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BIOL 1201 Thursdav Januarv 16 2014 De nition of science the use of evidence to construct testable explanations and predictions of natural phenomena as well as the knowledge generated through this process Key points on nature of science Scientists Science originates in questions about the natural world Science uses observations and evidence to construct explanations about phenomena and testable hypothesis The more observations and evidence that support a hypothesis the stronger the hypothesis Employ a variety of techniques to investigate the natural world Make their explanations public through presentations and publications Critique the explanations proposed by other scientists Ranges of conditions for life 1 P1999 Our quottypical experiencequotbody temp at 37 C and 1 atm The upper temperature for life is 132 C Cell body temperatures from 2 C to 132 C Ranges of pressure 1 atm to 1100 atm The most common habitat for life on the planet the deep sea Conditions at the average depth of the ocean 2 C to 4 C 380 atm of pressure no sunlight Anta rtic Fishes Live and have body temperatures at 2 C below freezing 1 Penguins Keep warm at similar temperatures endotherm 2 Diving Seals Deep sea sh Can hold their breath for as long as 90 minutes Dive down to 1500 m approx 1 mile for as long as 90 minutes Down to 700 m high pressure cold temp low food availability 1 Piezophiles Bacteria are quotpressure lovingquot 2 Thermophiles Bacteria thermophiles exist at temperatures up to 132 C grow at 122 C Found on sea oor at areas called hydrothermal vents hot water is vented 3 Sharks Live with 12 molar urea in their tissues 4 Halophiles Haophiic bacteria live in osmotic equilibrium with 3 molar salt 5 Tuna Raise the temperature of their muscles above ambient temperature as much as 15 C are endotherms in contrast to ectothermic sh other endotherms great white sword sh 6 Gutless tubeworms thrive at deep sea hydrothermal vents Midwater sh and invertebrates Organisms living in the water column achieve neutral buoyancy despite the high density Tuesdav Januarv 21 2014 Elements pure substances that cannot be broken down into 2 or more simpler substances 92 naturally occurring 118 known elements Atoms smallest unit which an element can be divided 0 Nucleus protons 1 charge 1 dalton mass neutrons 0 charge 1 dalton mass Atomic number number of protons in the nucleus Atomic mass of protons and neutrons in nucleus Electrical charge of electrons of protons In an ion the of electrons is not to of protons Compound substance which can be broken down to 2 or more elements 0 Composition is de nite and exact 0 Energy is involved in the synthesis or breakdown ie burning gasoline 0 elements lose characteristic properties of when they were individual Chemical Bonds gt Forces holding atoms together in molecules gt characterized as strong or weak depending on the energy required to make or break the bond Strong covalent bonds involve sharing of electrons Weak noncovalent bonds ionic interactions attraction of an opposite charges 1 atom donates an electron to another 0 hydrogen bonds Hvdroden bonds weak bond occurs between partial negative and partial positive charge Covalent bonds strong bonds share electrons lonic bonds weak bonds atoms gain or lose electrons to givereceive from another electron Polar Bonds unequal sharing of electrons partial and partial regions 0 What determines the number and type of chemical bonds Number valence Type electronegativity Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons Measure of the attraction an atom has for electrons Valence vs Valence electrons gt Valence is the number of electrons needed to ll the outermost shell of an atom o Valence electrons are the electrons contained in the outermost shell of an atom Moles and Molar Concentrations gt 1 Mole the mass of a substance equal to its gram molecular weight gt 1 molar solution solutions containing 1 mole of a substance per 1 liter of a solution 0 Fl D 7090 of weight of most life forms Sets the lower temp limit for life Sets upper temp limit Probably not result from hydrogen bonding Water behaves as a much larger molecule OOOOO Unusual properties 0 High heat capacity amount of heat needed to raise temp 1 degree for 1 g of water 1 cal per g of water High heat of vaporization amount of heat to vaporize 1 g of water 540 cal per g at 100 degrees C High heat of fusion amount of heat removed to freeze 1 g of water 80 cal per g Most dense at 4 degrees C High dielectric lonizations dissociation into acid hydronium ion and base hydroxyl ion High surface tension and capillary action due to hydrogen bonding Subercoolind aka undercoolind cooling of the liquid below its freezing point without the formation of ice crystals Below a certain temp molecular aggregates become larger Embryo crystal seeds the solutions when a critical radius is reached Ice forms spontaneously pure water can be supercooled to 40 degrees C lce nucleators prevent supercooling and a rapid freezing causes freezing at higher temperature ie proteins polysaccharides o Covalent HO 110 kcal per mole 0 Angle 1045 degrees 0 Weak 45 kcal per mole H bonding effectively makes water a larger molecule Freeze tolerant plant Lobelia Telekii mountainous regions of Kenya and Uganda holow and uid lled in orescence High heat capacity Alpine species experience temp from 10 degrees C to 10 degrees C lce formation uses ice nucleator and releases heat of fusion Induce freezing in central uid at highest possible subzero temp to prevent supercooling and explosive freezing Thursday January 23 2014 Acids Bases and Salts o acids produce H ions HCll H and Cl 0 Bases produce hydroxide ions NaOHD Na and OH 0 Salts produce neither NaClD Na and Cl H Scale l 1 pH log1H log H 2 log base 10 3 the difference between pH 3 and pH 4 is a 10 fold difference in the concentration of H The smaller the number the bigger the value in terms of concentrations 4 The difference in pH 3 and pH 5 is a 100 fold difference in the concentration of H 5 pH of 7 is neutral 6 pH below 7 is acidic 7 pH above 7 is basic pOH pOH log1OH logOH pH pOH14 Neutrality HOH logHlogOH Buffers Substances that help maintain a constant pH value Solubility Like dissolves like 0 Like in terms of polarity 0 Polar solutes dissolve in polar solvents o nonpolar solutes dissolve in nonpolar solvents Hydrophilic substances interact with water molecules Biological Molecules 0 Except for water all are built on a carbon skeleton 0 Large molecules constructed from smaller molecules 0 Polymers constructed from monomers Examples i water H Carbs iii Lipids iv Proteins v Nucleic acids Functional groups Hydroxyl groups are characterized by alcohol OH Carbonyl groups are aldehydes terminal carbons and Ketones Carboxyl groups are characteristic of acids COOH Amino groups are characterized by nitrogen with covalently bonded hydrogen amines Sulfhydryl groups are polar with SH Thiols Phosphate groups are characteristic of organic phosphates Methyl groups are nonpolar with CH3 PUN New Carbon skeleton The backbone Covalently linked Synthesis of polymers is covalent bond formation between monomer units Condensation dehydration synthesis Called this because a water molecule is removed Breakdown of polymers is breaking the covalent linkage between monomer units Hydrolysis breaking covalent bond linking the units by the addition of a water molecule Why make large biological molecules from small monomers a b Flexible system Fewer enzymes to make biological molecules than if quotstarting from scratchquot 1 Carbohydrates General formula CH20n eg if n6C6H1206 Saccharide sugars Monosaccharide1 sugardisaccharides2 sugars Both linear and ring formsring form is more popular Energy roles metaboic fuel Glucose and sucrose storage Starch plants Structural roles ceuose plants Chitin animals 2 Lipids Not based on structure but properties Water insoluble organic biomolecules Non polar compounds Structural components of cell membrane Storage and transport forms of fuel Protective surface coating Plants have waxy coating to prevent water loss Cell component in cell recognition Triglyceride storage form of fat not soluble in water 3 fatty acids From glycerol 3 carbons 3 hydroxyl groups COOH carboxyl contains the acid and provides linkage with the hydroxyl group alcohol Types of Fats 1 Saturated as many hydrogens that they can have no double bonds between adjacent carbons 2 Unsaturated liquid at room temp doube covalent bonds between adjacent carbons ower melting point kinks in the chain no a linear chain anymore disorganized Saturated fats are solids at higher temps Than unsaturated fats Acyl chains of unsaturated fats are kinky and therefore require a lower temp to become solid 0 2 3 D m L trigyceride phospholipids hydrophilic head and hydrophobic tails choesterol steroid ring structures hydrophobic Energy available per gram Fat93 Carb38 Protein31 1 nutrition cal1 kcal Lipids vs carbs Twice as much energy from fat Stored without water 0 lg of glycogen is stored with 25g of water Disadvantage to use fatnot as rapidly mobilized as carbohydrates Lipids metabolize in mitochondria and require molecular oxygen Examples 0 Camel up to 20 body mass is fat when food is plentiful Hump is lled with lipids Subatenous fat would cause thermoregulatory problems Hibernate 100 days without eating Metabolism survives off of energy stored in fat 0 Human Normal weight40 day reserve of energy Moderately obeseup to 1 year 3 Nucleic Acids Ring structure Nitrogenous hetercyclic bases Pentose sugar 5 carbon sugar Phosphoric acid Ex coenzymes NAD NADP FAD Genetic material ATP 4 Proteins Excellent example of a polymer Made of amino acids 20 naturally occurring amino acids are L isomers proteins vary in number and sequence of different kinds of amino acids FuncUons 1 Enzymes Protein catalyst Every chemical reaction in a cell is catalyzed by speci c enzyme 2 Storage Seeds Eggs 3 Transport Proteins Example hemoglobin transports 02 4 Contractile proteins In muscle Actin Myosin 5 Defensive blood proteins Antibodies 6 Toxins From bacterial Pertussin toxin whooping cough 7 Hormones and Receptors Hormones chemical messengers Receptors speci c recognition sites for chain messengers 8 Structural Proteins Silk Keratin hairs nails hooves 5 Amino Acids 20 kinds Monomers Structure Central carbon Amino group NH2 Carboxyl group COOH acid part Hydrogen R group 20 different R groups Types Polar hydrophilic interact with partial and charges of water Nonpolar hydrophobic no partial charges on R group Charged or Covalent bond between amino angles Peptide bond does not involve an R group Amino and carboxyl group are involved Primary Structure Sequence of amino acids in a protein or peptide Determines what protein will look like and how it functions Secondary Structure Alpha helix example brous proteins keratin in hair Beta sheet example silk core of globular proteins spiders web quotH bonds cause to form and stabilize these structures in the backbonequot Results from hydrogen bonding involving peptial backbone R groups are NOT involved Tertiary Structure Folding into 3D structure Folding is due to properties and interactions of the R group amino acids side chains R groups stabilize Hydrophobic and hydrophilic properties Hydrophobic R groups buried in interior of protein Stabilizes tertiary structure weak hydrogen bonds ionic interactions hydrophobic Strong covalent bonds disul de bridge Tuesdav Februarv O4 2014 Disul de bridges SH groups of 2 cystenines form covalent bonds Stabilize tertiary structure Quarternary structure Multiple polypeptide chains subunits t together to form a larger protein Can be identical subunits or different polypeptide chains Native and denatured proteins Native properly folded and functional Denatured unfolded and does not function Roles of weak bonds in biolodical svstems Easily made and broken at physiological temperatures Provide speci city If weak interactions were strong would crystallize the contents of a cell Attract and attach substrates to enzymes Determine molecular shape a compromise between backbone Antifreeze peptides 0 Small proteinspeptides that depress the freezing point of solutions 0 Noncolligative freezing point depression Colligative property dependent on number of particles molecules and not on the nature of molecules 0 Hysteresis proteins affect freezing point but not the melting point Freezes at 2C but melts at 0C Antifreeze peptides Hbond with ice Requires more energy to add water molecule to the curves surface of the ice crystal Temperature must be lowered to add molecule Decreased freezing point Proteins gone bad 0 Transmissible spongiform Encephalopathies 0 Genetic basis 0 Spread through medical procedures Tissues Instruments Examples 1 BSE mad cow disease 2 Scrapie sheep 1St recognized 250 yrs ago only New Zealand and Australia are free from scrapie CWD chronic wasting disease muledeer and elk CJD human formtypica onset at age 60 or later Kuru human form laughing disease in Papua New Guinea 6 vCJD early onset variant of CJD rst described in 1996 from eating meat from infected cows 155 Normal cellular form of prion protein Alpha helix Disease form Beta pleated sheet Same Amino acid sequence different secondary structures Disease form converts the normal cellyular form to the beta pleated sheet protein Cells Problems 0 Increased size 0 Relatively less surface area for a unit of volume 0 Problem moving materials into and out of the cell Cell structure Keeping cell distinct from the environment Organizing and coordinating metabolic processes 0 3 domains 0 Bacteria o Archaea o eukarya 2 categories 0 Prokaryotes archaea and bacteria 0 Eukaryotes eukarya Pro ka ryotes before the nucleus No internal membrane bound organelles quottrue Nucleusquot Have organelles bounded by membrane Cell wall of carbohydrates and peptides Ribosomes differ from eukaryotes in size and antibiotic sensitivity No nucleus or linear chromosomes histones complexed No internal membranes OOOOOOOO Eukaryotes animal plants fungi yeast 0 Larger cell size Need increased internal membranes Problem of intake of nutrients Problem of coordination and control of metabolism More opportunities as a heterotroph Plasma membrane 0 Present in prokaryotes and eukaryotes Semi uid mosaic Phospholipids Proteins Semipermeable barrier between contents of cell and environment Nucleus Present in eukaryotes Enclosed by a nuclear envelope a double membrane with pores Contains linear chromosomes Contains the nucleolus region of nucleus where ribosomal subunits are assembled Thursdav Februarv O6 2014 Endomembrane system Ribosomes Present in prokaryotes and eukaryotes Differ in size and antibiotic susceptibility prokaryotes have smaller ribosomes Two subunits Made of rRNA and protein Site of protein synthesis Occur free in cytoplasm or in association with the rough ER Endoblasmic reticulum ER Only present in eukaryotes Internal membrane system Mechanism of sorting material belonging in the cytoplasm from that which doesnT Lipids carbs and protein are synthesized in association with ER Ribosomes on the cytosolic side Sarcoplasmic reticulum calcium stores in muscle Prominent in cells synthesizing products destined for transport to other cells Egpancreas Smooth ER Golgi Lipid synthesis Detoxi cation of water insoluble compounds Eukaryotes only Composed of numerous sets of membranebounded cisternaedisc shaped Form a structure resembling a stack of pancakes Components are transported from ER to Golgi Components modi ed and packaged for transport Traf c control center of the cell Lysosome Eukaryotes only Vesicle containing digestive enzymes hydrolytic enzymes In plants called lytic organelles Why have digestive enzymes in vesicles lsolate these enzymes from cell components Mitochondria Eukaryotes only Two membranes Generates ATP use oxygen Lipids metabolized here Not part of the endomembrane system Inherited maternally in humans Contain circular naked DNA Ribosomes smallprokaryotelike Chloroplasts Only in plants Organelle where photosynthesis occurs Use energy in sunlight to x carbon Oxygen is produced as a byproduct Not part of endomembrane system 3 membranes Inner and outer membrane Thylakoid membrane stacks called grana Stroma Method of nutrition 1 Autotrophs a Plants 2 Heterotrophs a Animals Plant cell wall Cellulose Support and protection External to the plasma membrane Central vacuole Plants Membranebound structure keeps ces turgid Plants have 3 things not found in animals 1 Cell wall 2 Centralvacuole 3 Chloroplasts Cytoskeleton Provides structure to cytoplasm Initially cytoplasm ground substance was thought to be without structure improved techniques proved this wrong Flagella and Cilia Organelles involved in movement Bacteria have agella but are constructed differently than in eukaryotes Same structural design in agella and ciia 92 structureonly in eukaryotes absent in higher plants 0 Different than in bacteria Flagella larger and fewer than cilia Sliding laments Proteins involved in movement EX actin and myosin Molecular motors 0 Proteins Use energy derived from ATP Centriole In animals not in higher plants 0 Similar to base of a agellum or cilium Involved in mitosis and meiosis The problem a cell and its environment 1 The interior of a cell is different than its environment 2 How to defend the internal environment but still communicate with external environment Henridue and Hansen 1901 Raise pigs at different temperatures one in underwear and looked at composition of fat under skin of pigs 0 Higher melting point Membrane uidity can acclimate Thursday February 13 2014 Movement of Molecules Across Membranes Examples of small molecules that can move through membranes 1 Gases 2 Steroid hormones 3 Water Direction of movement Expect down the concentration gradient 0 What about against the gradient eg sodium 5 15 mM in the cell 145 mM outside how do you move sodium out of cell Transport process 0 Active transport doing work because you have to move something against concentration gradient Requires supplied energy ATP carrier molecule work must be done Moving uphill energetically Passivemoving down concentration gradient does not require supplied energy moving downhill energetically diffusion simple or facilitated Simple depends on molecular movement no required energy and does not use a carrier molecule Facilitated quotquotquotquotquotquotquotquotquotquotquotquotquotquotquotquotquot and is facilitated by a carrier molecule Equal Concentrations equal on both sides of barrier a molecules keep moving b there is no net change in solute concentration Semipermeable barriers only some types of molecules pass through Diffusion movement of molecules down concentration gradient 0 from regions of high concentration to lower concentrations 0 physical property of matter 0 individual molecules move randomly but the net effect is nonrandom what force causes net movement Membrane permeability size and shape of molecules solubility in lipids net electric charge 0 other chemical properties 0 water always freely permeable Aquaporins channel protein which facilitate water diffusion through the membrane Osmosis The net movement of water across through a semipermeable membrane Diffusion of water 0 From higher fewer solutes water potential to lower water potentialhigh solutes Hypertonic lower water potential more solutes dissolved Tend to gain water Hypotonic higher water potential fewer solutes dissolved Tend to lose water lsotonic equivalent water potential equivalent number of solutes dissolved No net movement of water Marine Invertebrates lsotonic with sea water Accumulate free amino acids to match the tonicity of sea water Marine elasmobranch sh sharks and rays lsotonic with sea water Accumulate up to 05 M urea Fresh Water bony sh teleost sh Hypertonic to fresh water gain water Marine Bony sh teleost sh 0 EXtuna o Hypotonic to sea water lose water Endocytosis ce engulfs object becomes membrane bound vesicle phagocytosis large object pinocytosis small object receptormediated endocytosis molecule on surface of cell detects a molecules that needs to be taken up Exocytosis membrane bound vesicle fuse with cell membrane and expels contents How do cells regulate metabolism Metabolic transformations a Chemical reactions b small steps c controlled processes d each step controlled by a protein catalyst enzyme Biological chemical reactions 0 O O Enzymes regulated by protein catalysts synthesis of energy carrier molecules to store energy transport it from place to place regulate its ow couple reactions together so that unfavorable reactions can occur at the expense of reactions that release energy protein catalysts not used up speci c reactions require speci c enzymes enzymes lower activation energy barrier enzymes speed up reaction by 108 1020 times faster do not reverse an energetically unfavorable reactions Thermodynamics study of the energy relationships of a system WM energy that is free and available to do work Gibbs free energy and Chemical reactions Spontaneous exergonic NonSpontaneous endergonic Saturday February 15 2014 Laws of thermodynamics 1 Within any closed system the total amount of energy remains constant 2 All spontaneous processes result in an increase in randomness and disorder in the universe And consequently in a loss of localized concentrations of energy a Entrophy is increasing b You must de ne the system c A closed isolated system d The earth is not a closed system Chemical Reactions Endergonic reactionsrequire the net input of energy heat to proceed Exergonic reactions energy heat is released from the reaction Only proceed spontaneously in the downhill reaction downhil exergonic reaction Example burning coal is exergonic Delta 6 Delta HT Delta S Delta Gfree energy change Delta Henthalpy change T Temperature degrees kelvin Delta Sentropy change Delta G Energy required for the favorable positioning of the reactants so the reaction can occur Enzymes accelerate chemical reactions 0 Reaction rates are increased because enzymes lower the activation energy barrier 0 Lower it because it brings together molecules so that reaction can occur with less input energy Enzymes cannot reverse energetically unfavorable reactions 0 Activation energy barrier is lowered because the enzymes positions the reactants in a conformation more favorable for the chemical reaction to occun Activation energy Delta G Energy necessary for the reaction to occur Temperature is a measurement of how many molecules will have achieved the activation energy Temperature The measure of the average kinetic energy of the molecules of a substance Low temperature low energy associated with molecules fewer molecules have energy greater than the activation energy the colder the temp the slower the rate How do you increase metabolic reaction rate 0 Increase amount of enzyme 0 Make a better enzyme Cold adapted enzymes 0 At a common temperature enzyme from coldadapted species converts substrate to product at a faster rate 0 Have lower Delta G values Going uphill Energetically unfavorable direction Anabolic biosynthetic reaction 0 Supply energy from ATP Coupling energetically unfavorable reactions with favorable reactions lgt t Adenosine triphosphate Nucleic acid 0 Two high energy bonds 0 When hydrolyzed exergonic Tuesday February 18 2014 ATP in bhosbhorvlation reactions 0 Transfer of high energy phosphate to another molecule Catalyzed by enzymes Delta G 0 Values are additive The energy available in ATP can be couples to an endergonic reaction Couolind reactions Exergonic reactions supply energy so that energetically unfavorable endergonic reactions can occur ATP is termed the energy currency of the cell 0 Compounds can be expressed in terms of their biosynthetic cost of ATP 0 Metabolites can be expressed in terms of ATP equivalents 0 Conditions for production and utilization a Are different b Must be controlled 0 By using ATP coupling processes can have thermodynamic feasibility in the appropriate direction Circe Effect 0 The act of luring the substrate into the active site Circe was a witchenchantress of Greek myth Lured Odysseus and his men with a song turned him and his companions into swine Positively charged arginine side chain lures the negatively charged metabolite into the active site Substrate turned into product Enzymes are affected by environment 1 Hydrogen ion concentration eweww Temperature Solutes Hydrostatic pressure Alter enzymes functional properties Denaturation Denatu ration 0 Protein unfolds due to broken weak bonds which stabilize the 3D structure 0 However under extreme conditions covalent bonds can be broken Thermophiles Bacteria thermophiles exist at 133 C grow at 122C Regulation of enzyme activity gt How are the controlled gt Can they be turned on and off Modulation of activity 0 Binding of ligands Covalent modi cation Competitive inhibition Substrate and inhibitor compete for binding to the active site of the enzyme Inhibitor is structurally similar to substrate 0 Most apparent at low substrate Noncompetitive inhibition Inhibitor binds at a site away from the substrate binding site 0 Causes a conformational change in enzyme 0 Not overcome by increasing the substrate Allosteric enzyme regulation 0 quotother sitequot 0 Modulator activator or inhibitor binds to a site other than the substrate binding site active site 0 Causes a conformational change in enzyme which changes the activity Cooberativitv Oxygen binding to hemoglobin 4 oxygen binding sites 0 Binding alters the af nity for 02 0 Binding for the rst 02 makes it more favorable for the next 02 to bind Metabolism hallmarks Chemical transformations in small steps 0 Each step is catalyzed by a speci c enzyme Pathway ADBDCDDDE AljB is enzyme 1 o Ble is enzyme 2etc o A X BDCDDDE Allosteric inhibition of the rst step in the pathway 0 Enzyme 1 Is inhibited Feedback inhibition by the end product of the pathway Rede Reaction 0 Reductionoxidation reactions 0 Biological Rede reactions involve transfer of electrons and hydrogens 0 Biological redox reactions employ carrier molecules Coenzymescofactors a Cycle between the reduced and oxidized forms b Reducing power 0 Reduction the addition of electrons or hydrogen to a molecule a Adds energy 0 Oxidation removal of electrons or hydrogen from a molecule a Reduces energy 0 Cofactorscoenzymes a NADP oxidized form b NADPH reduced form c FAD oxidized form d FADH reduced form 0 Control problem a Some processes require energy and quotreducing powerquot b Some produce energy and quotreducing powerquot c Some break down biological molecules d Some build biological molecules Spatial Separation Separate processes which are con icting Mitochondria Site of cell respiration Produce energy in form of ATP 39 m 0 m 0 3 D y S lsolate digestive enzymes from the proteins in cytoplasm Catabolic and Anabolic Reactions 0 Catabolism is exergonic break down large molecules 0 Anabolic processes require the input of energy biosynthetic Thursday February 20 2014 ATP is the major coupling agent between different processes 0 ATP is provided from the catabolic block to the anabolic block to drive biosynthesis Supplying Energy c When adequate oxygen is available 0 When oxygen is limiting F Burst activity results in inadequate oxygen delivery egsprinting Sprinting Oxygen availability Increase in power output Metabolism to support this work Energy sourcefuel OOOO Aerobic activity less intense allows adequate oxygen supply Energy Productions 0 Under aerobic and anaerobic conditions ATP during burst activity Myosin ATPase powers movement Vertebrates Creatine Phosphate recharges ADP back to ATP Invertebrates Arginine Phosphate Glycolysis is activated up to several hundredfold Glucose 686 kcal of energy Determined by combustionquot 34 captured in ATP during complete oxidation of glucose Oxidation occurs in small steps coupled to ATP production Enzymes control each step Cellular Respiration 1 Glycolysis a Occurs in cytoplasm 2 Citric Acid Cycle Tuesday February 25 2014 O 2 Combines with hydrogens to form H20 0 The 02 used in respiration is not used to for C02 Pyruvate branch point inadequate oxygen 0 No electron transport in mitochondria Need to regenerate NAD from NADH for glycolysis to continue Glucose fermentation o Lactate lactic acid a Anaerobic end product regenerating NAD b animals 0 Ethanol a Anaerobic end product regeneration NAD b Plants yeast LactateEthanol production without regenerating of NAD glycolysis would come to a halt no additional ATP is produced at this step Coldadapted gold sh and carp o Ethanol produced 0 No problem with blood pH 0 Ethanol voided into environment nontoxic Adaptations for diving l Metabolism more ef cient when diving ll Aerobic conditionsburns fats Ill Large onboard oxygen stores IV Small brain relative to body size Glycolysis allosterically regulated U 7 0 Fl 0 m 39lt 3 Fl 7 D m m o Recycles atmospheric C02 0 All coal oil and natural gas is from photosynthesis o Lightdependent reactions a Reducing power NADPH b ATP c 02 0 Reactions independent of light the calvin benson cycle a Uses ATP and NADPH form light reactions to synthesize sugars How is the energy of sunlight used to synthesize NADPH and ATP l Chlorophyll A and chlorophyll B and accessory pigments a In thylakoid membrane b Absorb light in visible spectrum ll Light energy a Used by Photosystem l and II thylakoid membrane b Drive the production of ATP and reducing power NADPH Ill Lightdependent reactions a H20 is split b Oxygen is released ATP and reducing power of the light reactions 0 Used in the calvin beson cycles the dark reactions 0 In stroma of chloroplasts Synthesize carbohydrates from C02 UV 0 Short wavelength Infra red Longer wavelength than visible Absorbed by water Thursday February 27 2014 Light reactions 0 Convert solar energy to chemical energy of ATP and NADPH Occur in thylakoid membrane Proton pumps in ATP generation Chloroplasts a Atp synthase 0 Generate ATP using proton gradient CalvinBenson cycle 0 Carbon xation Occurs in stroma Plants 0 Have chloroplasts and mitochondria Adaptation in hot regions a Overcome photorespiration b Conserve water Carbon dioxide 0 03 of gas in atmosphere 0 Must diffuse in through stomata Water will be lost through diffusion Types of plants in hot regions 0 C4 plants a Sharpens diffusion gradient b 4 carbon is produced to carry C02 to calvin benson cycle c Ex corn and sugarcane o CAM plants a Succulent plants b Ex cacti and pinapples c Take up C02 at night and store as crassulacean acids for use in the day Genetic material is DNA The daughter cells need the complete genetic complement Pro ka ryotes 0 Circular strands of DNA 0 Replicate DNA and pass it on to daughter cell 0 Divide by binary ssion Eukaryotes 0 Genetic material is found in linear chromosomes Cell Division Mitosis Cell cycles lnterphase a Generally 90 of cell cycle b Gap 1 Glincrease in number of organelles c S phaseDNA is duplicated d Gap 2 GZ centrioles replicate in animal cells Mitotic phase a Mitosis b Cytokinesis Thursday March 06 2014 Centrioles In animals 0 Found in centrosome 9 sets of triplet microtubules arrange in a ring Mitosis the cell division in eukaryotes to produce daughter cells which have identical genetic material to the mother cell Occurs in somatic cells 1 Prophase a Nucleoli disappear b Chromatin condenses c Mitotic spindle forms from microtubules in cytoplasm 2 Prometaphase a Nuclear envelope fragments b Microtubules of spindle invade the nuclear region and interact with the chromosomes via the kinetochore 3 Metaphase a Centrosomes at opposite poles b Chromosomes arranged at the midplane of the spindle 4 Anaphase a Sister chromatids separate 5 Telophase Nuclear envelope reforms spindle breaks down nucleoli reform chromatids become less densely coiled 1000 Cytokinesis division of cytoplasm Mechanism differs between plants and animals cells because plants have a cell wall Control systems for cell cycle checkpoints stop and go signals Glcheck and see if DNA is damaged GZchecks if DNA is replicated properly Mspinde assembly check for alignment 0 Go phase nondividing phase 0 Loss of cell cycle control cancer cells continue dividing Chromosome complement Each somatic cell has a characteristic number of chromosomes 1 the diploid chromosome number 2n 2 copies of basic set humans 46 2 the haploid chromosome number 1n basic set of chromosomes humans23 3 homologous chromosomes members of same pair same length same centromere position same staining pattern with dyes genes coding for the same characteristics Sex chromosomes X or Y All other chromosomes autosomal chromosomes of humans 46 chromosomes 2 are sex while 44 are autosomal Squot3939gt Meiosis Cell division for gamete production In specialized tissues Produces cells with the 1n chromosomes number 2 divisions 1 Meiosis 1 2 Meiosis 2 Asexual reproduction Mitotic division Identical offspring Ex hydra Sexual reproduction Fuse gametes from parents to produce a zygote Each parents contributes half of genetic material 0 Increase the diversity of offspring Thursday March 13 2014 Meiosis o Occurs in cells that give rise to gametes o Produces cells with the haploid 1n chromosomes number lnterphase As in mitosis During the S phase DNA is replicated giving rise to chromosomes consisting of 2 sister chromatids Prophase l Chromosomes condense Each chromosome consists of 2 chromatids from S phase of interphase Homologous chromosome pairs lie next to one another Crossing over of chromatids between pairs chiasma formation a Called chiasma chiasmataplural b Hold homologous chromosomes together c Can result in a physical exchange of genetic material between homologs Can result in a physical exchange of genetic material between homologs Metaphase l Chromosome pairs align on equator of spindle Kinetochores of sister chromatids are attached to bers going to the same pole Anaphase l Homologous chromosome pairs separate 0 Sister chromatids remain together Telophase l 0 Depending on the species 0 Nuclear membrane may reform Cytokinesis may occur Meiosis II 0 Cell division like mitosis but start with the haploid chromosome complement Gregor Mendel worked with edible pea plants ohn Goss i worked with the same plants 30 years before Mendel began his work observed green and yellow seeds in peas and followed them through a number of generations Why did Mendel succeed Chose the right organism to work with The plant usually selfpollinates and stigma are completely enclosed by petals until after fertilization Gene discrete unit of hereditary information consisting of a speci c sequence of DNA Often codes for a polypeptide chain Gene locusa partial position along a speci c chromosome where a given gene is located 32 alternative form of a gene Homozygous having 2 identical alleles for a trait Heterozvgous having two different alleles for a trait Genotype the genetic makeup of an individual Phenotype the physical appearance of a trait determined by genotype Dominant allele Allele that is fully expressed in the phenotype of a heterozygote Only a single copy is required to express the trait Represented by a capital letter Recessive allele o In a heterozygous individual the allele that is completely masked not expressed in the phenotype Represented by lowercase etter Generations o P a parent 0 F1 a Filial one 0 F2 a lial two yjYJ Y Yy Yy y yy yy Mendels rst law 0 2 members of a gene pair segregate from each other into the gametes 0 Each gamete ony carries one member of gene pairing Tuesday March 18 2014 Thursday March 20 2014 Sickle cell anemia Homozygous recessive autosomal Normal REC120 days Sickle cell1012 days 0 10 of patients total red cells destroyed Treatment Transfusions Hydroxyurea therapy Screening for diseases about 50 tests available for diseases 2 tests for rare diseases saves money Louisiana tests for 28 diseases screening fee is 30 Pedigree Analvsis Malessquares Femalescircles Autosomal recessive generations are often skipped Almost equal distribution among sexes If both parents affected all children should be affected Autosomal dominants generations not skipped Almost equal distribution among sexes Sexlinked recessive most affected are males Affected males have carrier mothers Approximately half of the sons would be affected Abnormalities in chromosome number Wheat hexaploid 6n Banana triploid 3n About half of owering plants are polyploidy such as corn cotton etc Most are lethal in animals Viable defects often involved in sex chromosome Euploidy complete chromosome sets Aneuploidy partial sets 1 or 2 chromosomes Aneuploidy involving Autosomes Down syndrome trisomic for chromosome 21 intellectual disabilities characteristic facial appearance and poor muscle tone in infancy Increases with mothers above age 40 A translocation can result in the equivalent of trisomy in younger women Molecular genetics Transforming bacteria DNA is the transforming principle Studies as viruses bacteriophage bacteria eaters Hershey and Chase 1952 used the bacteriophage T2 Sulfur in proteins phosphate in DNA Tuesdav March 24 2014 U z gt Double helix Antiparallel Base pairings a AT 2 hydrogen bonds b CG 3 hydrogen bonds Semiconservative means each strand of original double helix serves as new template for new strand 3 end has hydroxyl DNA synthesis CO 0000 Polymer synthesized from monomers Polymer grows by adding a new nucleotide triphosphate to 3 OH group of the growing DNA strand Single stranded DNA serves as template for new strand s primed with a short piece of RNA synthesized by enzyme primase DNA elongation is catalyzed by DNA polymerase DNA polymerase only works in 5 to 3 direction Treatment of HIVAIDS with AZT Block the production of viral DNA by reverse transcriptase Thymidine and azido thymidine 3 azido group instead of 3 OH group When AZT gets incorporated it stops addition of further nucleotides Cant form a covalent bond with a 5 phosphate Human DNA can proof read and notice when an alternate base has been included Reverse transcriptase does not have proof reading ability I Leading and Lagging strands Problem of DNA synthesis with antiparallel double strands Leading strand is synthesized 5 to 3 in the direction of replication fork Lagging strand synthesized 5 to 3 away from replication fork Okazaki fragments small fragments of DNA from each of starts of new DNA polymerase in laggings strands Linked together by enzyme ligase DNA damage Thymine dimer formation by UV light Ends are protected Telomeres noncoding repetitive DNA sequence laid down by telomerase Protects the ends of the chromosome from deteriorating Like the aglets on the end of a shoelace Telomerase Enzyme with a short of sequence of RNA Adds noncoding sequence of DNA to the template strand in some issues 0 The usual enzymes can now extend the new DNA strand Telomere prevents the erosion of chromosome ends during rounds of replication The central dogma DNA is transcribed into mRNA 0 mRNA is translated into protein exceptions a reverse transcriptase b telomerase RNA Ribonucleic acid ribosomal RNA rRNA 0 transfer RNA tRNA messenger RNA mRNA differs from DNA in having a hydroxyl group in the 2 position differs from DNA in that it has a uracil U instead of thymine T 0 base pairing rules a AU b TA c GC d CG rRNA serves as the scaffolding for the proteins of the ribosome tRNA serves as an adapter molecule to bring in the appropriate amino acid in protein synthesis Thursdav March 27 2014 o 3 bases of a codon can specify 64 amino acids 0 4 amino acids per base Codon sequences of 3 bases specifying an amino acid 0 non overlapping no punctuation codon can specify start and stop of the message RNA synthesis RNA polymerase Formed on the template strand of DNA RNA is antiparallel to the DNA RNA polymer grows in the 5 to 3 direction monomer added to 3 OH of polymer OOOO RNA processing Addition of a 5 GTP cap Addition of a polyA tail Removal of introns lntron is the noncoding sequence and is removed from the mature mRNA intervening sequence Exon codes for a sequence of amino acids expressed sequence a Code for protein domains i Modular architecture ii Functional units of the protein 0000 O Ribosome locations 0 Free in the cytoplasm Associated with the rough ER Pro ka ryotes Transcription and translation occur in same compartment Occur contemporaneously at same time Cell Communication 0 Coordinate metabolic processes 0 Receive messengers from both local and distant sources Respond to signal through a change in the metabolic processes of the cell 0 An extracellular chemical signal is transduced into an intracellular response 0 Communication occurs across the plasma membrane Extracellular signal is ampli ed within the cell via a signaling cascade Paracrine signaling diffusion of rst messengers over short distance between cells Synaptic signaling chemical signals from a nerve axon diffuse across a synapse to another nerve cell or a muscle cell 0 Hormonal signaling endocrine glands produce hormones hormones move through circulatory system to their targets Cell signaling 0 May involve a receptor in the plasma membrane 0 May involve intracellular receptor G protein coupled signaling Important class of signaling complexes More than 1000 different receptors in mammals Coupling receptors interact with G proteins G proteins link an extracellular signal and an intracellular response 3 components a Receptor in plasma membrane b G protein on intracellular face of the plasma membrane c Effector element such as an enzyme or ion channel 0 3 subunits labeled alpha beta and gamma 0 Interacts with receptor occupied by a signaling molecule OOOOO Effector enzyme Produces an intracellular second messenger Adenylyl cyclase is an integral membrane protein Gene protein coupled receptors GPCR Activated by binding of a rst messenger signal molecule 0 Example hormone neurotransmitter Interacts with a G protein Tuesday April 22 2014 Steroids intracellular receptors cycling between the cytoplasm and nucleus Activated receptors in the nucleus activate speci c genes by binding to DNA Ligands for steroid receptors steroid hormones thyroid hormones vitamin D Steroid effects are produced by increasing protein synthesis slow in onset duetothS Testes produce androgens testosterone Support sperm formation Ovaries produce estrogen Stimulates growth of uterine lining development and maintanance Stress and steroid hormones 0 Increased production of epinephrine and norepinephrine 0 Increased production of mineralo and guco corticoids steroids Short term stress response Glycogen break dow2n blood glucose increased Increased blood pressure Increased breathing rate Increased metabolic rate Change in blood ow 00000 Long term stress effects 0 Mineralocorticoids retention of sodium and water increased blood volume and blood pressure 0 Glucocorticoids breakdown of proteins and fats to increase blood glucose suppression of immune system 2 D C 0 3 U Process and act on sensory information Nervous systemrapid transfer of information through the body by electrical signals or nerve impulses 0 Contains the nucleus and organelles Clusters of cell bodies are ganglia Dendrites highly branched processes that come off of cell body Receive incoming info and carry it as an electrical signal to cell body 0 Axon longer processes only one per neuron Carry info to other cells and larger diameter with faster conducting OO
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