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Final

NATS 1610 Final: NATS 1610 Full Course Notes
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Department
Natural Science
Course
NATS 1610
Professor
Barbara Czaban
Semester
Fall

Description
LECTURE 2 ● characteristics of living things ○ take in energy and materials from the environment ○ sense and respond to stimuli ○ reproduce and grow ○ consist of one or more cells ○ maintain homeostasis ○ undergo evolution ● classification of organisms (domains) ○ bacteria ○ archaea ○ eukarya - it has 4 kingdoms ■ protists (protista) ■ plants (plantae) ■ animals (animalia) ■ fungi (fungi) ● taxonomy of humans (where do we belong) domain: EUKARYA order: PRIMATES kingdom: ANIMALIA family: HOMINIDAE phylum: VERTEBRATA genus: HOMO class: MAMMALIA species: SAPIENS ● characteristics of primates ○ grasping feet ○ forward-facing eyes ○ small litter size ○ complex social behaviour ● speciation ○ the formation of new species ○ Charles Darwin (1859) ■ modern species are descendants of ancestral species ■ evolution occurred by the process of natural selection - the descent through modification, over long periods of time ● criteria for evolution through natural selection ○ individual variation exists within a species - some variation is inherited ■ genes define traits ■ diversity is essential 1 ○ some people live longer and have more offspring than others ■ some characteristics make them better suited to their environment ■ organisms and environment are intimately associated ○ change occurs as the traits of the surviving people (those who reproduce) become more common in the population ■ less successful traits become less common ● modes of speciation (what causes new species to evolve) ○ allopatric ■ geographic separation restricts genes ○ sympatric ■ populations may be in overlapping geographical area ■ changes in gene flow ● chromosomal changes: mutations, exploitations ● behavioural changes: non-random mating - reduces gene flow LECTURE 3 ● lines of evidence ○ fossil ○ anatomical ○ biochemical ● fossil evidence ○ preserved remnants and impressions of past organisms ○ most fossils are mineralized in sedimentary rock ○ when assembled in chronological order, it shows the evolutionary changes ○ there can be non-decomposed fossils ■ when an organism dies, but doesn’t decompose because of its location ■ frozen in ice, trapped in resin, preserved in acid ● anatomical evidence ○ homologous structures suggest shared ancestry ○ resemblance early in development indicates common descent 2 ○ vestigial organs no longer serve any purpose to humans ■ a common ancestor used them - appendix, wiggling ears ● biochemical evidence ○ gene sequences that match closely were copied from a common ancestor ○ same genetic code - same cells and cellular components LECTURE 4 ● humans and environment ○ humans are dependant on it - ecology is the study of those interactions ○ things are needed to continue living ■ raw materials, oxygen, water, energy for metabolism ● macromolecules ○ LIPIDS → fat → glycerol/fatty acids ○ CARBOHYDRATES → polysaccharides → monosaccharides ○ PROTEIN → polypeptide → amino acid ○ NUCLEIC ACID → DNA/RNA → nucleotide ● photosynthesis (done by plants) ○ pathway where light energy, carbon dioxide and water are used to produce sugar ■ oxygen is a by-product 6CO 2 6H O2+ energy → C H6O12 6O 2 ● cellular respiration (done by all cells and organisms) ○ the oxygen-requiring pathway where glucose is broken down to create carbon dioxide, water and energy C6H12 6 6O →26CO + 62 O + 2nergy ● energy and raw materials ○ build and maintain molecular, cellular and body order ○ maintains ‘organization’ ○ metabolism utilizes energy to support homeostasis ● ecosystems ○ a specific geographic area ○ organisms exist in populations of individuals ■ interact among themselves and with physical environment ■ obtain energy and food ○ different populations organize into communities ■ live in the same physical conditions ● characteristics of ecosystems 3 ○ energy flow ■ energy cannot be recycled; it is used then is lost ○ chemical cycling ■ chemicals are not created or destroyed; they are reused ○ driven by photosynthesis and chemosynthesis ● trophic levels ○ feeding relationships within an ecosystem ○ follow transformation of energy ○ map movements of chemicals ○ two kinds ■ autotrophs - make their own food from inorganic substances (producers) ■ heterotrophs - cannot make own food; must consume to stay alive (consumers) ● producers ○ perform photosynthesis and chemosynthesis ○ fuel for cellular respiration and building blocks for growth ○ plants, algae, photosynthetic prokaryotes/protozoans, bacteria ○ chemosynthesis - uses energy from chemical reactions to make organic molecules, doesn’t use any light ■ hydrothermal vents - areas where hot, mineral-rich water enters seawater from the deep ocean floor ● some archaebacteria live here; they are chemoautotrophs ● they are the primary producers for organisms living here ● consumers ○ primary ■ organisms that consume producers (herbivores) ○ secondary ■ organisms that consume herbivores (carnivores) ○ tertiary ■ organisms that consume carnivores (omnivores) ● decomposers ○ they are consumers ○ get energy from non-living organic material ■ absorbs nutrients from dead organisms and decompose organic material ○ detritivores ■ animals that eat remains of dead animals; crabs, vultures, earthworms 4 ● energy ○ about 10% of the energy is passed on to the next trophic level - energy is lost because of cellular respiration and other energy-consuming processes ○ only the energy that is converted to biomass is available ■ biomass - dry weight of the organism; weight without water ○ ⅔ of the 10% of energy is used for cellular respiration LECTURE 5 ● biogeochemical cycles ○ nutrients are moved from the environment to organisms, then back to the environment ○ there are reservoirs of the nutrients in the environment ● water cycle ○ cycling of water molecules ○ between bodies of water to the atmosphere, then back to Earth, where the water is available to organisms 5 ● carbon cycle ○ movement of carbon-containing molecules from organisms and the Earth’s crust to the atmosphere and oceans, then back into organisms ● phosphorus cycle ○ phosphorus moves through rocks and living organisms ● nitrogen cycle 6 ○ movement of nitrogen from atmosphere, through nitrogen-fixing organisms in the soil and water, into plants and then to consumers; then back into the atmosphere ● disruption from human activity ○ human population growth ○ increased activities and technologies ■ causes global warming and climate change - greenhouse gases ● global warming ○ long term rise in Earth’s surface temperature; correlates with the rapid accumulation of greenhouse gases in the atmosphere ● renewable energy sources ○ can replace the use of greenhouse gases; better for the environment ■ solar energy, wind power, alcohol, hydrogen, methane LECTURE 6 ● defining life ○ condition that distinguishes organisms from inorganic objects and dead things ○ growing with metabolism, reproduction and adaptation ○ follows the characteristics of life ● characteristics of life ○ organism needs to have ALL of these, at some point during existence ■ order + organization ■ acquiring/using energy ■ metabolism ■ regulation ■ sensing/responding to stimuli ■ cells 7 ■ motion ■ growth/reproduction ■ ability to evolve ● chemistry of carbon compounds (what are organisms made of) ○ carbohydrates, lipids, nucleic acids, protein ● are viruses alive? ○ they are inert mixtures of protein and genetic material ○ not affected by antibiotics ○ tobacco mosaic virus, adenovirus, influenza virus, bacteriophage T4 ● viruses are ‘clever’ ○ they increase their numbers and evolve into new forms ○ use host cells ‘to do the work’ - LYTIC AND LYSOGENIC CYCLES ■ viral genetic material is released from virus ■ host cell processes the viral genetic material ■ produces more viral nucleic acid/ proteins, which makes more virus cells 8 ● RNA ○ some viruses have RNA as their genetic material; retroviruses, HIV ○ RNA must be copied into DNA, using an enzyme - reverse transcriptase ■ makes many mistakes and viruses readily mutate ● prions ○ infectious self-reproducing protein structures with no nucleic acid ○ they are a misfolded form of a protein that is normally present of the surface of nerve and brain cells ■ scrapie - disease in sheep ■ kuru - found in cannibals who eat brains ■ BSE (bovine spongiform encephalopathy) - mad cow disease ■ creutzfeldt-jacob disease - human version of BSE ○ create sponge-like holes in the brain, causing death ○ there is no treatment for any of the diseases ● how prions ‘reproduce’ ○ it converts the normal forms of the proteins into the prion versions LECTURE 7 9 ● chronology of life development ● theories on the origins of life ○ life was created by the action of one or more gods ■ natural phenomenon; not testable ○ life originated from non-living matter on Earth ■ spontaneous generation ■ chemical evolution ■ hydrothermal vents ○ life came from some other place in the universe ■ this causes other problems ● spontaneous generation theory ○ idea that life forms could arise from inanimate objects, instead of seeds or eggs ■ fleas from dust, maggots from dead fish ○ it was made obsolete by the work of Louis Pasteur ● Pasteur’s findings ○ 1859 experiment to see if living matter can spontaneously generate from nonliving matter ○ first showed that air is full of microorganisms ■ they can be killed with heat ○ second showed that spontaneous generation does not occur ■ conditions were very different many years ago 10 ● conditions of primitive Earth - 4.5 bya ○ 700 million years of meteor bombardment ○ intense lightening and UV radiation ○ Earth’s crust is hot and volcanic ○ too hot and hostile for life ● conditions of primitive Earth - 3.8 bya o ○ Earth cooled down (90-100 ) ○ less intense, but still strong energy sources (UV radiation, thermal energy) ○ little or no atmosphere oxygen (free O ) 2 ○ atmosphere gases mainly from volcanic eruptions (outgassing) - NH3, NH2, 2 , CO ,2CO, CH ,4H O2 ● chemical evolution ○ the chemical and physical processes in Earth’s primordial environment may have eventually produced simple cells ■ suggests that life evolved from chemicals ■ chemical complexity increased over 300 million years ● four stages in the formation of life 1. the abiotic synthesis of small organic molecules ■ abiont - synthesis outside the body of an organism 2. joining these small molecules (monomers) into polymers and macromolecules 3. origin of self-replicating molecules - genetic material 4. packaging these newly formed organic molecules into protobionts ■ protobionts - evolutionary precursors of the first prokaryotic cells 11 ● stage one ○ 1920’s: the idea of the ‘primordial soup’ - Oparin/Haldane ■ suggested that conditions of primordial Earth would have enabled life to first come into existence on early Earth ○ 1953: Stanley Miller/Harold Urey ■ tested Oparin/Haldane hypothesis with proposed conditions of early Earth ■ produced amino acids and other organic molecules ■ concluded that organic molecules can be synthesized abiotically ● another possible source is from space ● stage two ○ abiotic origin hypothesis predicts that monomers link to form polymers ○ similar conditions likely on Earth when dilute solutions of monomers splashed onto fresh lava or shores of oceans/lakes (also maybe in hydrothermal vents) ○ spontaneous assembly of molecules in these areas ● stage three ○ RNA world hypothesis ■ RNA was first genetic material that could replicate itself; DNA came later ○ DNA world - DNA replication - structure enables duplication ■ double stranded, making it more stable ■ complementary binding - A/T, C/G ■ passed on to new generations ○ RNA can also replicate and evolve ■ single stranded, making it less stable ■ complementary binding - A/U, C/G ■ occasional copying errors create mutations - this is what causes evolution ● stage four ○ formation of protobionts ○ single membraned sacs ■ they do form spontaneously LECTURE 8 ● chemicals ○ matter makes up everything that is of this world ■ made of chemical elements ○ we are made of more than 90 elements ■ they cannot be broken apart by normal means ■ typical human was worth $3.57-$4.50 (Sept. 2013) ■ 90% is carbon (18%), nitrogen (3%), oxygen (65%) and hydrogen (10%) ● atoms ○ in 2 areas 12 ■ central nucleus ■ pathways around nucleus (shells) - they orbit around ○ 3 types of particles ■ positive (protons) - in nucleus ■ neutral (neutrons) - in nucleus ■ negative (electrons) - orbit around ● atomic number ○ number of protons in nucleus ○ written as subscript to lower left of the symbol ● atomic weight ○ number of protons + neutrons ○ written as superscript to upper left of symbol ● electrically neutral atoms ○ they have the same number of protons and electrons ● electrons and their shells ○ electrons orbit around the atom nucleus in the shells ○ atoms try to lose, gain or share electrons until they have a full valence (octet rule) ○ 1st shell → holds up to 2 electrons ○ 2nd shell → holds up to 8 electrons ○ 3rd shell → holds up to 8 electrons (but can hold more, depending on atom) ● valence shell ○ outermost shell of an atom and it has valence electrons ○ atom is most stable when this shell is filled ○ not having a full valence shell makes the atom more reactive 13 ● isotopes ○ variations of an atom that have the same number of protons but different neutrons ■ they have a different weight ○ some isotopes are unstable - radioactive isotopes ■ they spontaneously decay, giving off different energy / subatomic particles ■ can be used as a dating tracer ■ radiation kills healthy cells and cancerous cells ● atoms reacting with other elements to form.. ○ molecules ■ groups of 2+ atoms, held together in a stable association ■ some molecules are made of only 1 element (oxygen 2 O ) ○ compounds ■ molecules containing 1+ type of element (water - 2H, 1O) ○ chemical bonds ■ hold atoms together in molecules or compounds ● chemical bookkeeping ○ chemical equation shows reaction: reactants → products ○ atoms are rearranged but never lost ■ accounted on both sides of equation; it is balanced ○ use symbols for elements when writing formulas ● what determines an interaction ○ the number and arrangement of the electrons ○ electron vacancies ■ unfilled valence shells make atoms likely to react ○ valence shell ■ an atom with a full valence shell will not bond (ex: noble gases) ● chemical bonds ○ the union between the electrons of neighbouring atoms ○ form in attempt to stabilize the outer shell of the interacting atoms ○ 3 types 14 ■ ionic bonds ■ covalent bonds ■ hydrogen bonds ● ionic bonds ○ formed by the attraction of oppositely charged ions 1. one atom loses an electron and becomes a positively charged ion 2. the other atom gains the electron and becomes a negatively charged ion 3. charge differences attract the 2 ions to each other ● covalent bonds ○ very stable bonds ○ forms when atoms share a pair of valence electrons ○ each atom’s attractive forces ‘pulls’ on the other atom’s unpaired electron ■ causes the 2 electrons to occupy a shared orbital LECTURE 9 ● basic information about water ○ 70% of total body weight is water - THE REST IS CARBON COMPOUNDS ○ life originated in water ○ its physical and chemical properties make life possible ■ capacity to dissolve or repel substances ■ cohesion and adhesion ■ temperature-stabilizing effects ■ liquid form over a range of temperatures (0-100 C) 15 ● polar covalent bonds ○ form when atoms don’t share electrons equally ○ in water, the oxygen atom’s nucleus has more protons, make it more positive ■ the compound still has the same amount of positive and negative charges, but the distribution makes it slightly more positive or negative ● hydrogen bonds ○ relatively weak bond ○ form by the attraction of a positively charged hydrogen end of a polar molecule to the negatively charged end of another polar molecule ○ can occur between different molecules or within the same molecule ● liquid water vs. ice liquid water ice molecules held together loosely molecules held together tightly water flows water is solid no spaces between molecules spaces between molecules ● cohesion ○ water molecules ‘cling’ to each other ○ polarity of water results in hydrogen bonding between molecules ○ surface tension ■ clinging at air-water interface ○ water flows as a unit because of this clinging ○ BROWNIAN MOTION 16 ● properties of water ○ liquid at room and body temperatures ■ other materials are gaseous at these temperatures ■ can be used to travel and carry materials ○ solvent for other polar molecules ■ permits chemical reactions because of its polar nature ■ ‘spheres of hydration’ ● layer of water around an ion ■ hydrophilic ● water loving; binds with water ■ hydrophobic ● water hating; repels water ○ cohesive and adhesive ■ when the same molecules stick to each other (cohesion) ● ‘pull’ on each other ■ when different molecules stick to each other (adhesion) ● ‘stick’ to structures ■ good for transporting nutrients in trees ● xylem (water) and phloem (food) ○ temperature rises and falls slowly ■ high heat capacity ● a lot of heat is needed to raise the temperature ■ protects organisms from rapid temperature changes ● maintains homeostasis ■ water in blood helps to distribute heat throughout the body ○ high heat of vapourization ■ a lot of heat is needed to vapourize the liquid ■ prevents overheating ■ water evaporating from a surface carries away heat, cooling the surface ○ frozen water is less dense than liquid water ■ hydrogen bonds are rigid; frozen water expands ■ ice floats, liquid water does not ● allows life to exist underneath ● water, acids, bases, pH and buffers ○ water molecules can dissolve (breakdown) to form hydrogen ions (H ) and - hydroxyl ions (OH ) ■ then they can re-bind to form water - it’s a cycle ● acids ○ pH: 0-6 ○ anything that can donate hydrogen ions (H ) 17 ○ increase H concentration in solution ● bases ○ pH: 8-14 + ○ anything that can accept hydrogen ions (H ) ○ decrease H concentration in solution ● pH scale + ○ measures the concentration of H in a solution and indicates how acidic/basic it is ● buffers ○ helps keep the pH within normal limits + ■ taking up excess H when concentrations increase ■ adding H when concentrations decrease ○ various buffer systems in the body maintain the correct pH level ● carbonic acid-bicarbonate buffering system ○ keep the pH of blood at 7.4 (fairly neutral) ○ if H level decrease, carbonic acid will dissociate to release H into blood (↑H ) + ○ if H level increase, it combines with bicarbonate ions, making carbonic acid (↓H ) LECTURE 10 ● shapes of molecules ○ carbon can form covalent bonds with 4 other atoms ■ tetrahedron shape ○ 2 carbon atoms can be joined with a double bond ■ flat structure tetrahedron flat 18 ● variation in carbon skeletons ○ shape changes because of the diversity of organic molecules ■ the skeletons vary in length ■ may be straight, branched or arranged in closed rings ■ skeleton may include double bonds ● hydrocarbons ○ hydrogen atoms attached to a carbon backbone ○ non-polar and do not dissolve in water (hydrophobic) ● functional groups ○ single or cluster of atoms, covalently bonded to the carbon backbone ○ replace one or more hydrogen atoms of the hydrocarbon skeleton ○ the number and arrangement of functional groups give each molecule its own unique properties ○ increase solubility in water ■ they are hydrophilic ○ they can act as acids or bases ● most common functional groups ○ hydroxyl (OH) ○ carbonyl (COH) ○ carboxyl (COOH) ○ amine (NH2) ○ sulfhydryl (SH) ○ phosphate (PO4) 19 ● carbon rings ○ carbons are numbered to identify them LECTURE 11 ● macromolecules ○ cells join smaller organic molecules to form larger molecules ○ 4 major classes ■ carbohydrates (monosaccharide) ■ fat (glycerol/fatty acids) ■ protein (amino acids) ■ nucleic acid (nucleotides) ○ the chemical mechanisms that cells use to make and break polymers are similar for all classes of macromolecules ● polymers ○ consist of many similar or identical building blocks, linked by covalent bonds ○ form chains of repeating subunits (monomers) ■ lipids do not form chains though ● condensation reaction (dehydration reaction) ○ process that joins monomers by covalent bonds ○ one monomer provides a hydroxyl (OH), the other provides hydrogen (H) 20 ■ these form water as a by-product (H O) 2 ○ aided by enzymes ■ synthetases ○ CREATING LONGER CHAINS BY GETTING RID OF WATER ● hydrolysis reaction ○ process that degrades polymers when covalent bonds connecting the monomers are disassembled ○ a hydrogen atom and a hydroxyl group from a split water molecule attach to where the covalent bond used to be ○ this reaction dominates the digestion process ○ aided by enzymes ■ hydrolases ○ USING WATER TO BREAK UP CHAINS LECTURE 12 ● carbohydrates ○ simple sugars and polymers (chains) of sugars ○ most names end in -ose ○ monosaccharide (GLUCOSE) ■ major fuel source for cellular work ■ energy is stored in chemical bonds between carbon and other atoms ○ disaccharide (MALTOSE) ○ polysaccharide (STARCH) ■ polymers of monosaccharides ■ fuel storage and structural roles 21 ● monosaccharide (one sugar) ○ classified by the number of carbons in the backbone ■ 6 carbons → hexose (C 6 12)6 ■ 5 carbons → pentose (C5H 10)5 ■ 3 carbons → triose (3 6 O3) ○ minor structural changes result in different sugars or formation of ring structure ■ ex: glucose and galactose (look at picture below) ○ aldoses ■ double bond is at the end of the chain ○ ketoses ■ double bond is somewhere in the middle of the chain ● disaccharide (two sugars) ○ sugars joined by condensation reactions ○ maltose → glucose + glucose ■ broken down by maltase ○ sucrose → glucose + fructose ■ broken down by sucrase ■ not synthesized in animals ■ water soluble, easily transported ■ cane sugar, beet sugar, pineapple ○ lactose → glucose + galactose ■ sugar in milk/dairy ■ broken down by lactase 22 ■ lactose intolerance is when people do not have lactase in their body, so they cannot break down dairy products ● polysaccharide (three or more sugars) ○ structure depends on kinds of sugar and the way they are joined ○ starch, glycogen, cellulose ■ they are all made of glucose, but linked differently ○ functions are energy storage and other polysaccharides serve as building materials for a cell or organism ● starch vs. glycogen starch glycogen storage form of glucose in plants storage form of glucose in animals (liver/muscle) long chains of glucose long chains of glucose many branching side chains more, but shorter, branches than starch ● cellulose ○ most abundant polysaccharide and organic material ○ in plant cell wall ○ unbranched ■ it is long, rigid fibrils, which are held together in ‘sheets’ ○ not digestible by humans ■ need enzyme, cellulase, to digest ○ ‘roughage’ or ‘fibre’ ■ helps food move through the intestines/colon LECTURE 13 ● structure of eukaryotic cells ○ cell membrane, nucleus, cytoplasm ○ cytoplasm is divided into cytosol and organelles ■ cytosol: gel-like fluid portion ■ organelles: solid pieces in the cell; with or without membrane 23 ● cellular metabolism ○ intracellular chemical reactions ■ degradation, synthesis, transformation of small organic molecules ■ linear or cyclic reactions ○ enzymes play a big role ■ they speed up reactions ■ mostly proteins, catalytic ■ keep optimum pH and temperature ■ interact with substrate at the active site ○ coenzymes ■ they help the enzymes ■ molecules that move hydrogen atoms and electrons to the sites of chemical reactions in cells ■ ex: NAD , FAD ● how enzymes and substrates fit together ○ at the active site, substrate molecules bind briefly and form a product ○ active site brings the molecules close enough so they interact and form a product ■ enzyme’s shape may change ○ once the product is released, the enzyme goes back to previous shape ● metabolic pathways 24 ○ anabolic ■ favour the synthesis of molecules to build organs and tissues ■ often condensation/dehydration reaction ○ catabolic ■ favours the breakdown of complex molecules into simpler ones ■ often hydrolysis reaction ● energy ○ energy source for the body is the chemical energy in the carbon bonds of ingested food ■ must be converted into a useable form of energy ■ ATP (adenosine triphosphate) ● the cell’s energy currency ■ the high energy phosphate bonds of ATP store energy ● ATP/ADP cycle ○ provides energy for cell activities ■ cells use ATP constantly, so it must always be replenished ● cellular respiration ○ three chemical pathways ■ glycolysis (anaerobic respiration) ■ kreb’s cycle (aerobic respiration) ■ electron transport chain (aerobic respiration) ● mitochondria ○ ATP is formed in its inner compartment ○ enclosed by a double membrane ■ inner and outer ■ allows for stockpiling of hydrogen ions and formation
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