Biochemistry 2280A Study Guide - Midterm Guide: Eosinophil, Lactase, Hydrolysis

• School: Western University
• Department: Biochemistry
• Course: Biochemistry 2280A
• Professor: Eric Ball

Document Summary

"deprotonated" o! amino"group" o! carboxylic"acid"group" o! side"chain"(some"amino"acids)" to"calculate"the"net"charge"of"an"amino"acid"you"need"two"things:" o! the"strength"of"the"group"to"attract"a"proton"(pka)" o! the"number"of"protons"available"in"solution"(ph)" see#document#in#meakin,#lec#2#tutorial#1#video" o! to"calculate"the"net"charge"of"a"group"at"a"certain"ph"we"multiply"the"fraction"of" ionized/unionized"group"by"its"respective"charge"and"find"the"sum"" at"ph"="pka,"50%"of"the"cooh"or"nh3"group"will"be"ionized" pka(c)"="2,"pka"(n)"="10" o! at"low"ph"(high"[h+])"amino"group"will"be"permanently"ionized"so"we"only" consider"the"carboxylic"acid"group"" at"ph"="2,"ph"="pka"so"there"will"be"50%"cooh"and"50%"coom" charge"of"the"carboxylic"acid"group"at"ph"="2:" o! (0. 5)(0)"+"(0. 5)(m1)"="m0. 5" at"ph"="1,"10x"more"h+,"less"cooh"able"to"ionize,"so"90%"cooh"and"10%" Cooh" charge"of"the"carboxylic"acid"group"at"ph"="3:" o! (0. 9)(m1)"+"(0. 1)(0)"="m0. 9" when"ph"moves"2"units"away"from"equilibrium"the"amount"of"h+"changes" by"100x"more"or"less" at"ph"="0,"there"is"100%"cooh"so"charge"is"(1)(0)"+"(0)(m1)"="0" at"ph" "4,"there"is"100%"coom"so"charge"is"(1)(m1)"+"(0)(0)"="m1"" o! so"at"high"ph"(low"[h+])"carboxylic"acid"group"will"be"permanently"ionized"so"we" only"consider"the"amino"group"" at"ph"="10,"ph"="pka"so"there"will"be"50%"nh3 the"same"steps"apply"as"above"except"you"re"considering"whether"nh2"is" able"to"ionize"(gain"proton)"based"on"the"[h+]" Understand!peptide!bonds! amino"acids"are"joined"by"an"amide"link"called"a"peptide"bond" proteins"are"long"polymers"of"amino"acids"whereas"peptides"are"shorter"(less"than"50" amino"acids)" there"are"electrostatic"interactions"between"amino"acids"caused"from"the"partial" charges"of"the"c"(m)"and"n"(+)"terminal"ends"or"from"charged"side"chains" o! the"force"of"attraction"is"weaker"as"the"distance"between"amino"acids"increases" o! electrostatic"interactions"are"weaker"in"water"as"the"water"molecules"shield"the" o! charged"groups"" inorganic"ions"in"solution"can"weaken"electrostatic"interactions"as"they"cluster" around"the"charged"groups" there"are"also"hydrophobic"interactions"between"amino"acids"with"nonmpolar"side"chains" o! water"forces"hydrophobic"groups"together"" o! these"are"not" hydrophobic"bonds "yet"an"attraction"caused"by"the"repulsion"of" water" distinguish!between!primary,!secondary!and!tertiary!protein!structure! 3d"arrangement"of"the"polypeptide"chain"(overall"shape"of"protein)" o! stabilized"by"bonds"between"side"chains"or"side"chain"to"backbone"or"backbone" to"backbone"" hydrophobic"interactions" hydrogen"bonds" van"der"waals"forces" ionic"bonds"(electrostatic" attractions)" +"one"type"of"covalent"bond:"disulfide"bond" between"cysteine"residues"(only"in"oxidizing"environments)" o! interactions"between"residues"that"are"distant"in"sequence" describe!the!characteristics!of!an!alpha!helix,!beta!sheet! alpha"helix" o! coil"spring" o! Define!and!describe!tertiary!and!quaternary!structure! on"top"of"the"characteristics"described"above"for"tertiary"structures,"the"concept"of" domains"is"also"extremely"important" domain:"distinct"region"of"a"protein" o! can"often"fold"independently"" o! provide"structure-and/or-function"" many"proteins"are"made"up"of"connected"domains"" related"domains"are"often"found"in"different"proteins"" "tertiary"structure" proteins"have"conformational"flexibility"" o! various"types"of"motion"possible"depending"on"structure" o! domains"can"usually"move"connected"by"flexible"linkers"(unstructured"peptide" chains)" denaturation"is"the"process"of"protein" unfolding "" o! things"like"ph,"high"temperature,"alcohol,"heavy"metal"salts,"detergents"can" cause"denaturation" urea"and"guanidine"hydrochloride"are"very"strong"denaturing"compounds" o! denaturation"breaks"weak"bonds"and"not"peptide"bonds"so"only"secondary"and" tertiary"structures"are"affected"and"not"the"primary"structure" o! some"proteins"are"able"to" refold "once"the"denaturing"agent"is"removed"(like" urea)"however"thermal"denaturation"is"irreversible" Understand!the!concept!of!protein!families! new"proteins"evolve"from"old"ones" protein"families"are"groups"of"proteins"related"through"evolution" similar"primary"sequence,"structures,"functions"and"domains" amino"acid"residues"that"are"vital"for"protein"function"are"found"in"all"members" o! conserved-residues" o! identifying"such"residues"by"comparing"amino"acid"sequences"often"helps"clarify" how"a"protein"functions"or"how"it"folds" Ubiquitination" a n g i s r o y t i l i b a t s r e t l.