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Pitt BIOSC 1000 - Exam 1 Study Guide
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Exam # 1 Study Guide Lectures: 1 - 7Lecture 1 (August 26)1. Foundations of BiochemistryMany scientific fields attribute to and overlap with biochemistry:Cell biologyGeneticsChemistryPhysicsEvolutionSome characteristics of Living OrganismsHighly complex structures with amazing microscopic organizationExtract usable energy from food or the environment to do mechanical and metabolic workDefined and regulated functionsResponsive to environmentReproduction (like begets like)Evolves overtimeCellular FoundationsThree domains of LifeBacteria – single-celledInhabit soils, surface waters, tissues of decaying/living organismsArchaea – single-celledExtreme environments (salt lakes, hot springs, acidic bogs, ocean depths)EukaryaEvolved from ArchaeaDifferences at the cellular levelBacterial and archaeal ribosomes are smaller than eukaryotic ribosomes, but serve the same function of protein synthesis from an RNA messageCommon structures of bacterial and archaeal cells:Cells are ~2 microns by 1 micron in sizeNucleiodPiliFlagellaCell envelopeEukarya cells~5-100 micronsnuclear envelopeorganellesSources of EnergyPhototrophs – sunlightChemotrophs – oxidation of chemical fuelsFurther division:Autotrophs – directly from CO2Heterotrophs – require organic nutrients made by other organismsExamples:Humans – chemoheterotrophsCyanobacteria – photoautotrophsChemical FoundationsBiomolecules achieve a high degree of variation while utilizing a modest number of low AMU elementsSmall atoms form stronger chemical bondsMost of the dry mass of any cell is composed of H, C, N, O. several other elements are used by all cells in smaller amounts. Some trace elements are only used by a few life forms.The chemistry of biological molecules is centered on carbon, which is weakly reactive. Reactivity is achieved by functional group substitution associated with carbonCellular Foundations – Basic Biochemical Building BlocksAmino acids are the building blocks of proteinsEach amino acid (20 total) have:H3N+COO-CHR-groupNucleotide are the building blocks of Nucleic AcidComponents of Nucleic Acids:Nitrogenous base (Uracil, Thymine, Cytosine, Adenine, Cuanine)Five carbon sugar (α-D-Ribose, 2-Deoxy-α-D-ribose)Phosphate ionFatty acids are the building blocks of lipidsSome components of lipidsOleatePalmitateCholineGlycerolPhosphate ionChemical FoundationsChiral Molecules – rotated molecule cannot be superimposed on its mirror imageAchiral molecules – rotated molecules can be superimposed on its mirror imageStereoisomers – molecules with the same chemical bonds and formul but different configuration (the fixed spatial arrangement of atoms, which is conferred by double bonds or chiral centers)Geometric isomers (cis-trans isomers) – differ in arrangement of their substituent groups with respect to the nonrotating double bond)Maleic acid and fumaric acidEnantiomers – stereoisomers that are mirror images of each otherDiastereomers- not mirror imagesRacemic mixture – equi-molar solution of the two enantiomersShows no optical rotationRS systemAssign a “priority” (Higher priority based on highed atomic number atom linked directly to the carbon)-OCH3>-OH>-NH3>-COOH>-CHO>-CH2OH>-CH3>-HRotate molecule so that lowest priority pointing away from viewerClockwise = R; Counterclockwise = SConformation – spatial arrangement of substituent groups free to rotate around a single bondBiomolecules extensively built on carbon skeletonsAll chemical bonds have preferred lengths and angles therefore biomolecules exhibit specific shapesSingle bonds may rotateEclipsed & staggered forms only separated by very small energy difference, so rapid & spontaneous interconversionDouble bonds are planar and rigidInterconversion of double bonds requires bond-breaking that enzymes can accomplish, but such an interconversion cannot happen spontaneously at a low temperatureCells contain a set of nearly universal small moleculesTypically MW≈ 100 to ≈500mostly water-soluble compoundsalmost always polar or chargedincludes monomeric building blocks (AA, nucleotides, sugars) plus many more complicated molecules (like Ac-CoA)most types found in all cellsPhysical FoundationsLiving organisms are in dynamic steady state, NOT in equilibriumInputs of energy and fresh material are regularly required to produce and maintain the molecules of life and for reproduction of living organisms“Dynamic Steady State” implies continual input of new material and energy as well as continual discharge of waster products and heat energyGibbs Free Energy ∆G = ∆H –T ∆SFree energy content (G) can be defined in three terms:Entropy (S) – randomness of a systemEnthalpy (H) – number and kinds of bondsAbsolute Temperature (T) – in KelvinExergonic – reaction in which the products have less free energy than reactants – releases net free energy (- ∆G)Endergonic – unfavorable, energy-requiringTo carry out these reactions, cells couple them with reactions that liberate free energy (exergonic reactions)Exothermic – reaction that releases heat to surroundings (-∆H)Endothermic – reaction that absorbs heat from surroundings (+∆H)Changes to either Enthaply or Entropy alone do NOT determine whether a reaction is thermodynamically favorable or unfavorableOnly ∆G for the reaction determines thermodynamically favorability!By convention:∆S is pisitive when entropy increases∆H is negative when heat is released to surroundingsT(Absolute temperature) is always a positive valueActual free energy change = system function of actual conditionsStandard free energy changes represent standard conditions∆G depends upon conditions of the reaction:reactants and product concentrationstemperatureionic environmentpHstandard conditions are ∆G°:298K1 M reactants1 atmosphere pressure (101.3 kPa gas)as most biological reactions occur near pH 7, ∆G’° coefficients for biochemists are adjusted for pH = 7Two or more reactions may be coupled, allowing a net unfavorable reaction to be part of a favorable sequence of reactions and thus to be possible, or even highly efficientEnzymes lower activation energy (free energy) barriersChemical reactions usually require breaking existing bonds and forming new bondsBreaking existing bonds generates transition stateSome enzymes bind tightly to transition state, accessing lower free-energy barrier for reaction and thereby increasing reaction rateGenetic FoundationsGenetic information is stored and inherited as DNAMust


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Pitt BIOSC 1000 - Exam 1 Study Guide

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