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Lecture 1 - Biology 200 Winter 2012 Classroom ...

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Unformatted text preview: Biology 200 - Winter 2012 Classroom Instructors: Jim Mullins, Ph.D., Professor, Dept. of Microbiology Hannele Ruohola- Baker, Ph.D., Professor, Dept. of Biochemistry Course Coordinator: Ben Wiggins, Dept. of Biology Teaching Assistants: Chelsea Kidwell, Dan Grunspan, Elisha Harris, Elizabeth Abshire, James Chiang, Josh Kessack, Lola Yelistratova, Lyndsie Slakey, KaRe Dobkowski, Ryan Miller, Sara Lee, Tim Janetos 1 Grading Components of the Course •  4 exams –  Each held within class periods –  Worth 90, 110, 90, 110 points 400 •  Mullins – Will be short answer & cover lectures, labs and text readings •  Ruohola- Baker –MulRple choice •  In class parRcipaRon 65 •  Laboratory sessions 80 –  Clicker quesRons –  ~80 quesRons, each worth 1 point –  Day’s points lost if found accessing irrelevant web pages –  9 labs, one per week, none during first or exam weeks –  You MUST a^end your first lab or you will be dropped from the course –  Talk to Ben a_er lecture if this is a problem –  Online quizzes / small assignments 15 560 2 Goals of Course •  Become aware of and learn basic life processes" •  Learn to think like a Biologist" •  Apply scientific thinking to your outlook on life" •  Evolve your learning style" –  Recall, Understand and Apply biological principals" 3 My recommendaRons •  Be proacRve –  Take advantage of course resources •  Before class –  Read the textbook assignment •  Come to class –  Avoid distracRons (use computer for class notes only) –  Ask quesRons –  Answer clicker quesRons •  Exam preparaRon –  Answer quesRons in the Study Guide at the end of each chapter –  Write down quesRons as they occur to you –  Come to review sessions and office hours and ask your quesRons •  Beforehand: Review and integrate lecture material and readings –  Take the pracRce exams •  One pracRce exam will be available at least 1 week before each exam •  No answer key will be provided, although quesRons can be discussed at review sessions 4 Course Resources •  •  Syllabus with reading assignments Textbook –  “Biological Sciences” Sco^ Freeman 4th ediRon –  Textbook and textbook website has features to help you grasp the concepts in mulRple ways •  •  •  Laboratory Manual –  Professional Copy N Print, 4200 University Way Lecture materials on course website –  h^p://proRst.biology.washington.edu/biol200/ –  Lecture slides (2 and 6 slides per page) –  In class and addiRonal videos on class website –  PracRce exams –  Videos and podcasts of lectures Office hours –  14 Instructors are here to help at all Rmes! –  Mullins •  Weekly review session on Thursdays, 12:30- 1:20, Kane 120 •  Available during most lab sessions in HCK 143/147 prep room –  Full schedule of all office and review sessions is on the course website 5 Where Biol200 fits in: !99(*,*3&( 2)($%&*.0 ,(*&"%#31 !"#$%& '()*+%#, -#.(&/.(0 4#,$*"%#3 !"#$%&$ =)#/6)" '"()%$*+# >()*+%#, 3%4245# ,-.%/%.012 64&%(*# -*&,#$#.(&/.*,0 2(..1 1",/&"/,(1 -*&,#$#.(&/.*,0 4/3&"%#31 53(,67 2*"*.71%1 -#.(&/.*,0 8(9,#:/&"%#3 2(../.*,0 8(6/.*"%#3 ;(+(.#9$(3"0 #40$/."%&(../.*,0 #,6*3%1$1 <,6*3%1$*.0 8(9,#:/&"%#3 ;%1(*1( 6 Why discuss physics and chemistry? •  Life most likely originated via Chemical Evolu2on: –  Simple chemicals that existed in earth’s atmosphere and oceans reacted with one another to form more complex molecules –  ConRnued reacRons of these chemicals led to the origin of life, and the start of biological evoluRon –  Increasingly complex, carbon- based molecules formed with energy supplied by sunlight and high temperatures –  Molecules became capable of self- copying (replicaRng) 7 Hydrogen Common Elements in Biological Systems Helium Number of unpaired electrons = valence Electron shell Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon Valence = 1 2 3 4 3 2 1 0 •  Electrons move in specific regions called orbitals (holding up to 2 electrons) •  Orbitals are grouped into levels called electron shells •  Elements whose outer shells are filled are nonreac2ve •  Elements whose outer shells are not filled are reac2ve •  Elements commonly found in organisms have at least one unpaired valence electron (they are reacRve) 8 Chemical bonds Single bonds – 1 pair of electrons is shared between two atoms Atoms with more than one unpaired electron in its valence shell can form mulRple single bonds and double (CO2) and possibly triple (N2) bonds 9 Types of Chemical Bonds Electronegativity – tendency for an atom to attract electrons to itself •  Covalent bonds •  Electrons are shared –  Nonpolar •  Equal sharing; both atoms have similar electronega7vity –  Polar •  Unequal sharing; the more electronega7ve atom holds the electrons more Rghtly •  Ionic bonds •  The more electronegaRve atom *takes the electron, giving it a negaRve charge and the other atom a posiRve charge (*very small degree of covalency) •  van der Waals forces •  Weaker than chemical bonds, they correspond to the total of the other a^racRve and repulsive, primarily nonpolar, forces between molecules; important to organic (carbon- containing) structure and solubility 10 The importance of Carbon to life •  Carbon is the most versaRle atom on earth –  With its 4 valence electrons it can form many different types of covalent bonds and an almost limitless array of molecular shapes Hydrogen cyanide C6H12O6 (Glucose) Evolution Our food C8H18 (Octane) Our cars 11 The importance of water to life 1.  It is an excellent solvent*, due to its capacity to H- bond * A substance that dissolves another substance to form a soluRon Forms hydrogen bonds (H-bonds) between water molecules It dissolves ionic and other polar substances, stabilizing the ions away from each other It excludes nonpolar molecules δ+ δ- 12 2.  Its adhesion and cohesion properRes –  It adheres to other substances via H- bonding –  It coheres with itself via H- bonding •  Creates surface tension –  Resists forces that increases its surface area –  Behaves like an elasRc membrane 3.  It is denser as a liquid than as a solid –  Contrary to most substances –  Its open lasce structure in ice is more loosely packed than in liquid water, in which bonds are constantly being broken and reformed 13 4.  It has a very high capacity for absorbing energy –  Very high specific heat* *Heat required to raise the temperature of 1g of a substance by 1oC –  Very high heat of vaporizaRon¶ ¶ Heat required to change 1g of liquid to a gas See video on class website 14 What does this graph tell you about the relaRonship between entropy (disorder) and temperature? 1.  Entropy increases with temperature 2.  Gases have a higher entropy than liquids 3.  Phase transiRons result in a large increase in entropy 4.  All of the above 15 Does sweaRng cool your body? 1.  No, the capacity of water to absorb energy keeps heat in, making my body’s core ho^er 2.  Yes, especially when sweat evaporates - a lot of heat energy is transferred from my body to the water to cause vaporizaRon It depends on the humidity of the environment: 3.  Only in low humidity environments 4.  Only in high humidity environments 16 5.  Water’s polar nature renders it unstable –  Water molecules conRnually undergo a chemical reacRon, called “dissociaRon”, forming ions A molecule that will give up a proton during a chemical reaction, and raise the hydrogen (H+) (or hydronium, H3O+) ion concentration in water is an acid A molecule that will acquire protons during a chemical reaction, lowering the hydrogen ion concentration (noted as [H+]), is referred to as a base 17 pH and Buffers •  All chemical reacRons in our bodies take place in a water (aqueous) environment –  Water makes up ~65% of our bodies •  Living Rssues are extremely sensiRve to changes in [H+], typically found at 1 x 10- 7 M (molar) •  pH = - Log [H+] –  Thus living Rssues have a pH of ~7 •  Buffers are compounds that minimize changes in pH –  Most buffers are weak acids, e.g., •  CH3COOH (AceRc acid) combined with NaCH3COO (Sodium acetate) –  Water has very li^le buffering capacity 18 Chemical Energy •  Energy is the capacity to do work –  It is neither created nor destroyed, but it can be transformed –  Poten2al energy of an object derives from its posiRon or structure –  Kine2c energy is the energy of moRon Uptight but controlled Relaxing but uncontrolled (A lot of potential energy, Ep) (A lot of kinetic energy, Ek) 19 Chemical ReacRons •  Spontaneous chemical reac2ons –  Occur without any conRnuous external influence such as the addiRon of energy –  ReacRons tend to be spontaneous if: •  The products have lower Ep than the reactants •  The product molecules are more disordered than the reactants 1 Methane (CH4) Electrons are held “loosely” in bonds between atoms with equal electronegativities 2 Oxygens (O2) Energy ac7vates the reac7on* Poten7al energy drops Electrons are held tightly by highly electronegative atoms 1 Carbon dioxide (CO2) 2 Waters (H2O) 20 Energy changes in chemical reacRons Can this reaction be spontaneous? •  In exergonic reacRons (example shown above), energy is released into the surroundings •  Endergonic reacRons absorb energy, they require energy to flow in from the surroundings See video on class website 21 What would an endergonic reacRon look like? 1 2 Endpoint has the same Ep Free Energy Free Energy Endpoint has lower Ep Progress of reaction Progress of reaction 4 Endpoint has higher Ep Progress of reaction Free Energy Free Energy 3 Progress of reaction 22 IniRaRon of Chemical EvoluRon •  Life had a problem gesng started –  Organic compounds are typically formed by endergonic reacRons –  FormaRon of life required a lot of environmental energy •  Ancient atmospheres could provide the needed energeRc impetus for these reacRons 1.  The earth’s atmosphere was filled with volcanic gases, and li^le to no ozone •  Ozone is highly reacRve, absorbs high energy photons (light) •  Large quanRRes of high energy photons bombarded the ancient earth 23 2.  High energy photons can create free- radicals –  Free radicals have unpaired electrons in their outer electron shells and are extremely reacRve 24 First ReacRons of Chemical EvoluRon •  The products of chemical evolu2on have more poten2al energy than the reactants •  The energy of sunlight is captured and stored in the chemical bonds •  This potenRal energy is called chemical energy Forma7on of Formaldehyde O CO2(g) + 2 H2 Sunlight H2O (g) + H2CO(g) C H H 25 Temperature (T) and [ConcentraRon] impact chemical reacRons •  Increases in either T or [C] increase the rate of reacRons –  When temperatures are raised (energy is added) the molecules move faster and hit each other harder, increasing the likelihood of a chemical reacRon –  When the concentraRons of reactants are raised, more collisions occur and the reacRons proceed more quickly 26 Today the atmosphere and our needs are different •  The reacRve molecules of chemical evoluRon are the poisons of today •  Ozone gradually accumulated to block high energy photons from the sun •  AnRoxidants evolved that scavenge free radicals in our bodies “Shield yourself from the aging effects of free radicals and oxidative stress! Resveratrol may also help activate the longevity enzyme, boosts antioxidants, and enhances heart health” 27 ...
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