Berkeley Biology 1A Spring 2016 Lecture Reader Part 1

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This is a marked up and annotated copy of UC Berkeley's Biology 1A course from Spring 2016. It was taught by Dr. Doudna, a famous DNA researcher.

Text of Berkeley Biology 1A Spring 2016 Lecture Reader Part 1

  • Bio1A:Introduc/ontoBiologySpring2016

    PartI:JenniferDoudna

    Guestlecturer:RossWilson

    DoudnaocehoursMondays12-1pm

    Fridays2:30-3:30pmVLSB2084

    Text:BIO1A/BUC,Berkeley

    Reading:Chapters1&2

    Lectureoutline:ThechemistryoflifeProperTesofwaterareessenTalinbiology

    Lecture#1:Biology&Water

    BiologyisthescienTcstudyoflifeonEarth Evolu/onbynaturalselecTonistheprocessofchangethathasproducedthediverselifeweobserve

    BiologistsaskquesTonssuchas:Howdoesasinglecelldevelopintoanorganism?Howdoesthehumanbrainwork?HowdoorganismsinteractincommuniTes?

    Overview:InquiringAbouttheWorldofLife DeningLife

    Compartmentaliza/on Hierarchicalcomplexity Sensi/vity Reproduc/on Energyu/liza/on Homeostasis Adapta/on

    WhyLifeDoesNotReallyExisth]p://Tnyurl.com/on-dening-life

  • Evolu/on:theOverarchingThemeofBiology

    EvoluTonmakessenseofeverythingweknowaboutlivingorganisms

    OrganismslivingonEartharemodieddescendentsofcommonancestors

    Thenatureofthelastuniversalcommonancestor(LUCA)andtheoriginofliferepresentbiologysgreatestunsolvedmysteries

    ChemicalFounda/onsofLife

    BiologyisamulTdisciplinaryscience

    Livingorganismsaresubjecttobasiclawsofphysicsandchemistry

    YoushouldknowbasicdeniTonsofma]er;chemistryofwater;chemistryofcarbon

    Elements,Compounds,Molecules Ma]erismadeupofelements AnelementisasubstancethatcannotbebrokendowntoothersubstancesbychemicalreacTons

    AcompoundisasubstanceconsisTngoftwoormoreelementsinaxedraTo

    AcompoundhascharacterisTcsdierentfromthoseofitselements

    Amoleculeistwoormoreatomsheldtogetherbychemicalbonds

    Elements,Compounds,Molecules Ma]erismadeupofelements AnelementisasubstancethatcannotbebrokendowntoothersubstancesbychemicalreacTons

    AcompoundisasubstanceconsisTngoftwoormoreelementsinaxedraTo

    AcompoundhascharacterisTcsdierentfromthoseofitselements

    Amoleculeistwoormoreatomsheldtogetherbychemicalbonds

    Isoxygenanelement?compound?molecule?Whataboutiron?Water?Carbondioxide?

  • Sodium Chlorine Sodiumchloride

    Saltissaferthanthesumofitsparts Essen/alElementsofLife

    Onlyabout25ofthe~80stableelementsareessenTaltolife Carbon,hydrogen,oxygen,andnitrogenmakeup96%of

    livingma]er Mostoftheremaining4%consistsofcalcium,phosphorus,

    potassium,andsulfur Traceelementsarethoserequiredbyanorganisminminute

    quanTTes

    h]p://umbbd.ethz.ch/periodic/spiral.html

    TheBiochemicalPeriodicTable

  • Nitrogendeciency

    EectsofDecienciesofEssen/alElements

    Iodinedeciency:Goiter!

    The abundance of water on Earth's surface is a unique feature that distinguishes our "Blue Planet" from others in the Solar System.

    Water:TheMoleculeThatSupportsAllofLife

    Water is the biological solvent on Earth All living organisms require water more than

    any other substance

    Most cells are surrounded by water, and cells themselves are about 7095% water

    The abundance of water is the main reason the Earth is habitable

    Thepolarityofwatermoleculesresultsinhydrogenbonding

    The water molecule is a polar molecule: the opposite ends have opposite charges

    Polarity allows water molecules to form hydrogen bonds with each other

    Polarity also promotes interactions between water and polar molecules or dissolved ions

  • Hydrogen bond

    H

    +

    H

    O

    + +

    +

    Fourproper/esofwatercontributetoEarthstnessforlife

    Cohesive behavior Ability to moderate temperature

    high specific heat high heat of vaporization

    Expansion upon freezing Versatility as a solvent

    acid/base properties dissolves many (but not all) molecules

    CohesionandAdhesion

    Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion

    Cohesion helps the transport of water against gravity in plants

    Adhesion is an attraction between different substances, for example, between water and plant cell walls

    Protonsdissociatebetweenwatermoleculesinaprocesscalledautoioniza/on

    hydroniumionorproton

    hydroxideion

    H+ or

  • ThepHscaleislogarithmicanddescribestheconcentra/onofhydroniumions,[H+]

    pH = log[H+]

    HCl H+ & Cl

    NaOH Na+ & OH The Celsius scale is a measure of temperature using Celsius degrees (C)

    A calorie (cal) is the amount of heat required to raise the temperature of 1 g of water by 1C

    The Calories on food packaging are actually kilocalories (kcal), where 1 kcal = 1,000 cal

    The joule (J) is another unit of energy where 1 J = 0.239 cal 1 cal = 4.184 J

    Unitsoftemperatureandenergy

    Biologicalbuildingblocks:covalentconnec/onsbetweenC,H,O,N

    Biologicalbuildingblocks:covalentconnec/onsbetweenC,H,O,N

    C N O H

    single bond

    double bond

    N/A

    available electrons

    4 3 2 1

    C C

    N N

    O

  • Lecture#2:Biologicalpolymers

    Reading:Chapter3

    Lectureoutline:MolecularbuildingblocksofthecellSugars/carbohydratesFats/lipidsAminoacids/proteinsNucleo>des/nucleicacids

    Overview:TheMoleculesofLife

    Alllivingthingsaremadeupoffourclassesoflargebiologicalmolecules:carbohydrates,lipids,proteins,andnucleicacids

    Withincells,smallorganicmoleculesarejoinedtogethertoformlargermoleculesBuildingblocksofthecell: Largerunitsofthecell: Sugars Polysaccharides FaEyacids Lipids/membranes Aminoacids Proteins Nucleo>des Nucleicacids

    BefamiliarwiththecontentsofFigure3.2inyourbook!

    Dehydra>on/condensa>onvideo:hEp://>nyurl.com/Bio1A-vid1Hydrolysisvideo:hEp://>nyurl.com/Bio1A-vid2

    Carbohydratesasfuelandbuildingmaterial

    Carbohydratesincludesugarsandthepolymersofsugars

    Thesimplestcarbohydratesaremonosaccharides,orsinglesugars

    Carbohydratemacromoleculesarepolysaccharides,polymerscomposedofmanysugarbuildingblocks

  • Sugars

    Monosaccharideshavemolecularformulasthatareusuallymul>plesofCH2O

    Glucose(C6H12O6)isthemostcommonmonosaccharide

    MonosaccharidesareclassiedbyTheloca>onofthecarbonylgroup(asaldoseorketose)Thenumberofcarbonsinthecarbonskeleton(pentoseorhexose)

    Monosaccharidesserveasamajorfuelforcellsandasrawmaterialforbuildingmolecules

    H

    CH2OH

    H

    OH

    OH H H

    H

    C C C

    C C

    C C

    H

    C H

    HO OH H

    OH H C

    OH H C OH H C

    H

    O H

    C H H OH

    H OH

    H O H

    H

    OH

    H

    OH H H

    H

    C C C

    C C O

    OH

    OH H H

    H

    C C C

    C O C

    OH

    OH

    O H 2 3

    5

    1 4

    6 5 4 3 2 1

    2 3

    5 6

    1 4

    2 3

    5

    1 4

    -glucose or

    -glucose

    O O

    CH2OH

    Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

    Fischer projection

    Haworth projection

    C C

    H

    C

    HO H

    O H C

    H C H C

    H 6 5 4 3 2 1

    H

    O H O H O H

    H O

    Fructose Glucose Galactose

    H OH

    O

    C

    C

    C

    C

    C

    C

    H

    H

    HO H

    H OH

    H OH

    H OH

    H

    O C

    C

    C

    C

    C

    H

    H

    HO H

    OH

    H OH

    H OH

    O C

    C

    C

    C

    C

    C

    H

    H

    H

    HO H

    OH

    H OH

    H OH

    C H OH HO H

    Stereo- isomer

    Structural isomer

    Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

    ketose hexose

    ketohexose aldose hexose

    aldohexose aldose hexose

    aldohexose

  • Disaccharides 2 monosaccharides linked together by

    dehydration synthesis Used for sugar transport or energy storage Examples: sucrose, lactose, maltose OH

    Sucrose Fructose -glucose HO

    CH2OH H

    OH

    H OH H

    H

    H

    O H OH H

    H O HO

    H

    OH

    H OH O H H

    H

    O H OH OH H

    H O +

    Maltose HO

    H

    OH

    H OH O H H

    H

    O H

    OH

    H OH

    OH H H

    H

    O OH

    HO H2O

    CH2OH CH2OH CH2OH CH2OH CH2OH

    CH2OH CH2OH

    Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

    ThisisanexampleofacondensaConreac>on,inwhichtwomoleculesbecomecovalentlylinkedwiththelossofawatermolecule(dehydra>on).Thereversereac>on,inwhichwaterisadded,iscalledhydrolysis.

    Polysaccharides

    Long chains of monosaccharides Linked through dehydration synthesis

    Energy storage Plants use starch Animals use glycogen

    Structural support Plants use cellulose Arthropods and fungi use chitin

    Glycogen

    Amylose + Amylopectin

    3.3 m

    Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

    -glucose

    HO

    CH2OH H

    OH

    H OH H H

    H

    O OH 4 1

    -14 linkages

    CH2OH

    OH

    H OH H H

    O CH2OH

    OH

    H OH H H

    O CH2OH

    OH

    H OH H H

    O O O

    H

    -14 linkage

    - 16 linkage

    CH2OH

    O H

    OH

    H OH H H

    H

    O

    CH2 H

    OH

    H OH H H

    H

    O O

    CH2OH H

    OH

    H OH H H

    H

    O

    7.5 m

    Starch:

    4 1

    branched

    unbranched

  • ThechemicalformulaforglucoseisC6H12O6.Whatstheformulaforaglycogenpolymer

    composedof10glucosemolecules?a. C60H120O60

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