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Bundle of Chapter 1 Notes

by: Liz Fish

Bundle of Chapter 1 Notes STAT 1200 - 03

Liz Fish
GPA 4.0
Introduction to Biological Systems with Laboratory
Joel Maruniak

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Here are all of my chapter one notes. Enjoy! All of the underlined/bolded words are crossword words.
Introduction to Biological Systems with Laboratory
Joel Maruniak
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This 12 page Bundle was uploaded by Liz Fish on Thursday September 17, 2015. The Bundle belongs to STAT 1200 - 03 at University of Missouri - Columbia taught by Joel Maruniak in Summer 2015. Since its upload, it has received 42 views. For similar materials see Introduction to Biological Systems with Laboratory in Biological Sciences at University of Missouri - Columbia.

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Date Created: 09/17/15
The Origin of Life Universe 137 Billion Years Old 0 Earth 46 Billion Years Old What is Life a All Life 0 Early Earth Hadean Period 46 38 Billion Years Ago asteroids and geologic seduction destroyed ancient rocks and almost none can be found from that time Archean Period 38 25 Billion Years Ago only prokaryotes evolution of 1st life bacteria prokaryotes existed 38 billion years ago 0 no large continents until late Archean sun was 13 times dimmer days 15 hours long Proterozoic Period 25 Billion 540 Million years ago simple life existed period before abundant complex life 0 oxygen increased in oceans and atmosphere 0 a number of ice ages occurred Sometime between 18 28 Billion years ago Eukaryotes formed 1st cell with nucleus Oldest multicellular fossils are 12 billion years old algae Phanerozoic Period 540 million years ago present 0 a period of abundant animal life Consists of 1 or more cells that grow develop and reproduce via DNAbased heredity has ATP based metabolism maintains homeostasis stable internal environment 0 When life 1st evolved the atmosphere consisted of Nitrogen N2 Carbon Dioxide CO2 Methane CH4 and Ammonia NH4 but no Oxygen 02 o This made it a reducing atmosphere which favored the formation of organic molecules compounds with CC and CH bonds Lots of heat lightning and radiation provided the energy 0 No oxygen meant no ozone layer so the high amounts of UV from the sun broke down organics as they formed 0 There is growing evidence that life may have begun at the site of deepsea vents 0 right reactants and conditions exist there chemoautotrophic bacteria and archaea live around them Early Life 0 The 1st evidence for life is found in fossil carbon grains in 38 billionyearold rocks that have a 12Carbon to 13Carbon ratio these ratios are only found in living organisms or their remnants c There are 35 billionyearold fossils stromatolites found all over the world 0 formed only by colonies of cvanobacteria All life requires energy Carbon and Hydrogen sources Photosynthetic or Chemoautotronhic prokaryotes can make organic molecules 0 others have to use existing molecules Some of the first photosynthetic bacterias more that 35 billionyearsago had a photosystem that split Hydrogen Sulfide H2S to get Hydrosulfide HS 0 Released Sulfide S2 as a waste product 0 Photosystem l evolved about 35 billionyearsago from the first photosynthetic bacteria this is the most efficient energy collecting process known almost 100 efficient Photosystem ll evolved from Photosystem about 32 billionyearsago in cyanobacteria it was able to split water H20 to get Hydrosulfide HS and produced Oxygen O2 as a waste product Methanogens were chemoautotrophs that collect Hydrogen H2 and Carbon Dioxide CO2 for use in the metabolism and give off Methane CH4 0 they exist in sewage garbage dumps swamps cow rumen etc Appearance of Aerobic Life From about 32 billionyearsago when Photosystem ll evolved until about 25 billionyearsago the Oxygen O2 produced was used up in oxidizing organic waste in the ocean 0 About 25 billion years ago free Oxygen O2 began to first accumulate in oceans and then in the atmosphere Dated sediments show that the ocean was rich in dissolved Ferrous Fe2 more than 25 billionyearsago 0 About 25 billionyearsago Oxygen O2 that was liberated by Photosystem ll began to oxidize Ferrous Fe2 and Ferric Fe3 which is insoluble in water and forms rust Fe203 Over time oceans and then the atmosphere became enriched with free Oxygen O2 Prokaryotes 2 types of prokaryotes evolved Bacteria and Archaea they form 2 of the 3 domains of life 0 3rd is Eukarya o Bacteria split from the last common ancestor about 35 billionyearsago o Archaeas and Eukaryotes split about 18 28 billionyearsago many believe that Archaeas are more closely related to Eukaryotes than Bacteria o The only problem in establishing relationships is horizontal gene transfer in prokaryotes So many genes were exchanged that the early tree of life may have really been a ring of life from the 3 domains that emerged Prokaryotes have little internal structure 0 Most individual species have a repertoire of 1030 compounds for energy 0 Some are autotrophs and some are heterotrophs o Autotrophs organism that can create energy from inorganic substances don t eat 0 Heterotrophs organisms that create energy through organic substances these ones eat 0 DNA is double stranded with single circular chromosomes located in the nucleoid region and in the plasmids o Plasmids are small nonchromosomal loops of DNA a Exchanged in horizontal gene transfer 0 Can carry genes for antibiotic resistance 0 Scientists use them as vectors to insert genes into bacterial and eukaryotic cells Prokaryotes have a strong outer cell wall to protect against damage 0 Bacteria but not archaea have a wall made of sugar molecules that are crosslinked by peptides m 0 Some bacteria and archaea walls stain purple with gram stain these are Gram Positive Gram Positive cells have a single thick wall that absorbs purple stain Gram Negative cells have a thin wall that absorbs pink stain o The penicillin class of antibiotics blocks the crosslinking of peptides to sugars in gram positive bacteria 0 This causes the walls without crosslinks to become weak and rupture a As the cell walls are naturally broken down and restructured the links are blocked so the walls simply fall apart antibiotics using this mechanism do not work with gram negative bacteria or archaea good thing archaeas aren t human pathogens 0 Many symbiotic bacteria are gram negative 0 They live in stable conditions and therefore don t need a strong wall 0 Example E Coli in animal guts 0 Instead they have two membranes one inside the wall and one outside 0 the outer membrane of gram negative bacteria prevent penicillin from getting into its walls 0 Antibiotics for gram negative cells or penicillinresistant bacteria work by inhibiting the bacteria s metabolism OR the proteinDNNRNA synthesis Eukaryotes have cells with a nucleus and other organelles The classification of groups in eukaryotic cells is in flux 0 Molecular and genomic studies reveal that many organisms in the former singlecelled kingdom Protista should be grouped with fungi plants or animals Features of a Eukaryotic Cell 0 Has a nucleus containing most of its DNA in linear form in chromosomes 0 Has organelles which are structures that compartmentalize Eukaryotic cells and allow a complex metabolism 0 Most have cell walls except animal cells Organelles Membranes o Lasma Membrane is the covering or the outer skin of the cells 0 Acts as a barrier gatekeeper for movement inout of the cell c Membranes divide the cell into compartments 0 Made of lipids and phospholipids 0 Most common lipid in the animal plasma membrane is Cholesterol 0 Phospholipids have some properties as detergents One end is polar other is nonpolar o Amphipathic a Polar end dissolves in water then nonpolar end dissolves in oil 0 The membranes are arranged as a bilayer sandwich 0 Polar ends face water inside and outside the cell c Nonpolar ends are hidden from water inside the bilayer 0 Because the middle is a thick nonpolar layer the membrane is impermeable to most polar water solubles Such as amino acids sugars proteins nucleic acids andions o Allows nonpolars to pass easily 0 Membrane Proteins Customize membranes A bilayer forms a matrix proteins perform specific functions Form channels that allow ions and water to pass in and out of the cell Form transporters to move impermeable molecules in and out of the cell Act as antennas for incoming signals Act as enzymes Extracellular surface parts uniquely identify the cells Attach a membrane to other cells or the cytoskeleton 0 Movement Across the Plasma Membrane o Diffusion is the movement of molecules down their concentration gradient Nonpolars diffuse through the membranes polars don t Movement of water down its concentration gradient is called osmosis lons can only cross membranes through channels and transporters o Transporters are large membrane proteins They move impermeable compounds from one side of the membrane to the other e The rate is saturable because the number of transporters is finite o Facilitated Transport moves import molecules faster down their concentration gradient No energy used Glucose enters the cells this way insulin turns the transports on 0 Active Transport is like facilitated diffusion except it uses energy to move molecules up and down the concentration gradient 0 Many compounds are too big to use channels or transports 0 These use endocytosisexocytosis o Endocytosis the plasma membrane invigilates folds into itself to form vesicles 0 Exocytosis the vesicle fuses with the plasma membrane and the contents are exported c There are 3 types of endocytosis Cytoskeleton Phagocytosis particulate matter is engulfed o lmmune cells do this to viruses and bacteria Pinocytosis extracellular liquid is taken in ReceptorMediated Endocvtosis a forming vesicle is lined with receptors for specific molecules 0 Cholesterol is endocytosed via HDL and LDL receptors 0 Eukaryotic cells have a skeleton made of 3 types of protein filaments o Actin the finest filament it forms long thin filaments Most abundant protein makes up 10 15 of all of the protein in the body Involved in cell movement and structure also in muscle contraction Intermediate Filaments tough fibrous structural proteins like keratin ln brain cells these are tangled in ALS and Parkinson s o Microtubules the largest filament hollow form internal scaffold that determines the cell s shape Forms the spindle apparatus in cell division Moves cilia and flagella Organelles and vesicles are moved along these Degenerate and tangle Neurofibrillarv Tandles in Alzheimer s and athletes with repetitive head trauma 0 Head trauma causes E Chronic Traumatic Encephalopathy CTE groups intellectual and memory deficits anger depression early Alzheimer s in players of contact sports Organelles and Internal Components Endoplasmic Reticulum ER extensive network of membranes 0 Derived from the plasma membrane 0 Divides the cell into compartments forms an assembly line for synthesis or breakdown of molecules forms vesicles 0 Rough ER Studded with ribosomes these are proteinRNA complexes that synthesize proteins 0 Smooth ER has enzymes where carbohydrate and lipid synthesis occur 0 There are lots in cells that produce steroid hormones c There are also lots in detoxification tissue like the liver that use Smooth ER enzymes to break down toxic compounds Golgi Apparatus or bodies Golgi stacks of membranes derived from the Endoplasmic Reticulum Collects and modi es molecules then packages them in vesicles and distributes them Animal cells contain about 1020 Golgi bodies Plant cells have hundreds of Golgis Proteins and lipids from the Endoplasmic Reticulum go to the Golgi to get carbohydrate or phosphate groups added 0 This helps them become glycolipids or glycoproteins and phospholipids or phosphoproteins Golgi are plentiful in secretory cells where they make vesicles for export Golgi also make lysosomes equivalent to vacuoles in nonanimal cells for its cell39s use 0 Contain digestive enzymes that can break down most organic macromolecules White blood cells kill bacteria viruses etc by putting them into lysosomes There are a number of lysosomal storage diseases about 50 such as TaxSachs A defective gene causes an enzyme that breaks down a lipid to be absent in TaySachs causing liquid to accumulate in neurons leading to brain damage and death by about age 5 Silicosis and Asbestosis result from indigestible silica and asbestos bers being trapped in lysosomes which they pierce and cause to leak Enzymes leaking from lysosomes damage lungs Nucleus Has a Nuclear Envelope that39s 2 layers of membrane 0 It39s continuous with and derived from the Endoplasmic Reticulum There are a number of big pores in an envelope 0 Many proteins and smaller molecules can39t pass 0 Allow 2 types of large molecules to pass 0 Proteins needed in the nucleus are made in ribosomes RNA going from the nucleus to the ribosomes o The number of pores varies with metabolic activity 0 More metabolic activity more pores Nucleus contains a Nucleolis o This is a region on chromosomes where a lot of rRNA is being made for ribosome protein synthesis stations 0 Nuclear pores are made from about 50 different proteins Mitochondria 0 Proteins are directed for import into the nucleus by NLS39s Nuclear Localization Signals short sequences of amino acids 0 Importing and Exporting are complex and require energy Pores are positively charged so compounds passing through have to be negatively charged Originated when Alpha Proteobacteria entered Eukaryotes very early Perform aerobic respiration for our cells About the same size as these bacteria Mitochondria have their own DNA which is circular like bacteria Eukaryotes don39t manufacture Mitochondria existing mitochondria ssion like bacteria 0 The nucleus controls ssioning Aerobic conditioning raises the number of mitochondria o Metabolically active cells have more mitochondria Antibiotics that inhibit bacterial ribosomes inhibit mitochondria o Mitochondria don39t have a cell wall Organelles unique to plants Chloroplasts arose from engulfed cyanobacteria Metabolism Double outer membrane Have own genome reproduce by ssioning Plants have a large central vacuole that can be greater than 75 of the cell39s volume Stores water metabolites digestive enzymes wastes Performs many functions of animal lysosomes Provides water pressure turgor that keeps plants from wilting 3 Major Types Photosvnthesii synthesis of organic molecules from C02 and H20 using energy from the sun Catabolism breakdown od organic molecules to obtain energy and materials Anabolism synthesis of organic molecules from materials to energy All life uses ATP as an energy molecule which implies that ATP evolved early Glycolysis only type of metabolism that almost all living organisms perform ls anaerobic uses no oxygen All reactions occur in cytoplasm none in organelles Glycolysis is a series of 10 reactions Essentially cuts glucose in half to produce two 3carbon molecules of pyruvate Energy is required to make ATP from ADP and is produced by breaking bonds Inef cient because only 2 of 10 reactions produce enough energy to make ATP Glycolysis produces a net of only 2 ATPsglucose Average person needs 2000 calories a day 236 pounds of solid ATP Only about 17 ounces of ATP is in the body at any given time ATP has to be regenerated over and over Aerobic Respiration o Pyruvate is actively transported into mitochondria This is immediately decarboxviated loses carbon dioxide to acetyl CoA 2carbons Acetyl CoA enters the Krebs Cycle lt39s H39s are stripped off and Carbons are breathed out as Carbon Dioxide Fats and proteins can be converted to acetyl CoA and run through the Krebs Cycle Generation of ATP by Mitochondria Mitochondria inner and outer membranes form 2 chambers Krebs cycle occurs in the inner chamber lt regenerates 2 ATPs by bondbreaking like glycolysis However most ATPs are generated by energy extracted from Hydrogens stripped off acetyl CoA in the Krebs Cycle Hydrogens are picked up by carrier molecules NAD or FADH Taken to ETC Electron Transport Chain on the inner membrane Energy of H39s is stripped off and Acetyl CoA resides in their electrons These high energy electrons are used in the ETC to pump H39s into the outer chamber 0 Builds a high concentration of H in the mitochondria39s outer chamber The High concentration of H and its charge create 2 forces that act to drive H into the inner chamber Chemiosmosis o 1 force is the concentration gradient 0 Second force comes from positive charges repelling But the inner and outer membranes are impermeable to H Only place H39s can go is at a specialized protein called ATP Synthase This enzyme harnesses forces driving H back into inner chamber to generate ATPs Carbon Dioxides that were clipped off in the Krebs Cycle are breathed out The oxygen that we breathe in and some spent electrons combine with extra Hs left after pyruvate is dismantled all to form H20 Aerobic Respiration provides an extra 28 ATPs after Glycolysis yields 2 Each H carried by NAD yields about 25 ATPs Each H carried by FADH yields about 15 ATPs FADH produces fewer ATPs because of where H enters the ETC This is less than the theoretical yield of 38 ATPsGlucose Because energy has 2 be used to actively transport pyruvate ADP and P04 and 2 NADHs from glycolysis into mitochondria And mitochondria membranes are a bit leaky to Hs o Fermentation When muscles don39t get enough Oxygen pyruvate undergoes fermentation anaerobic metabolism lt39s reduced has hydrogens added to it to Lactate Because pyruvate can39t diffuse easily out of cells but lactate can Otherwise pyruvate would build up and create product inhibition which would slow the production of ATPs by glycolysis Yeast produce alcohol ETOH from pyruvate o Photosynthesis Chloroplasts perform photosynthesis Using disklike structures called Thylakoids A stack of which is called a granum Cytoplasm is called Stroma Chlorophyll is a pigment in most photosynthetics lt39s green because green is the only wavelength not absorbed o Photosystems linked arrays of chlorophylls that collect light energy Cyanobacteria evolved Photosystem II to be used in combination with Photosystem Photosystem ll allowed them to get Hydrogens from H20 Light absorbed by chlorophyll excites an electron that is routed to a reaction center chlorophyll that can export it to the ETC Photosystem ll works rst makes only ATP using an ETC as in mitochondria via chemiosmosis Pumps Hs inward across the thylakoid membrane ATP is made as Hs move out through ATP synthesis At the end of the ETC electrons are handed off to Photosystem This electron has given up about half of its energy in the ETC to make ATPs Photosystem l absorbs light boosts this electron to an excited state again Energy from this excited electron is used to make NADPH from NADP and Hs NADPH is the source Hydrogens used to make organic molecules Photosystem I also makes some ATPs because Photosystem ll can39t provide all the ATPs needed to make glucose NADP is different HydrogenElectron carrier than NAD Allows plants to keep catabolism and anabolism separate Photosystem ll gave Photosystem I an electron which is given to NADP along with an H Photosystem ll now needs a replacement electron badly It gets one by splitting H20 into Hs electrons and Oxygen Hs go to chemiosmosis and NADP Electrons replace those given to Photosystem l Oxygen is released as a waste 0 Calvin Cycle reactions that make glucose 0 Uses 18 ATPs 12 NADPHs and 6 C025 to make one glucose C025 are run through the cycle oneatatime Each C02 is xed by adding by adding to RuBP ribulose 1 5 bisphosphate a 5Carbon sugar Catalyzed by Rubisco most common protein on Earth Essentially glucose is made by running glycolysis in reverse occurs in stroma 0 Cell Reproduction 2 types of cell division by most Eukaryotes o Mitosis occurs when cell makes a copy of itself Meiosis provides gametes for sexual reproduction Most eukaryotic cells have pairs of chromosomes Diploid Humans have 23 pairs of chromosomes Pair members similar structures and are called Homologs Gametes sperm eggs spores pollen are Haploid Life Cycle of a Cell 0 lnterphase 0 G1 growth of a cell 0 GO working phase most cells in body are in GO not growing or dividing just doing it39s thing 0 S DNAchromosomes replicate beginning of cell reproduction G2 Chromosomes begin condensing organelles replicate 2nd step of cell reproduction Mitosis M moves parts duplicated in S and G2 into 2 compartments 3rd step of cell reproduction Cytokinesis o C division of 2 compartments into 2 daughter cells 4th step of cell reproduction Interphase Chromosomes are diploid not visible 0 In S phase our chromosomes are replicated to produce 92 sister chromatids Sisters are attached at the centromere the pinched point when looking at a chromosome where the chromatids come together Number of chromosomes always equals the number or centromeres Have a kinetochore that microtubules attach to Mitosis begins when chromosomes become visible 0 4 stages Prophase Metaphase Anaphase Telophase PMAT o Prophase Chromosomes become highly condensed Transcription of DNA stops nucleolus disappears In animals centrosomes move to opposite poles These are organelles that organize the spindle apparatus 0 Nuclear envelope breaks down so the microtubules can get to the chromosomes Microtubules form spindle apparatus and attach to kinetochores o Metaphase chromatids are lined up in the center of the cell by microtubules Called the metaphase plate 0 Near the end of Metaphase molecules holding the chromatids together dissolve freeing the sister chromatids o Anaphase Shortest phase only a few minutes Microtubules pull sister chromatids to opposite poles and push against those poles to stretch the cell Telophase returns cell to Interphase Chromosomes uncoil transcription begins again Spindle apparatus is dissembled Envelope forms around each new nucleus 0 Cytokinesis physical division of cell into 2 parts after telophase o By contraction of a belt of actinmyosin laments which forms a cleavage furrow can only be done in cells without cell walls Plants build a new cell membrane and wall in between the daughters to split them cell plate Meiosis provides gametes for sexual reproduction O 0 Fusion of haploid gametes produces a new diploid cell fertilization or syngamy o Offspring carry traits from both parents Mitosis vs Meiosis o Mitosis and meiosis begin with the dame chromosome duplication in Interphase o PMAT stages in Meiosis l are called P1 M1 A1 and T1 0 ln Mitosis duplicated homologs line up individually along the metaphase plate O In meiosis I duplicated homologs pair during P1 and stay paired along metaphase plate during M1 In anaphase of mitosis each chromatid of a homolog is pulled to a different pole In anaphase I of meiosis each duplicated homolog is pulled to a different pole In humans Meiosis I produces 2 new cells with 23 chromosomes23 centromeres Each chromosome is 2 sister chromatids attached at a centromere Meiosis II performs mitosis on cells produced by Meiosis I Pairing of homologs in P1 Synapsis Genes from each chromosome are aligned sidebyside by the synaptonemal complex Crossing over between chromatids exchanges corresponding sections of DNA In humans 23 crossingovers occur per chromosome pair resulting in nonidentical sister chromatids In mitosis kinetochores are on opposite sides of the centromere in Meiosis I kinetochores of each homolog pair face the same pole Pulling paired homologs apart in Anaphase 1 2 chromatids and their centromere go to each pole 0 At the beginning of meiosis egg and sperm precursors have 2 copies of the 23 chromosomes This can produce 223 or 8 million possible gametes Fertilized egg is from 2 gametes and has 64 trillion possible permutations 8 million x 8 million Crossingover further increases variability to a mindboggling degree And it allows genes from mom and dad to end up on the same chromosome


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