H+ + OH- ​ Single bonds ​ Alkane ​ Double bonds ​ Alkene ​ Triple bonds ​ Alkine BIOCHEMISTRY Carbohydrates ○​ Contain hydrogen, carbon, and oxygen ​ The 3 most basic sugars ○​ C6H12O6 ​ Glucose ​ Galactose ​ Fructose ○​ All are Isomers, they share the chemical formula C6H12O6 ○​ C12H22O11 ​ Sucrose ○​ H:O = 2:1 ○​ Starch ​ Chain of glucose molecules ○​ (C6H12O6)n ​ n represents # of glucose molecules bonded together ○​ Glucose is a monomer ○​ Monomer: a small, basic molecule that can bind chemically to other identical or similar molecules to form a larger structure called a polymer. Ex: glucose ○​ Polymer: a large molecule made up of repeating units called monomers, which are chemically bonded together. Ex: starch ​ Made up of repeating units known as monomers ○​ Glucose is soluble in water ○​ Starch is insoluble in water ○​ Disaccharide ​ Made up of two monosaccharides ○​ Maltose is a disaccharide ​ Composed of two glucose molecules ○​ Hydrolysis: break apart by adding water ​ Uses H2O to break down molecules ○​ Dehydration synthesis (condensation): join together by removing water  ​ Removes H2O to form larger molecules ○​ N-1 ​ Water added or removed ○​ N ​ # of glucose ○​ Polysaccharide ​ Polymer ​ Ex. glycogen, starch ​ Activation energy (EA): Energy necessary for reaction to proceed ○​ Lower Ea by using an enzyme ○​ Energy released ​ Exothermic reaction ○​ Polymers made up of glucose ​ Cellulose ​ Cellulose is linear ​ Not soluble in water ​ Found in cell wall of plants ​ Linkage is beta 1-4 linkage ​ Starch ​ Found in plants ​ Not soluble in water ​ Alpha 1-4 linkage ​ Glycogen ​ Found in animals ​ Soluble in water ​ Alpha 1-4 linkage ​ Starch and glycogen are branched ○​ Glycogen is highly branched ○​ Roughage ​ Fibrous indigestible material in vegetable foodstuffs which aids the passage of food and waste products through the gut. ​ We do not have an enzyme to break the bonds in cellulose ○​ Therefore, for us, cellulose is roughage ​ Cows also don’t have enzymes, yet they can break down cellulose ○​ Bacteria (gut microbes) in the digestive tract that digests cellulose for them. ​ Example of a mutualistic relationship Simple sugars ​ Glucose ​ Glucose + fructose -> sucrose (table sugar) ​ Glucose + glucose -> maltose ​ Glucose + galactose -> lactose ○​ All disaccharides ​ Fructose  ​ Galactose ○​ Glucose ​ Use in cellular respiration to obtain energy for life processes ​ If we don’t need glucose, it can store as lipids and/or glycogen Enzymes ○​ Type of protein ○​ Catalyze reactions ○​ Enzyme is not a reactant in the chemical reaction ○​ Enzyme is regenerate and therefore you don’t need lots of enzymes ○​ Enzymes are proteins ○​ Active site ​ Place on enzyme that the substrate binds to ○​ Substrate ​ Substance that binds to an active site ○​ Enzymes are specific to their substrates ○​ Lock and key ​ Substrate fits into enzyme’s active site analogous to a key fitting into a lock ○​ Induced fit ​ Enzyme molds itself around the substrate ○​ Heat denatures enzymes ○​ It loses its 3D shape and therefore its function ​ Cold does not denature enzymes ○​ Optimum temperature ​ Temperature in which the enzyme works the best ○​ Denature ​ Molecules start to move so fast that the enzyme loses its 3D shape ○​ Less effective collisions b/c molecules are moving slowly (colder temp) ​ Means less chance for substrate to effectively collide with enzyme ○​ Enzymes are organic catalysts ​ Inorganic catalyst (MrO2) does not denature and so activity will keep increasing with increased temp ○​ Optimum pH ​ pH that enzymes work the best ○​ Enzymes lower the activation energy ○​ Constant amount of substrate ​ All of the substrate is bound by the enzyme ○​ Constant amount of full enzymes ​ All active sites of enzyme are occupied ○​ Inhibitor ​ Molecule fits ​ No activity ○​ Similar shape to actual substrate ○​ Competitive inhibition  ​ Regulates enzyme activity ​ Inhibitor binds to the same site as substrate and prevents substrate from binding to active site ○​ Non-competitive inhibition ​ Inhibitor binds to allosteric site ​ Allosteric site ○​ Where inhibitor binds in noncompetitive inhibition ​ The substrate can still bind to its active site but the enzyme can no longer catalyze the reaction ​ In competitive inhibition, if I increase substrate concentration, I increase the chance of substrate binding over the inhibitor binding to the active site ○​ Feedback inhibition ​ Allosteric regulation of metabolic pathways ○​ NaCl ​ Ionic ○​ Amino acids, glucose ​ Covalent ○​ Starch, protein ​ Too big to get into the cell ○​ Cell membrane ​ Less dense than the cell contents ○​ Oil is less dense than water ​ Infer: cell membrane is composed of lipids ○​ Amino acids ​ Monomers of proteins ​ Carbon, hydrogen, oxygen, and nitrogen are the elements that make up proteins ​ Different amino acids have different R-groups ​ Amino group ○​ Base ​ Acceptor ​ Carboxyl group ○​ Acid ​ Donor ​ Protein donors ○​ Acids ​ Protein acceptors ○​ Bases ​ The R-group is what determines its properties ​ Amino acids are classified as basic, acidic, polar, and hydrophobic based on their R-group ​ Amino acids make up proteins (polypeptide) ​ Peptides are made up of amino acids ​ They are not polymers ​ Polypeptide (protein) are polymers ​ Need enzymes for synthesis and hydrolysis ​ We can make so many different proteins because: ​ Different order of amino acids ​ Different number of amino acids ​ Different type of amino acids ​ DNA is in the nucleus ​ DNA codes for protein ​ Eukaryotes: Membrane bound organelles ○​ Ribosomes ​ Site of protein synthesis ​ Prokaryote ​ No membrane bound organelles ○​ Ribosomes ​ DNA -> RNA ​ Transcription ​ RNA -> protein ​ Translation ​ Primary structure ​ Chain of amino acids ​ Covalent bonds between the amino acids and therefore will not dissociate in aqueous solution ​ Secondary structure ​ Attractive forces between atoms are the hydrogen bonds ​ Coiled structure -> alpha helix ​ Beta pleated sheets ​ Tertiary structure ​ Globular shape (conformation) of the protein ​ The order of amino acids determines the shape of the protein ​ DNA codes for the order of amino acids ​ Quaternary structure ​ Two or more polypeptide chains ○​ Ex. hemoglobin (4 polypeptide chains) ​ Disulfide bond (bridge) ​ A strong covalent bond ​ Sulfur is found in the amino acids cysteine and methionine ​ Heat a protein, I can disrupt my hydrogen bonds, but not the covalent bonds ​ Denatured my protein with heat ​ Lost it’s tertiary structure and therefore its activity ○​ What’s left is the primary structure ​ Need an enzyme to break primary structure ​ Protein can be denatured with heat, acid or base ​ Denature  ​ Loss of shape and therefore loss of activity ​ Shape (conformations) determines proteins activity’ ​ SHAPE DETERMINES FUNCTIONS ​ Functions of proteins ​ Motile (movement) actin and myosin in muscle ​ Enzymatic ○​ Enzymes are proteins ​ Transport (hemoglobin(hb)) proteins in cell membrane that facilitate transport ​ Storage (of nutrients) ○​ Ovalbumin in egg whites, seeds ​ Protective ○​ Antibodies ​ Regulatory ○​ Protein hormones ○​ Insulin ​ Coordination of organisms activities ○​ Receptor proteins ​ Response of cell to chemical stimuli ​ Structural ○​ Strengthen and protect cells and tissues ​ Collagen Lipids ○​ Fats ​ Fats provide more energy than carbs and proteins due to all the bonds in fatty acids ​ Lipids are not polymers because there are no repeating units (monomers) ​ They are just large molecules ○​ Oils ○​ Waxes ○​ Steroids ○​ Phospholipids ​ Cell membrane is composed of phospholipids ​ Phospholipids self assembles ​ Doesn’t need info to assemble ○​ Lipids ​ Tails ​ Hydrophobic ​ Non-polar ​ Head ​ Polar ​ Hydrophilic Cell Membrane  ○​ Lipid soluble substances can passively diffuse across the cell membrane by simple diffusion ○​ Ions can enter cell via protein channels ○​ Water enters through protein channels known as aquaporins ○​ Protein channels are specific ○​ Cell membrane is a fluid mosaic model ​ Fluid ​ Movement in the membrane ​ Mosaic ​ Small fragment like pieces of colored tile cemented together ​ Fluid mosaic model ​ Has diverse proteins embedded in a framework of phospholipids ○​ Semi permeable ​ Allows for only certain things to pass ​ For the cell membrane, it’s small and non-polar substances ○​ Facilitated diffusion ​ High -> low concentration ​ Involves protein channels ○​ Active transport ​ Low -> high concentration. ​ Requires energy ​ ATP ​ Requires transport proteins ○​ Butter ​ Solid at room temperature ​ Saturated fat ○​ Oil ​ Liquid at room temperature ​ Unsaturated fat ○​ Saturated fat ​ No double bond ​ Maximum # of hydrogens ○​ Unsaturated fat ​ Double bond ​ Can have a triple bond ​ Double or triple bonds causes a “kink” or a “bond” ○​ Kink keeps molecules further apart and therefore you get a liquid DNA ○​ DNA codes for proteins ○​ Most DNA found in nucleus of eukaryotic cells ○​ DNA is negatively charged ○​ DNA is a polymer ○​ Nucleotide is the monomer  ​ Phosphate group ​ Nitrogenous base ​ Adenine, guanine, thymine, cytosine ​ Deoxyribose sugar ​ DNA ○​ A-T ○​ G-C ​ Base pairing ○​ Double helix ○​ Sugar phosphate backbone ○​ Deoxyribose ​ Sugar ○​ Hydrogen bonding between the base pairs ​ 2 hydrogen bonds between A-T ​ Adenine and thymine ​ 3 hydrogen bonds between G-C ​ Guanine and cytosine ○​ Information in DNA is contained in the order and # of base pairs. ○​ Sequence of nucleotides are your genes ​ RNA ○​ Single stranded ○​ Uracil ​ No thymine ○​ Ribose ​ DNA ○​ Double stranded ○​ Thymine, no uracil ○​ Deoxyribose ○​ Most of our DNA are like each others, since we all need certain molecules to survive ​ Insulin ○​ Our differences are due to different DNA sequences and base pairs ​ Purines ○​ Guanine ○​ Adenine ​ Pyrimidine ○​ Cytosine ○​ Uracil ○​ Thymine ​ Cells Cell Theory ​ All living things are made up of one or more cells ​ All cells come from pre-existing cells ​ Cells are the basic unit of structure What cells needs to do ​ Cells need to have energy to carry out life functions ​ Cells need to be separated from outside environment ​ Need to be able to direct activities ​ Need to be able to exchange molecules from inside and outside the cell Building of a cell Nucleus ○​ Contains DNA ​ Nucleus membrane ○​ Contains nuclear pores ​ Allow large macromolecules to enter and leave ​ Double membrane composed of lipids ​ Each membrane is a lipid bilayer ​ RNA is transcribed in nucleus off of the DNA code ​ Ribosome RNA is made in the nucleus Eukaryotic cell ​ Membrane bound organelles ​ Nucleus has a double membrane ○​ Both membranes are lipid bilayers ​ All organism’s cells contain ribosomes ​ mRNA = messenger RNA ​ Prokaryotic cell ​ Has a nucleoid ○​ Not membrane bound ○​ Contains circular DNA ​ Doesn’t have membrane bound organelles ​ Found in bacteria ​ Reproduces through binary fission ​ Contains 70S ribosomes ​ Smaller than eukaryotic cells ​ Usually has cell wall ○​ Usually a plant cell Endomembrane system ​ Membranes related either through direct physical continuity or by transfer of membrane segments in tiny vesicles ​ Includes:  ○​ Nuclear envelope ○​ Golgi ○​ Lysosomes ○​ ER ○​ Cell membrane ○​ Various vacuoles Endocytosis ​ Phagocytosis ○​ Food (not specific) ○​ Prokaryotic cells cannot perform phagocytosis; only eukaryotic cells can ​ Pinocytosis ○​ Fluids (specific) ​ Receptor mediated endocytosis ○​ Molecules (not specific) ​ Food gets into amoeba by phagocytosis ○​ Ingestion ​ Membrane pinches off and forms a food vacuole ○​ Food vacuole = phagosome ​ Phagosome needs to get to the lysosome ○​ Cyclosis ​ Cytoplasmic streaming ​ Membranes of the phagosome and lysosome fuse to form a phagolysosome (secondary lysosome) ​ Food gets digested in the phagolysosome ○​ Once food is digested, it diffuses out of the phagolysosome ​ Phagolysosome travels to cell membrane and fuses with cell membrane in a process known as exocytosis to get rid of undigested material Tay Sachs ​ Lysosomes contain lipid digesting enzymes ○​ These enzymes are inactive or missing in people with Tay Sachs ​ This leads to accumulation of lipids in the brain and eventual death ​ Plants don’t have lysosomes ○​ They contain a large central vacuole ​ Vacuole functions: ​ Storage ​ Breakdown of waste product ​ Absorption of water ​ Autophagy ○​ Digesting cell organelles ​ Apoptosis ○​ Digesting entire cell Amoeba ○​ Needs food  ​ Phagocytosis ○​ Needs to get rid of waste ​ Substances moved from high to low concentration ○​ Requires concentration gradient ​ Random motion (kinetic energy) of atoms and molecules ​ O2 gets into cell by diffusion ○​ High -> low concentration ​ O2 is low concentration inside the cell because it’s used for cellular respiration ​ CO2 diffuses outside of cell ​ Dynamic equilibrium ○​ Rate of the forward = rate of the reverse ​ Concentrations on each side are constant ​ They don’t have to be equal ​ O2 and CO2 enter and leave cell by simple diffusion ​ Water enters cell via protein channels known as aquaporins ○​ Specific for water ​ Cell permeability can be regulated by insertion or removal of protein channels ​ Diffusion of water is known as osmosis ​ Active transport ​ Low -> high concentration ○​ Up a concentration gradient ​ Uses a protein to transport ​ Na+K+ pump ○​ Couples the hydrolysis of ATP with movement of materials across cell against concentration gradient ​ ATP + H2O -> ADP + P1 ○​ Hydrolysis of ATP ​ Facilitated diffusion vs active transport ○​ Facilitated diffusion ​ Requires transport protein ​ High -> low concentration ​ No ATP ○​ Active transport ​ Requires transport protein ​ Low -> high concentration ​ Requires ATP ​ Solutions ​ Animal cell ○​ Isotonic ​ Concentration of solutes same inside and outside the cell ​ Dynamic equilibrium ○​ Animal is happy ○​ Hypertonic  ​ Solution with higher concentration of solutes outside the cell is hypertonic ​ Cell shrinks ○​ Animal is sad ○​ Hypotonic ​ Solution with lower concentration of solutes outside the cell is hypotonic ​ Cell burst (lyse) ○​ Animal is sad ​ Plant cell ○​ Isotonic ​ Plant cell wilts ​ Plant is sad ○​ Hypertonic ​ Plant shrinks ​ Plasmolysis ○​ Plant is sad ○​ Hypotonic ​ Cell wall is firm and tough and pushes back, creating turgor pressure. ​ Keeps herbaceous plants upright ​ Turgor pressure ○​ The force within the cell that pushes the cell membrane against the cell wall ​ Contractile vacuole pumps out H2O ○​ Requires ATP ​ As surface area increases, more substances can diffuse across and if the volume decreases, substances have to travel ​ As the cell gets bigger, the cell membrane is unable to keep up with the needs of the inside. ​ If the SA/V ratios is small, your SA is not large enough to supply nutrients to the inside of the cell ​ The volume inside the cell is bigger than SA; diffusion takes longer is more effective ​ Substances cannot diffuse across the membrane at a sufficient rate and is less effective ​ Besides being small, cells can achieve a favorable SA/V ratio: ○​ Branches ○​ Villi (folds) ○​ Flat and long ○​ Red blood cells ​ Expel nucleus and organelles soon after being born in bone marrow ​ Minimizes O2 capacity ​ Serial Endosymbiosis ​ The original host is a heterotrophic bacteria with DNA ​ Multiple aerobic bacteria (mitochondria) enter the bacteria ​ After lots of time goes by, this results in a eukaryotic cell (animal fungi, some protists) ○​ Or, cyanobacteria (photosynthetic bacteria) become chloroplasts and are engulfed by the cell, which results in a eukaryotic plant cell (and some protists) Organelles Ribosomes ○​ Function is to synthesize proteins from amino acids ○​ rRNA carries the code as specified by the DNA ○​ Ribosomes are made from rRNA and protein ​ Ribosomes are not membrane bound ○​ Ribosomal RNA made in nucleolus ○​ Protein made on ribosomes in the cytoplasm enters the nucleus via nuclear pores ○​ rRNA and proteins associate in the nucleolus ○​ Subunits (rRNA and proteins) leave nucleus via pores and associate in cytoplasm to form ribosomes ○​ Site of protein synthesis ○​ Made of protein and rRNA ○​ Not a membrane bound organelle ○​ Free ribosomes in cytosol ​ Fluid portion of cytoplasm ○​ Bound ribosomes on the endoplasmic reticulum ER ○​ RER (Rough ER) ○​ Rough endoplasmic reticulum ​ Contains and transports bound ribosomes ○​ Smooth ER ​ Contains no ribosomes ○​ Bound ribosomes are on the RER ○​ Protein formed on bound ribosomes depart from ER in vesicles that bud off ○​ Some proteins are modified in ER ○​ Membrane factory for cell ​ Grows in place by adding membrane proteins and phospholipids to its own membrane ​ ER membrane expands and is transferred in form of vesicles to other components of the endomembrane system ○​ Hydrolytic enzymes and lysosomal membrane made by rough ER ○​ Vesicles that leave ER travel to golgi apparatus Smooth ER ○​ Synthesizes lipids and steroids ○​ Metabolizes carbohydrates ○​ No ribosomes ○​ Stores calcium ​ In muscle cells; sarcoplasmic reticulum ○​ Detoxifies poison Lysosome ○​ Contains digestive enzymes ○​ Enzymes in the lysosome work best at pH = 5 ○​ We use lysosomes to digest old cells or damaged organelles ​ Autophagy ○​ When organelles are digested, the organic monomers are returned to the cytosol for reuse ○​ Some human cells do phagocytosis ○​ These cells are our white blood cells ​ White blood cells ingest pathogens lysosomal enzymes digest tay sachs Golgi ○​ Packing, sending and sorting ○​ Sends substances to other parts of the cell or for secretion ○​ Receives vesicles from RER ○​ Vesicles from RER fuse with golgi and release contents ○​ Substances get modified in golgi ○​ New vesicles from from golgi carrying specific proteins to other locations in cell or to cell membrane for secretion Vesicles emerging from golgi ○​ Carry proteins for secretion ○​ Mature into lysosomes ○​ Carry proteins for insertion to cell membrane and carry membrane components insertion to cell membrane and carry membrane components Mitochondria ○​ Cellular respiration ​ Aerobic, ATP generated ○​ Glycolysis occurs in cytosol, not mitochondria ○​ Characteristics of mitochondria ​ DNA ​ Circular chromosome ​ Circular DNA is also found in bacteria (prokaryotic cells) ​ Cellular respiration ​ Aerobic ​ Two separate membranes ​ Outer and inner  ​ Ribosomes ​ Mitochondria reproduce by binary fission, just like bacteria ​ Mitochondria reproduce independent of the cells reproducing ​ Mitochondria has the ability to make its own proteins ​ DNA -> mRNA -> proteins ​ 70s = prokaryote ​ Found 70s ribosomes in mitochondria ○​ Came from prokaryote ​ 80s = eukaryote ​ Prokaryotic ribosomes are less dense that eukaryotic cells ​ Inner membrane of the mitochondria have enzyme and transport systems homologous to those found in the plasma membrane of prokaryotes ○​ Binary fission ​ Asexual reproduction ​ Occurs organisms that do not have nucleus ​ Mitochondria splits in half and the DNA replicates Cell membrane (not an organelle) ○​ Regulates substances that go in and out of cell ○​ Transport ○​ Homeostasis ○​ Semi permeable ​ Size ​ Lipid solubility ○​ Lipid biliary consistency of salad oil Chloroplasts ○​ Found in plant cells ○​ Site of photosynthesis ○​ Mitochondria and chloroplasts were originally organisms ○​ Eukaryotic cells (plant and animal) contain mitochondria ​ Both animal and plant cells need to perform cellular respiration ○​ Maybe mitochondria and chloroplasts got engulfed by phagocytosis ○​ Two membranes ​ Inner and outer ○​ Contain 70s ribosomes ○​ Contain circular DNA ○​ They don’t perform cellular respiration ○​ Have internal system of membranous sacs ​ Thylakoids ​ Contain chlorophyll in membrane ○​ Also grow and reproduce in cell Tools Tools Microtome ○​ Consists of a blade holding unit and a mechanism for adjusting the desired thickness ○​ Tissues are hardened by replacing water with paraffin or substance is embedded in wax or plastic ○​ The substance will harden and allow the specimen to be cut Cryostat ○​ Medium is used to freeze sample and keep it stable enough to cut without fracturing Centrifuge ○​ Separates based on density ○​ Break open cell using a blender ​ Forms a homogenate ​ Contains organelles and chemicals Electron Microscopes: ○​ Light travels ​ Waves ​ Wavelengths (λ) ​ Particles ​ Photons ○​ Distance from crest to crest is the wavelength ○​ The resolution of a microscope is limited by the shortest wavelength of light used to illuminate the specimen ​ X electrons (0.005 nm) ○​ When electrons travel through the air, they scatter all over ​ Use a vacuum ​ No air ○​ Two types of electron microscopes: ​ Scanning ​ 3D ​ Electrons bounce off specimen ○​ Specimen is coated so electrons can bounce off ​ Transmission ​ 2D ​ Electrons pass through ○​ Density difference cause different patterns Electromagnets ○​ Used to focus electrons Spectrophotometer  ○​ Used to measure absorbance or transmittance of light ​ Light → cuvette → reading absorbance ○​ Pigments ​ Absorb and reflect light ○​ Concentration of pigment in each tube is known ​ Absorbance in each tube can each be measured ○​ Make a standard curve (line of best fit) ​ Use a linear relationship in order to determine the line of best fit ​ Interpolation ​ In between known values ​ Extrapolation ​ At unknown values, line is extended beyond known points Cell Fractionation Sucrose Gradient Centrifugation 1.​ Sucrose is used to make a density gradient 2.​ Add homogenate to top of the gradient 3.​ Centrifuge the mixture 4.​ The organelles will be at the place in the tube where the density of the organelles equals the density of the sucrose 5.​ Use a needle to puncture the bottom of the tube and a machine counts the number of drops and they make an entire series of test tubes 6.​ Use gel electrophoresis to separate DNA 7.​ Use a functional assay to look for signs of mitochondria ○​ ATP production ○​ O2 consumption ○​ CO2 production ○​ Heat production ​ Differential Centrifugation ​ Have cell homogenate ○​ Disrupted cells ​ Heavier particles come out in pellet at lower speeds and when centrifuged for a shorter period of time ○​ Lower speeds ​ Pellet contains larger components ○​ Higher speeds ​ Pellet contains smaller components ​ You are centrifuging a homogenate at various speeds for different times. ○​ The heavier components come out first in the pellet. ​ For each spin the supernatant is removed from the and the supernatant is centrifuged for longer and faster speeds Paper Chromatography ​ Used to separate substances that have similar size and density ​ Based on different chemical properties  ○​ Solubility ○​ Affinity ​ H2O = solvent ○​ Polar ​ Substance trying to separate is also polar ​ Solvent moves up paper by capillary action ​ Solubility vs affinity for the paper: ○​ Blue is more soluble in H2O and has less affinity for paper ○​ Yellow is less soluble in H2O and has more affinity for paper ​ Size of paper strip influences the degree of separation ○​ Longer strip gives better separation of substance Gel Electrophoresis ​ Separates on a basis of size and charge ○​ DNA is all negatively charged so it only separates based on size and density ​ Electricity moves the sample through the cell ​ Electrolytic cell ○​ Cathode ​ Negative charge ○​ Anode ​ Positive charge ​ Buffer solution is used ○​ Ions in the buffer ​ Ions conduct electricity ​ When the electric current is turned on, the ions in the buffer carry the current ○​ DNA will move towards the anode since DNA is negatively charged ​ Agarose gel ○​ Use different percent agarose gels depending on size of DNA you are separating ​ Largest size DNA moves the slowest so when the gel is stopped, the larger size will not have moved as far into the gel as the smaller sized DNA Digestion Different Organisms (Digestion) Protist (Eukaryote) ​ Paramecium 1.​ As paramecium swims, food moves in with H2O 2.​ Cilia in the oral groove moves food to the gullet. When food particle gets to the end of the gullet, it puts pressure on the gullet 3.​ Forms food vacuole by process of endocytosis a.​ Phagosome 4.​ Phagosome fuses with lysosome to form a phagolysosome 5.​ Food gets digested (hydrolyzed) in the phagolysosome. Digested food diffuses out of the lysosome.  6.​ Egestion of undigested food via endocytosis ​ Amoeba ​ No gullet, no oral groove. Ingests food by phagocytosis using pseudopods Fungi (absorptive heterotroph) ​ Large surface area ○​ Facilitates absorption of nutrients at a sufficient rate 1.​ Secretes enzymes outside of its body 2.​ Digestion occurs outside of its body 3.​ Absorb digested nutrients a.​ Monomer Hydra ​ 2 layers of cells ​ Can ingest food bigger than its cells ​ Sessile ○​ Doesn't move much ​ Phylum: Cnidarian ​ Mesoglea ○​ Structural function ​ Gastroderm (endoderm) ○​ Contains gland cells 1.​ Tentacles contain stinging cells called nematocysts. They sting their prey and then use tentacles to stuff prey into their mouth 2.​ Digestion takes place in the gastrovascular cavity. Known as extracellular digestion a.​ Takes place outside of cells 3.​ Enzymes are secreted from the endoderm cells a.​ Chemical digestion 4.​ Flagellum circulates food in gastrovascular cavity and facilitates digestion 5.​ Muscle fibers in endoderm and ectoderm allow hydra to crush food which increases the surface area for digestion by enzymes a.​ Mechanical digestion 6.​ Following chemical digestion in the gastrovascular cavity, monomers diffuse into endodermal cells and also diffusion of monomers from endodermal cells to ectodermal cells 7.​ The endodermal cells can also absorb food particles by phagocytosis a.​ Intracellular digestion 8.​ Hydra egests through its mouth a.​ Two way digestion Earthworm (Phylum: Annelids) 1.​ Muscular pharynx sucks food in through the mouth a.​ Crop -> Storage -> Ability to expand 2.​ Gizzard -> mechanical digestion occurs. Gizzard is muscular so can crush food. Gizzard contains pebbles a.​ Ingested with soil that aid in mechanical digestion  3.​ Chemical digestion takes place in the intestine and monomers are absorbed from the intestine into circulatory system 4.​ Small intestine is long a.​ Increased surface area for absorption of monomer i.​ Diffusion and transport ​ Grasshopper ​ Mandibles ​ Pair of salivary glands ○​ Secrete saliva and enzymes known as amylase ​ Digests starch ○​ Exocrine ​ Secretions go into a duct ​ Chitin plate ○​ Toothlike protection in the gizzard ​ Gastric caeca contains digestive enzymes that are secreted into the stomach and food is completely digested. Monomers are absorbed from stomach into circulatory system ​ Undigested food passes from stomach to intestine to rectum and out via anus ​ Intracellular Digestion ○​ Digestion inside a cell ​ Coelomate ○​ Organisms that contain a coelom ​ Space between the body wall and the digestive tube is called a coelom. The coelom contains other organs ​ Mandibles ○​ For chewing and grinding ​ Rectum ○​ Reabsorption of water ​ Teeth ○​ Crushing and tearing of food to increase surface area ​ Saliva ○​ Softens our food, making it easier to swallow. Also contains amylase ​ Tongue ○​ Shapes food into a bolus; pushes food to the back of the oral cavity ​ Hard palate ○​ Roof of the mouth ​ Soft palate ○​ Back of roof of the mouth ​ Zymogen is a general name for inactive form of enzymes ​ Afferent vs Efferent ○​ Afferent means leading toward or bringing something to an organ, while efferent means carrying something away from an organ. HUMAN  ​ When food hits the end of soft palate, it causes the swallowing reflex ○​ Swallowing is both voluntary and involuntary ​ The larynx has a flap on it called the epiglottis. When you swallow, the larynx moves up and the epiglottis covers the trachea ​ Peristalsis ○​ Muscle contractions that start in the esophagus and go through the entire digestive system. Smooth muscle is responsible for peristalsis ​ Smooth muscle is involuntary ​ Contractions are behind bolus ○​ Keeps bolus moving in one direction ​ Orientation of stomach muscles ○​ Aid in mechanical digestion by crushing food in from different directions ​ Stomach storage capability ○​ Stomach has folds called rugae. Rugae can expand ​ Chemical digestion of proteins starts in the stomach ○​ pH=2 in stomach ​ Acidity of stomach denatures proteins, making them easier to hydrolyze ​ Pepsin ○​ Enzyme in stomach that digests proteins ​ HCL ○​ Denatures proteins, kills some bacteria ​ Mucus is secreted by cells in stomach ○​ Mucus helps protect stomach lining from acid ​ Cell division adds new epithelial layer every three days, replacing cells eroded by digestive juices ​ Pepsinogen is activated to pepsin in the stomach by HCL. Acid cuts the part of the enzyme that blocks the active site and pepsinogen is now in active form (pepsin). Pepsin can then clip other pepsinogen to expose the active site, therefore generating more pepsin. ​ Gastric glands contain three types of cells: ○​ Mucus ○​ Chief ​ Secrete pepsinogen ○​ Parietal ​ Secrete HCL ​ Action of crushing and mixing by muscular stomach and enzymes, food becomes a nutrient rich broth known as chyme. Sphincter regulates passage of chyme from the stomach to the small intestine. Chyme leaves the stomach one squirt at a time Small intestine ​ The longest section of the alimentary canal ​ Major organ of digestion and absorption ​ Lot of surface area for absorption of nutrients ​ Long and thin and has many folds ​ Digestion is completed in the small intestine  ​ Proteases in the pancreatic juice ○​ Carboxypeptidase, Chymotrypsin, Trypsin, Endopeptidase, Exopeptidase ​ Most digestion takes place at the beginning of the small intestine and the remainder of the small intestine is for absorption ​ Secretion from salivary glands (exocrine glands) ○​ Secretion via ducts ​ Bile salts are produced in the liver and stored in a gallbladder and are released to emulsify the fats, making fats more susceptible to attack by enzyme (lipase) ​ Emulsification by bile = mechanical digestion ​ Bile gets into small intestine via ducts, where it emulsifies the fats ​ Lipase works at pH = 8 ○​ Acid chyme from the stomach enters the small intestine. The pancreas secretes bicarbonate through a duct into the small intestine. This causes pH = 8 Pancreas ​ Exocrine gland ​ Endocrine gland ○​ Secretes insulin and glucagon directly into blood ○​ Ductless ​ Secretions from gastric glands goes to the stomach ​ Secretions from the pancreas and the liver go to small intestine ​ Monomers absorbed from small intestine by diffusion and active transport ​ End products of digestion: ○​ Glucose ○​ Nucleotides ○​ Amino acids ○​ Glycerol ○​ Fatty acids ​ Inside the villi of glycerol and fatty acids are lacteals, which are part of the lymphatic system ​ Digested materials diffuse/active transport into the circulatory system Blood ​ Formed elements ○​ Cells ​ Plasma (liquid) ○​ 90% H2O, plasma proteins ​ Antibodies, albinum, fibrinogen ○​ Nutrients, CO2, O2 and waste products of metabolism are carried in the plasma ​ Material of lymphatic system is called lymph and the function of the lymphatics is to carry our digested fats and also has an immune function Large Intestine ​ Absorbs H2O via osmosis ​ Contains E. Coli bacteria in lumen ○​ Vitamin K helps blood clot, also several B vitamins contain folic Anus  ​ Get rid of undigested waste ○​ Egestion Rectum (terminal part of large intestine) ​ Undigested material stored in rectum until we need to defecate ​ Sphincter between rectum and anus ​ Voluntary and involuntary ​ Urge to defecate is due to contractions by colon Accessory organs ​ Never see food but participate in digestion ○​ Pancreas ○​ Salivary glands ○​ Gallbladder ○​ Liver ​ Capillaries from small and large intestines converge into veins that lead to the hepatic portal vein. The liver gets first access to nutrients absorbed from a meal. One of the main functions of liver is to remove excess glucose from blood and convert glucose to glycogen which is stored in the liver ​ Also synthesizes plasma proteins albumin and fibrinogen, as well as lipoproteins that transports cholesterol to body cells Diseases ​ Cancer ○​ Rapid growth of cells ​ Infections ○​ Bacteria, virus, parasite ​ Gallstones ○​ Crystals of cholesterol or bilirubin ​ Diarrhea ○​ Large intestine fails to reabsorb H2O ​ Constipation ○​ Large intestine absorbs too much H2O ​ Throwing up ○​ Reverse peristalsis ​ Acid reflux ○​ Acid from stomach goes into esophagus ​ Ulcer ○​ H.Pylori ​ Acid burning lining of stomach Hormones ​ Stimuli ○​ See food ○​ Smell food ​ Stimulus initiates a response ​ Nervous system  ○​ Sends messages through nerves ​ Message = action potential ​ Electrical impulse ​ Endocrine system ○​ Uses hormones that travel through the blood to their target tissues ​ Hormones ○​ Gland secretes hormones into blood ○​ Hormone binds to receptor on target tissue ​ Receptors are proteins ​ Receptors are specific ​ Reflex Arc ○​ No thinking/cognition ○​ Involuntary ​ Stimulus -> ​ Food ​ Sensory nerves -> ​ Afferent ​ CNS -> ​ Brain ​ Spinal cord ​ Motor nerves -> ​ Efferent ​ Salivary glands ​ Mouth water ​ Salivary glands secrete saliva via a duct into the mouth under neural control ​ Stomach ○​ Nervous and endocrine control ​ Intestine ○​ Nervous and endocrine control  Factors that Source to Hormone which Target Tissue Actions stimulate release… goes to… which then release causes… causes… Distention of the Stomach Gastrin Gastric glands in Stimulates gastric stomach by stomach glands to secrete HCL food. Also smell and pepsinogen Acid chyme Small intestine Secretin Pancreas Secretion of sodium acting on the bicarbonate intestinal mucosa Partially Small intestine CCK ​ Pancreas ​ Stimulates digested wall ​ Gallbladder release of proteins. Also digestive fats enzymes ​ Stimulates of bile ​ Negative feedback ○​ A primary mechanism of homeostasis whereby a change in a physiological variable that is being monitored triggers a response that counteracts the initial fluctuation (reverses a trend) ​ Ex. CCK inhibits gastrin HUMAN DIGESTION ​ You ingest your food one bite at a time ​ In the oral cavity, chewing begins mechanical digestion, and salivary amylase action on starch begins chemical digestion ​ When you swallow, food passes through the pharynx and esophagus to the stomach\mechanical and chemical digestion will continue in the stomach, where HCL in gastric juice breaks apart food cells and pepsin begins protein digestion ​ In the small intestine, enzymes from the pancreas and intestinal wall break down starch, protein, and nucleic acids to monomers ​ Bile from the liver and gallbladder emulsifies fat droplets for attack by enzymes ​ Most nutrients are absorbed into the bloodstream through the walls of the small intestine ​ Fats travel through lymph ​ In the large intestine, water is absorbed from undigested material, and our feces are eliminated