Intro to biology week 3 of notes
Intro to biology week 3 of notes BIOL-L 105
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This 16 page Class Notes was uploaded by Katelyn Scott on Wednesday September 9, 2015. The Class Notes belongs to BIOL-L 105 at Indiana University taught by T.J. Sullivan in Summer 2015. Since its upload, it has received 46 views. For similar materials see Introduction to Biology in Biology at Indiana University.
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Date Created: 09/09/15
91114 Acids and bases l Molecules break and reform constantly H20 lt gt H OH l H is a protonOH is a hydroxide ion l The concentration ofprotons in a solution determines its pH Acids and bases l pH logH are used to indicate concentration i More H gives you a smaller pH value i More H means more acidic l Substances thatgive up protons easily are acids Acids and bases l Water is a weak acid l Atequilibrium H20 lt gt H OH 1000000000 2 i This ratio is a constant 91114 91114 Acids and bases Suppose you add extra H20 and throw off the ratioWhatwill happen H20 HH OH 91114 Acids and bases C ompounds thatreduce the concentration ofH in a solution are called bases n water NaOH gt Na OH Ifthere are extra H in the solution H OH gt H20 Oven cleaner Household bleach Household ammonia Milk of magnesia Baking soda Seawater 7 323233 Neutraurw 7 fm 39 Logarithmic scale Urine Black coffee Tomatoes Wino Wnegar soft drinks beer Lemon juice Stomach acid pH 1 pH unit10xH Doubling H 03 pH units 2 pH is 10x greater than 3 pH 91114 91114 pH buffering l Living cells can t tolerate big changes in pH i Homeostasis maintaining a constant internal environment l C hemicals called buffers can absorb or release H in order to maintain a constant pH Weak acids Noteverything v dissociates completely 39139 AP Notall the H will H C C leave the molecule I acetic acid 91114 Homeostasis l C02 carbon dioxide reacts with H20 water to form carbonic acid HZC O3 C02 H20 lt H2CO3lt H l Can we test this 91114 Homeostasis C02 H20 lt gt H2CO3lt gt H l Reactions actually go both directions Finds an equilibrium point Ratio ofproductszreactants is constant Reaction is going the same rate in both directions 91114 C hemical reactions C02 H20 lt gt H2CO3lt gt H Adding carbon dioxide to your blood makes it more acidic Removing carbon dioxide from your blood does what make it more basic Amino acids and polymerization Building blocks ofproteins are amino acids 20 differentamino acids all have the same basic structurea C at the center that bonds to the following side chainsfunctional groupsRgroups amino functional group NH2 carboxyl function group COOH a hydrogen atom an Rgroupside chain 91114 Amino acids and polymerization a Nonionized form H o of ammo acrd Amino N C Carboxyl group group OH R Side chain b Ionized form H H O of ammo acrd i Amino 1 7 Carboxyl H N C C group I y group H n 0 Side chain 91114 Amino acids and polymerization n wateramino acids exist in ionized form why would this be importantfor living things because they can dissolve in water b Ionized form H H of amino acid I l 0 Amino Carboxyl H N v C i C group I 1 group H R Side chain 91114 91114 Amino acid Rgroups side chains Rgroups group ofatoms that define the differentamino acids Rgroups create the variation in chemical properties for the different amino acids 3 main types of Rgroups nonpolar polar electrically charged 91114 Nonpolar groups Nonpunv H 0 D um H 0 0 4 N39 c c My 7 c c n u c c o o n N c c NN39 c c 4 he 0 390 on o 39 1 39 cu 2 2quot rcquot an 939 axv quot lhva n 01mm GI Alumna A Vnne m L ucar IL lwlcucmo m Gly AL V Lou m H 0 N Now c c o N o o quot quotV c c HN39 c c a o 139 FW 0 r 3 ya Melhomne mu Phcnylalnnne m Pwlme 4m Mo m We How could you tell these are nonpolar 91114 Atoms don t always share equally The atoms that are more greedy with the electrons are more electroneg ative OgtNgtCH 91114 Polar groups 0 gt1 mm H H u N c c u N c c 0 0 0 N N c c 0 mm c c H N c c N N C C CH cu 0 C I o cquot 0 cut 0 I c C u no c 544 I o Vc quot M o thponmo m cwem It Ty me or Awalraghna ul cm no 0 1h 5 m m cm 91114 91114 C harged groups 1 Linking amino acids Ma ny large biological molecules or 3 macromolecules are made up ofsmaller w o M 2 c building blocks 3 3 o c single block monomer 54 if t bunch oflinked blocks polymer la quot N I A wna mlb outagmuu Lymom mm39ztmp mummy 1m monomer amino acid polymer protein or polypeptide 91114 91114 Key points about Key points about polypeptides polypeptides 1 Rgroup orientation 2 Directionality side chains stick out from the backbone Amino group atone end Nterminus can react with each otherother molecules and carbOXyl atThe other C39terminus or water a Polypeptide chain Ammo acids iomod by pcptido bonds Nlermmus 1 c a Polypeptide chain Ammo acids iomod by pjcptido bonds C terminus Nlermmus I 7 C terminus H H o N M o H u o M H o H u o u H o n H o H N o Peptide H H o N M o H u o M H o H u o u u o n H o H N o Peptide l 1 l l l l 1 l l i u 39u c c u c c u c c u c c u c c u c c u c c n c c 039 mm u 39u c c u c c u c c u c c u c c u c c u c c n c c 039 mm 4 I i I I backbone 4 I i i I backbone u u 601 cu 39 ion on cu cu u u 601 cu 39 4 cu cu cu i quot 9 x 2 V i if x Ammo 0 39 39 8quot Caiboxyl Ammo 0quot 39 39 8quot Caiboxyl qriznp v quotV group 1mm WV group Side chains on Side chains 91114 91114 91114 Key points about polypeptides 39 Flexibility Single bonds on the backbone and connecting the Rgroups can rotate Polypeptide is wiggly a Polypeptide chain Ammo acids jomod by peptide bonds Nlermmus l group i i Cterminus u H o H u o n H o H H o H M o u u o n H o H H o Peptide i f i r u v i i H 1 H 39u c c u c c u c c u c c n c c u c c u c c n c c o bonded 4 t i 1 c backbone u u as cu GI 5va CH cu 39 j A v t Ammo 0H 4 l s Cmboxy flilil V 1 Side chains on 91114 Protein versatility Proteins are the workers in the cell Usually exist in large numbers Hemoglobin Carries 02 in the blood Every red blood cell has 300 million copies 91114 Protein functions in Catalysis Speed up chemical reactions enzymes 2 Defense Antibodies 39 Movement Muscles 91114 Protein functions 4 Signalingregulation C arry information between cells insulin 59 Structuresupport Fingernails haircollagen a Transport Hemoglobin 91114 91114 Protein structures Protein structures de ne their functions a Normal amino acid sequence b Single change in amino acid sequence tTPro rt Glu 6 4 2 pr6 aural rerquotvalu39 c f 6 7 5 6 7 1quotquot Normal Sickled red blood red blood cells cells 91114 Protein structure Primary structure Unique sequence ofamino acids Lots ofvariation possible 20 amino acids For a 2 amino acid peptide there are 2020 combinations For a 3 amino acid peptide there are 202020 203 combinations 91114 Protein structure For a 10 amino acid polypeptidethats 2010 possible sequences About 10000 billion Proteins can be 105 ofthousands ofamino acids long 91114 Titin largest protein Found in muscle 35213 amino acids C hemical formulas Water H20 Titin C 169723H270464N 456880 522435912 In vivo halflife 30 hours 91114 91114 Protein structure Secondary structure The polypeptide strand can fold back on itself and hydrogen bonds will form between atoms on the backbone a Hydrogen bonds torm boiwoon peptide chains 91114 Protein structure tertiary structu re Tertiary structure Larger scale structure Interactions between Rgroups or Rgroups and the backbone Variety ofpossible interactions involving Rgroups wide range ofpossible 3D shapes a Interactions that determine 1 cu on o Hydrogen bond between side chain and carbonyl group on backbone H 0 CM Von n ccquot H Hydrogen bond between two Bade chains 91114 Protein structure tertiary structu re Tertiary structure depends on secondary structure a Interactions that determine the tertiary structure of proteins row on 0 Hydrogen bond between rum chum and carbonyl group on buckme a o ti gtchz on on in cc H hydrogen bond between me moo than Hydrophobic ricnax fWEbZ ccngcn Ionic bond cwvi si ecm Dlwl do bond mmmcuons van der Weak Interactions 91114 Protein structure quaternary structu re Interactions between 2 or more polypeptide chains For Cro2 copies ofthe same polypeptide chain a Cro protein a dimer lL 91114 91114 Protein structure quaternary structure b Hemoglobin a tetramer C xquot J For hemoglobin2 copies of2 different polypeptide chains 91114 Protein structure summary wx39vx v lurjl a Protein Structure lcvel Deanlptlon Sublllzed by 1 sz Hemoglobin arimary lrv s m MC 1 Julquot Am r H 6 Gun 1 I m wprrm m L Snondaw Yenuxy 91114 Protein structure key points Protein structure is hierarchical Primary structure determines secondary structurewhich determines tertiarywhich determines quaternary Huge variety of possible protein shapes 91114 Importance of protein structure FORM AND FUNCTION ARE INTERTWINED Proteins need to be folded into their proper structure before they are functional 91114 10 91114 C hange the form change the function Ribonuclease protein folded Ribonuclease protein denatured unfolded Dlsullrde bonds form Hydrogen bonds form Disulfide bonds and hydrogen bonds are broken C hange the form change the function Denaturing unfolding a protein Denatured proteins do notfunction Ribonuclease protein folded Ribonuclease protein denatured unfolded Dlsulltde bonds form bonds form Dlsullide bonds and hydrogen bonds are broken Protein folding Enzymes proteins thatwork l5 iDrrleoir Slmnum Sublle sampleMemo nNn Primlry 3 quotquot6Il4 39i1 gm 15M 5mm Enzymes are used by cells to speed up chemical reactions like a catalyst m Bring substrates reacting molecules close together Position the substrates so less energy is If you put a hemoglobin peptide in water itwill needed for the reacuon form the tertiary structure on its own automatically 11 91114 Enzymes proteins thatwork H Energy for reactions Transition state is a high energy state rm mam Theoretical chemical reaction Need to invest some A BC lt AB C energy to getthe reaction done 91114 91114 Energy for reactions 1 Energy for reactions Enzymes lower the activation energy required for a reaction Makes the transition state more stable The energy needed to make the reaction go is the activation energy rm mam rm mam Makes the reaction go much faster millions oftimes faster 91114 91114 12 91114 Energy for reactions Al 00 7 A va 39 0 Transition state gt 9 53 with g enzyme a o E Reactants AG 0 39G does 39 AB c not chang quotquotquot r r r 7 Products V Progress of reaction 91114 Energy for reactions Enzymes are catalysts Catalyst substance thatlowers the activation energy ofa reaction causing it to go faster without being consumed qunnso39nncuon Enzymes are the same atthe beginning and end ofa reaction 91114 Energy for reactions Enzymes can catalyze the same reaction many times C arbonic anhydrase 1000000 P 39 m reactionssecond 91114 How do enzymes work Substrate It s all about the shape WWquot Lock and key 513 Enzyme has an active site thatwill bind with a specific molecule 91114 91114 How do enzymes work How do enzymes work When the substrate binds to the active site the enzyme may change shape Induced fit Notezenzyme is much bigger than the substrate Substrate locus in J Only a fraction ofthe enzyme is partofthe active site nzyme ncxokmm This can change the shape ofthe substrate too which makes the transition state easier More specifically only a fraction ofthe Rgroups interact with the substrate 91114 91114 How do enzymes work How do enzymes work 239 Transition State PROCESSAMODEL or ENZYME Action A B C A B C 1 I n 0 n substrates 1 o n Iransmon state Bring substrates to Orient the substrates each other mm such that the Don t have to rely on them bumping into each other 1 lnltiatlon Reactants bind to the active site in a speci c orientation forming an enzymesubstrate complex 91114 transition state requires less energy Position in the active siteinduced fit 2 amnion state facilitation Interactions between enzyme and substrate lower the activation energy required 91114 14 91114 How do enzymes work 1 Enzymes PROCESS A MODEL OF ENZYME ACTION A B C 3 Termination o Wm Enzyme does not l Some enzymes need a little help bind to the products C ofactors 31 ermina onzProduct5have lower amm 3907 ac ve me Enzyme returns to its andmm swe n zymss small organic molecules coenzymes unchanged after the reaction beginning shape 91114 91114 Enzyme cofactors Enzyme cofactors C arbonic anhydrase with Zn2 ion in the active site Vitamin B3 niacin 91114 91114 15 Enzyme cofactors i Ifyou re missing cofactors thiamine B1 deficiency beriberi vitamin C deficiency scurvy vitamin D deficiency rickets zinc deficiency hair loss problems with eyesight taste memory 91114 91114 16