ELEMENTS OF BIOL CHEM
ELEMENTS OF BIOL CHEM BICH 303
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This 27 page Class Notes was uploaded by Sylvester Mante on Wednesday October 21, 2015. The Class Notes belongs to BICH 303 at Texas A&M University taught by Timothy Devarenne in Fall. Since its upload, it has received 26 views. For similar materials see /class/225849/bich-303-texas-a-m-university in Biochemistry at Texas A&M University.
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Date Created: 10/21/15
Biochemistry the study at the molecular level of the chemical processes that occur in living organisms a 2505 amnme mmm Origins of Biomolecules Early earth gases like NH3 H28 CO C02 MillerUrey experiment H20 gas and liquid lightning mimics early earth atmosphere conditions spontaneous formation of biomolecules in presence of electricity Smpmck 3 r WWMW take sample analyze l I I W components formaldehyde HCHO l i hydrogen cyanide g HCN lupcuck I amino acrds ozmsamvcmmmu bIOCkS of proteins Heal mum Two types of cells Prokaryotes lack of nucleus or cellular organelles before the nucleus examples bacteria cyanobacteria Eukaryotes presence of nucleus and cellular organelles true nucleus examples animals plants fungi single cell complex organisms yeast paramecium euglena etc H r 39 1 AEF SS gp B V 39 Escherichia coli i if f Aquot greefactsorg Arabidopsis thaliana Cellular structure animal cell ml mambranc NuLIcus Enduplnsmi remmum with mmmmhcd Main difference between plant and animal cell plant cell Cllluloplasl 332mquot Plants cell wall quot 39 chloroplast mprokaryotic cell Rihummas 39 Plum membrane Cell wall nmsmawcch mnum Nucleus Location of genome storage DNA amp RNA synthesis Double Porc in Nuclenlus membrane membrzme I Vacuole Chromatin Immature gmnules chm nplasm ems WonThurman Mitochondria location of energy production Golgi apparatus OulcrmcInlmuu39 Innt39rmembrane Matrix Irismr Ribusmms Rnugll unduplztsmir Stack Of attened Wlimllllquot membranous vesicles 02m BlowCM Trauma woos Emukslcal 7 human Endoplasmic reticulum transport system for proteins and other compounds protein synthesis of membrane localized proteins Chloroplast location Of phOtOSyntheSiS Endoplasmic Ribosome Cell membrane reticulum Double membrane Grana Microtubule 7 39 4 MilOClIOIKII iOl zms humCue Thanmn a 2005 amencote Thurman Functional groups define properties of molecular compounds Chmderltlic Namth Fumlnnd Gmup Panama Group Example mm m m nnr a it lmlml Rb UH llnlmul gtnup L l u I on lhu mm 70 7 um rnmp m u H mi RINH v N Alninntmmp LILNIL 1qu RSII Sullhwln39I guilty llel 0 0 ll ll Aldehydm 17 mimnu gum Li L H H 7 R any carbon kenmes icik Im bnmlmnup mic mm H W containing group arid R7 70H ialeml gmup 1 I KIOH u ll mm B Wuv wont On a molecule With U 0 ll ll 39 Wt Rikiing AMc WWW multiple R groups they 0 ll HEW may be different or 0 H the same ll NlI 0 u u l hnrplmrk ucid ll ll ll mm o i oi U quot oil Fluuplimh mm H o i 1 Hun on an Emmy 0H thplwnr mii U l U 0 0 Manama ll ll ll ll 7 u H Ri i ini ii i i ini i Plumpllum lloilrioiffiuH 0 m on u uxlllWlndu gmin zunn amused mum Water H20 6 5iOH6 The O and H share electrons unequally more toward 0 making the 0 H bond polar Bonds such as C H share electrons equally thus this bond is nonpolar This makes water a polar molecule and the 0 H bond is at an angle of 1043 Dipole moment Dipole bond with and ends r aaaaaaaaaaaaaaa an Water basis of life 6 6HOH6 Polar nature of water allows it to act as solvent A solvent is a liquid that dissolves a solid liquid or gaseous solute resulting in a solution Electrostatic attraction between opposite charges ie opposites attract attracts attracts Dissolves ionic compounds NaCl KCI etc polar compounds with partial charges alcohols ketones etc Hydrophilic waterloving Hydrophobic waterhating Hydrophobic Polar covalent Compounds eg alcohols Nnnpular covalent Compounds such as 131 101 1 ethanol and ketones eg hydrocarbons such as such as IHI acetone IDHH hexane Sugars Fatty acids cholesterol Ionic cmnpounds egg lx Cl Amino acids phosphate esters Water basis of life 5 Dissolving of polar hydrophilic compounds in water E HOH6 The of H attracts charged ions or other dipole compounds The of O attracts charged ions or other dipole compounds ls thermodynamically favorable a 6 5 1 1 52 H 51 0 0 5H H6quot 6 H 5 y at I H H052 skoH 52 IDS 5H 14 H 511 b a 052 5IIOHS 5 5 H H 52 Mmhol 6 R 39 r5 Kamila HOsz 52 0 Hzi R 5 R 1 5 25 s H H O 331 145 Water basis of life 5 Hydrophobic waterhating compounds do not 5HOH5 dissolve in water Nonpolar No charged ends to interact with charged parts of water Compounds such as hydrocarbons chains of C and H oil fatty acids Nonpolar compounds and water do not mix Form two layers H III a CH I O I I O I 3 I O I IO I mix 39 4 5 oil Li39l If water I i a Water basis of life Amphipathic a single molecule with both polar hydrophilic and nonpolar hydrophobic regions Example phospholipid membrane lipid has polar head group and nonpolar tail Micelles a formation of an amphipathic molecule in water where the polar head groups interact with water and nonpolar tails associate away from water is spherical Pnlzu39 Nrmpnlm39 tzlil llrzul 0 O 2am amscaie 1mmquot ma aaaaaaaaaaaaaaa u AcidBase Chemistry Importance the acidbase properties of a compound HCI NaOH etc can affect the biochemical behavior of that compound Acid proton hydrogen ion H donor HA ee HA HQHQQQ acid complete dlSSOCIatIOl l In H20 conjugate base Weak acid 33593 Prom acceptor incomplete dissociation in H20 AOHee OH base conjugate aCId Dissociation constant acid Ka Ka W A39 denotes concentration HA in molarity M moleL large Ka strong and pH Measurement of the concentration of H ions in a solution or measurement of acidity HA H A39 acid dissociation HA H20 H3O A39 dissociation of acid in liquid H20 Actually measuring H3O pH of H20 at 25 C H20 H OH39 self dissociation of H20 Monoprotic acid releases one H per molecule Thus for H20 H OH For pure H20 at 25 C H 1 x 107 M OH39 KW ion product constant for water KW H1 OH1 KW 1 x 10 1 x 107M KW1X1014M pH Scale To express wide range of W concentration pH og1OH pH og101x107 acidic pH 7 basic more H more OH less OH1 neutral Less H O 7 14 Logarithmic increase of one pH unit is a 10 fold increase in H increase of two pH units is a 100 fold increase in H Calculatin H Acid 9 p What is pH of 0001M HCI HCI H Cl39 is monoprotic 0001M 0001M 0001M pH ogH pH og0001M pH 3 Base What is pH of 00001M NaOH NaOH Na OH39 is monoprotic 00001 M 00001 M 00001 M NaOHiyOeehmHOH 00001M 00001M 00001M H OH 1 x 1014M from KW H 00001M 1 X1014 14 pH 39IogH H 1 Bgt3381 pH og1 x103910M 39 pH 10 H1x103910M Calculating W from pH pH 39IogH negative inverse log H or log negative 1OX Ex pH of 85 what is W 85 logH E W log ln calculator enter 85 and then press 1OX W 32 x 10 What is OH1 pOH measurement of OH39 If PH 85 pOH 55 55 logOH39 POH 409 OH39 OH39 log OH39 316x10396 pK a A numerical measurement of the acid strength of a compound a protein an amino acid side chain an amino acid ls analogous to pH in that it uses the log of Ka dissociation constant pKa log10Ka Smaller value stronger acid Relationship between pH and pKa HendersonHasselbalch equation A39 conjugate base H Ka Io p 390 giHAigadd If A39 HA then pH pKa A39 0AM 1 H A 05M pH pKa Iog1 pH pKa 0 pH IoKa Arid HA K I39mn u xrid Funnil Aud u mmunium in mm qu 1 mm MM 12 Mulul 39nud 1 LIm39IL and 21 5 iL uul h Mal mid L77 sucriu u md 1 3 id 1 m mm 2 uhuxm and H7 mm Irid l iuk mid All Lurir acid 21 Muir arid 3 l huiplmr n mmphom Immphmu ma 5 ZH UOLIX 1H on ma muumm H 39 gt HI x 1001le 7IH Hoot 394 1001117 2 7 gt 7 Hrt In 1H 7tllt 0 411100 H K 039 UJ39UOHCUI Hm L 7UH17UH 7L1 r t r 2 Hl X IU H 7 39l 10039 2HHZNH xr on 00 7rlt Hym HI O Equot P0 7 J r 1 Mix 10quot NHX 10quot 7x x l 7 w x llrh x 10quot x10quot 38x 1w macs mmcm Thurman Calculating pH using the HendersonHasselbalch equation Useful for determining the pH of solutions when adding bases to acids A solution of 1 mole acetic acid is titrated or pH d with 03 moles NaOH 03 mole NaOH will react with acetic acid to form 03 mole acetic acid ion A39 leaving 07 mole acetic acid HA 07 mole acetic acid remaining HA A what is the pH of the solution CH3COOH NaOH gtCH3COO39 H Na OH 1 mole 03 mole 03 mole Acetic acnd pKa 476 A 03 pH pKa Iog jg unreacted CH3COOH remaining 07 mole HA 07 03 H K p pa 0307 03 H 476 lo p g 07 pH 476 log 043 pH 476 037 pH 439 Why is pH of a solution important Pepsin Trypsin Lysozyme E 2 S n u x m E E E nudismmt manen Buffers A mixture of a weak acid and its conjugate base Maintains the pH of an aqueous solution in the presence of moderate amounts of strong acid or base me If f j l i i if J 1m 7 157 Unlzni39imml aunt pH in Add 1 mum Mim I J a p11 mam7f L 39 f3 u it 74 quotv2 xi lt E 11 g 39nlmlll wd BIIHL39I pH7Ji Add 1 mL Ll M NuOH Ex phosphoric acid HZPOA weak acid HPOi39 conjugate base i Q E s v L V A M J i i 1lllitlt il piimihn pi mmh pii Jam lnu cx ill butler high with Imlll x ErZ UEErnuks Cuic Tnumsun 7120 Add 1 quot1101 MIN 17 39 j M I mbl ill Im m 1 1 pg i lnlmllLnwl Bullu 1120 p11 7 11 Add 1 mLUl M NuOH 1 z quot 39Illlrlr Q ZOUSE39nnks Cme r an 1 ml of 01M HCI added to 100 ml of H20 HCI 0001M pH ogH BU erS cont d 1 ml of01M HCI added to 100 ml of buffered phosphoric acid in ratio H2PO 01 M HPO 0063M HCI 0001 M phosphoric acid pKa 72 1 remaining 3 after reaction from HCI l 0062M i m39 1nd R MN HPO4239 H H2PO439 0063M 0001M 0101M A39 HCI gtH Cl39 pH pKa IOgHA pH og0001 pH3 0001 M 0001 M 0001 M HPOZ Hzpoi 0062 0101 pH 72 log 061 pH 72 021 pH 699 pH pKa log pH 72 log Buffers cont d H1303 Buffers are optimal at one pH unit of pKa Ratio of conjugate base to weak acid changes the farther the pH H2POZ gets from the pKa 4 3 5390 100 Relative abundance 70 Thus buffer can no longer maintain pH of solution If the pH equals The ratio of base formacid form equals plg 3 11000 pKn 2 1100 pKu 1 110 pKA 11 pKu 1 101 pKa 2 1001 pKa 3 10001 macs Eunicme aaaa an Synthetic buffers Physiological buffers Used in in vitro experiments in I b t buffer pKa location a ora ory Phosphoric acid HZPOA 72 mOSt39lfl lt ge39m39ar Carbonic acidbicarbonate 637 blood buffer pKa H2003H00339 Tris 83 HEPES 755 MOPS 72 PIPES 68 Conditions for selecting buffers 1 2 3 4 5 Suitable pKa No interference with reaction or assay Suitable ionic strength of buffer No precipitation of reactants or products caused by buffer Nonbiological nature of buffer
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