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CHEM!3653 Fall2009 Exam Versi0n:. .1 b_ame/ID:_-i _"... (r(

- qlulnllt B .....

", _ Instru " " "" , • " " " '• _ ctions: * " ' '

_1) Write your name'(legibly) and your student ID on this cover sheet and on th_ answer'sfiedt. ....

" " :"2) Y'o_ shouldhave a working (i.e., new batteries)non-programmable; scientificcalculator(i.e.,'no g/ai_hing . . -calculators) and your student ID. Youwill not be all6wed tO "borrow" anoihei" student's calculator• 'Any students Who : •

"_ do so (both the borrower andthe lender) wdl recewe an F on this exam and will be charged with academic : , -, . _ _ "-misconduct. . . , .. _,. - . - . . ,. ._.

3)No cell phones or any:other electi'onic communicatic;n devices such as pagers, FM_receivers, headphones etc.. ! _vill" '*e ,

be allb'_ed?Any students who are Observed having such a device will'receive a'n F for ihis exam ands.will be chgged

," = ,with academic misconduct subject to sanct|ons m accordance with the Norman Campus Academic Misconduct Code•:I routinely.r'e'commend "F" foi"the course mid'expuliion, from the I:/niversit,j for any such violationg. _r, • ' . .'"' .- ,

4)*YouwilI' record your answers to the exam questions•fly:.l) writing your answers on the exam and 2) w_tlng_" : "• your answers on the answer sheet:*The'angwers on the•answer sheet will be graded_'but theworK'that led to thew

w h_

• answers (whic h you will record on the ex_.m)m_iyObe checked as well. Any dlscrepancies between thelwork' _ _' ' *"shown on the exam and the ans_ve_ written on the answer sheet will be counted as[ncorrect. Make sure that..

- • • _the,work you record on the exam does in fact lead to the answer that you record on the answer sheet• Any . _.• patterns of inconsistencies will be gi'ounds for aca_lemic mis_onduct, as d'iscussed above'in #3. :_ " : ?, • . " " ...;

: ==>.Foldyour answer sheet vertically down the center such that_your answers.are not vi§ible:'Keepyour answer _-et - . •:. . .•_ sheet folded in this manner at all tim'es except when you are recording fin answ .

- -, 5) Wi_en you are done with the exam, turn in to the TA.the completed exam and the'compl&ed afiswefsheet. Also," sh6w.the TAyour student.ID.,Any stud_nt_ who do not folloffthese instructions Will receive an F for this exam and -,

-will be charged with academicmisconduet as discussed al_ov& ".: • ;.. .- . - .......

. t . ., _]-• e ,t _-.

3 -

_ . . 2"" - _

#

- - 1. Match each of the following• To record your answer• list the letters'that correspond to.the Roman numeral ch6ices: in incre_ing Roman'numericalorder. For example, if yon felt that choice "A" matched Roman numeral 'T' and that

• , _- choice "B" matched Roman.numeral "II" and that choice "E" mfitched Romiin'numeral "III" and so on; you would. record ABE .... for your answer .... _ . _ "- -

_9 II. -RTO-P(O)(OH)2: , ']_A lII. :P(o)IOH-o:P(O)OH:, " " . ' ......

:" D_)._Phosphateester . _ IV. R-O-P(O)OH-O-R'- E_hosphate diester - • _V. >C-=NH-

. .. 2.,,Which statement is _ important _pect of the hydrophob c effect? - . .t - ! ,'

_ (A) The AH isnear _ero or positive when hydr6phobic:molecules are:excluded from water .... • ' :- B)Th " ' "' " hyd ph ..... " .................; e entropy of water increases when . ro ohm moleculesare excluded f/om water, . . . ,-

,5. ./_,drdphobic molecules have a strong affinity to interact frith each other instead of.water,/" _ _,.. . .. _-- . ' : I_'J'The larger the surface areg of a hydrophobic molecule, the greater the loss of entropy by iriteractifig s'61vent water. , 'k_

-" E) All of the above s'tatements are important aspec_ of the hydrophobic effect.•F) None of the above statements represents an important.d_pecL'of_e hydrophobic effect.- _ " - - . , " .2'

3. Match eachof the_following?To record y6ur answ6r, list the le_ers that correspond tb ihe Roman nu/r[eral choices - -.

in'increasing Rgman numerical order;For example, if you felt that choice '_A" matche_t Roman nuineral 'H" and that "., choice "B" matched Roman numeral "II" and that choice "E" matched Roman numeraF"IIl;i and 'so.on, you would

record "ABE:.." for your answer. - "''k" , " r ." -

: .,A-)--Hydrogenbond _ I. -_0.4 kJ/mol - - . -

__.__._B) London dispersign forces. _,_ -.,,,., -,t_.II. '_20kJ/mol _ !_7_ Cj__._. :" . .. - .... "_.-_ovmentoono _m.-_lOKJtmo( . , . • , ,., ,: .I_-dipole interaction C.IV. -_400kJ/mol • - . . _

• _raction _-V. _80kJ/mol ", " " - "-" -' "'

...... 4. Which of the following statements is/are true? ' - -- ' " . "_ m

b

- . - . • _-o

. ,_(pK_, = 4.76) is an effective buffer against acid at pH 3.76 : " . ,. , • " "_,."

- _cetic.acid (pK_ = 4.76) is an ef(ective buffe_:against acidat pH 5.76 i - " " " ": -:' " -.,•'."': . _Ll_mmonium hydro:_ide (pK_ =_.25) is an effective buffer .against base at pH 8.25: ". ,._

" _onium hydroxide (pK, -_ 9.25) is an effective buffei against base'at pH 10.25 - • ." , "'- " . • •. • -1

: "_I only -" ;. B) Ii 0nly, . . . - , c) iii only _ D)'IV:only- - E) I ,,.2 I1.3al) _" "

" F)]'ai_IIIonly Q_LI'_':dP, rz=ly ,_ I) II and iv only J)lllhndIVSnl3; "_'£(-

5. Carbonic acid (H_CO_)'has pK_'s of 3.60 and 10.25_ To n4ak6 a buffer at pH 3.60 starting with One liter of 10 raM-." carbonic acid, you could add . . _ _ ..........

t :%% . • .... :. . ....'._) 5 mmol of HCI '@ mmoi o_'KOH'. C) 5mmol of NaCl':. " _mol of H+. %

_.4Oml/nol K* "_ " : F-)-l(kmmol of KOH " _01 of KC)_ .,' "- ",H).None of the ithove-

_ 6. What is the molecular geometry ofihe ammonium ion (NFI_*)? " "

A) In'ear " -\

_,__l:t_,h_,nt = " -: ._. . -.. -. :_ - , "'-n

- E}octahedral ..... . , . :. . .,,

. t is the mosi likely e ectron configuration of the calciu in i_ b.You may want to u_e the blank"_eriodic table (question.#23) to orient yoursblf _ , ' , ' "" - F

"'. ", .. _ . _'t:]_S I . . ,." __' : l_)JAr]" _1 2-. F) [P/i']3_2"', ,' . _ f__[Ar]4s : . _ " J) [Ar]3d? .

. - 8..Erwin Chargaffstudied DNA structure and composition: What observation(s) did he make? _ " "•• . r /"

-"- I. Nucleotides are nbt all present in the'sa_me amount, _. ., " " ,"II. Nucleotide comi_6sitjon varies4tmong siaecies. - o -

-lilt-The ratios ofA to'C and of G to T are 1:1 regardiess of species. " ._+C - ' " " • " ' "

_Ai I only B) II only _, C) 11Ioniy, "_- D)IV •only " - _ -: " _:":'_

-, .,< ?27F_x_&IIw_I._h_. _ G) I &"IV only .... H).II.& HI only _ " ) II &. IV only _ J) Ill& IV'6nly"" _ _"" _'_, ' " • L) I, II, & IV'only ." M) II, IIl;& IV 6nly i.. " .- : ) ,• ;

_" " " " by" _"9: The experiment .of Av__, MacLeod, and McCarty In which nonvirulent bacteria were made virulent

..... ransform jdn'wassignifican '' =- , ._t at t because it showed that: .... _,: .

_ria c_in undergo transformation'. - ' ' " -" "' _ " .'_ _ • ..;., " _ is the molecule of heredity. - "-

• , ,.l_ice-ai'e more susceptible.to pnbumonia than are . - - ._ . -_" ;:, 2" " -'h'umans. _ " - - '-"

Darpheumonia can be cured by transformation: • _ytli- • _,_ . _-_-heatrcan.destro e transmissible factor.

,.'_ " " ?_10._VJaichone of the following scientists generated the X-ray diffraction photograph.used to determine.the structure:'_ : "ofDNA? " '" "

_ ", " '-'-A)M/uirice WilkinU _-- -" • L.;"B) MaxPerutz . .? - - " " - :.

" ' " _" ..C) Linus Pauling : ' " ' : '_i d Frankl_" E) Francis Crick • • .... '. . -

:. - _ F) James Watson - ".... - • ., . .,. -. _-G) JohnKendrew" . .- " "" " " : "- . " "- ..... •

-: _ _ __q _oC,.,_ .... ' ' " , " -• 11: If a 32 base-pair;segment of double:stranded DNA contains _enine residues, how many gfianine residues are.:

- - th6Fe? '"_-- ' _ , ': - " '_-_,_ "".... -: ....

"" ' _ " : " fromthe info_raation given " .- ,_) It is not possible to eaiculate" " " ' : , _ -

, E) 32 _ ' " ...._'_' Y:F) None of the above. - • •"'

.,., . . _. - r. .'. . , .

12. If a peptide made up'exclusively of _m_residues (of sufficient length to form an a-helix) was in solution at -:" p'H 7, would it likeiy form an a-helix? --F . _ " . --- " " " "

" " ' ldfonna h li "" "'-' - A) Yes, itlikely wou n _- e x <

• _lik ly uidnot fo h li " -..,, -.. e WO rlnano_- e X ." .

• . C) It is not p0ssible'to make a reasonable predictioil - "

?t -. : 13. In b6thRNA and DNA synthesis, the phosphodiester bond is formed.when the hydroxyl at the terminus of.... - the growing clJg_inattacks the '_ phosphorus of theincoming NTP or dNTE

- .

" _r ianerrfiost) -_-"_r innermost)

. . . "-C--)"2"j13"-f(_middle)-, . _ - .

- D)-3_-(Or middle) . .

" "_routermost) . . , , ". " ' "F) 5'; ct (or innermost) .. ,. -"G)--.5_.'d_:(ormiddle) , . . . , . :' '

H):_6r outermost) ." '. - " • "J ".

" nsider the titration curve of phosphoric acid with NaOH shown below..What species are present at the p nt in

.-.._ '._..thetitrati0n cu_elindicated by.#3? "_. ". " " _- ". , . . _.

• " .d_ ..... sPO4 oa,u ,12, 04-

-" (_sentially all H2PO4- : , lo

. D)59:5J)M_PO4- and HPO42- . " " "'" - .E) essentiatly-all4-IPO_ 2....... on .. ' ..... ,.. 6

_ . F) 50:50 HPO42SandPO, 3- , " _

•; _)._,_se..ntially.all poa3_ .- _ . " 4

" 7 -' . "" 0

15. At physiological_pH, in the side'chain 0nlof_. how many o.s." _.Ow_o__i_o_t_152.0 .: zs . ,ao . . .-- carboris, hydrogens, and nitrogens are present? ..... " .... • . . -

- • ".... ,4 _."'

. - . " _)-8"enr4_; 10 hydrogens, and 2nitrogens . . - t.

- ' J_t::R2_hm_, 6 hydrogens, and' 1 nitrogefl "" .. .. ' . " . " " : .....

"...._.:. " D9(,._._9_ns, 8 hydrogens, and 1 nitrogen ia . ,: E)9'qarbons, 9hydrogens, andqnitrogen ' ' ' • "' ; "

F] 9 carbons, 10 hydrogens, and 1 nilrogefi:" _,".G) 9 carbons,.10 hydrogens,'and=aq_i_[_ t4 .. - .'... - '_.

- , " H) None of the above " " " : : '....... -

. -: 16. At physiological pH, guaninehfis " ," " " _.."_' . -i I. , ,: • -

_s, 5 hydrogens, 1 ox_r_/w-_'_U_ell_ns _. _ _.¢ "'-" " '"" '" "'_ carbohs,5 hydrogens,. 1 oxygen, and_5.nitr0gens ,: .- _-:

••'( _- _::.C) 5 carbons, _/hydrogens, 1 oxygen,and 4 nitrogens )_• " . . ,

" l_8_arbons, 7 hydrogens, 1 oxygen, and 5 nitrogens • - . -.E) None bfthe above " " : "

" _ :." ich c ice (or choices listed below provides an acceptable description of _com_ ?'" ":_ " "_ B) iionly . - _)i-_iii2 .... . : . --

" ': .,A :i.__ :- _ an L-amino acid CH2SH ."

: E_&-4v-- F) ii & iv - ii) It is a D-amiito acid + :'71 " " _

: "" iii) It has the R- " HaN _ C "" COO-_' ' :

.: configuration .. • ] • • -:.- :.... iv)'It has theS- ; : " "" ,_: . , - configuration H

_",,." L" "- '_" •" :" =' - i; _ ." , "'_ .7_;:)V," -'-.,. -

- " .. .+ .+ .'+ .

.- + •• , • " . " - . . .-, . . . " • " .

- . . _'2. or'_._) ng ea_. "-r-1 en l;a " " ' + " " '_ " "... , hydrogen bond can be represented as D-H.-.HT_3x_ere _ :

,.D:H Is a weakly acidic "d0nor'_ group such as.O,"H, N-H, Or sometimes S-H, andHZ is a weakly basic "aci_eptor".+" - • .atom such as HO, HN,.or occasional!y HS. Write !'T" or "F" on the answer sheet to indicate'true or false, respectivelyC : . °

.19. The binding of ligand (oxygen) to t_ein can be described by the Hill equation shown beiow.

A) The.ab0ve statement applies only to hemoglobin . , ' :: "' "rT]n' " 5

(_i6ove statementapplies only to myoglobin:.,. . . . . " " : +r ---_ "" I'L't .i' 'above statement applies both to hemoglobin and to myoglobln : [L]n -I- [ISs0 ]? •

D) The above statement does not apply either to hemoglobin or to m3,oglobifi ....

-, 20. Consider the pept[dd shown below and to the right.' : - ,,

:, What.is the sequence of this peptide? Use the one" NH2 _: " .' -letter'code to convey your answer• . -- "--- _ ......... .,.: ..... . c=o . '-_."x,-Jn';_ ! --" ....

; ' " ' + " .... " " ' L I '+ ' + ' "l ...... '" " "U +'., , - :+ + , ' " ' H--N + , -/.C /CH" + +jC "t.GH N +, " C " ':j +,, . . : , • + j-+. 1. >+-V"-+n./.

.:: "+. :"- 21. Still considering the adjacent peptide wl_atwould " H.Sq_-_ I n I._ .[ "::+, I_1..'./I-.. -+ ".

: -, .- _..betl_enetchargeofth,spept(deatpH 13?.+ +. ' , :-' ' C_+'k_O, , " _ _", ._H_ " _ • " [i" r . 1 a " ..

. - CU2 +

-- +. • . _

", + . _ '+NH+ . •

--" .... ' "22.'Cleavage ofa_g with trypsin yielded twO"and a Ne, the amino acid compositions of•+ :.' -._+ ++which are shown on the below.:Cleavage of, the hepta-15eptideWith ch_sirl yielded'two dipeptides and a " " ... ,tripeptide_ the'amino acid compositions of.which also are shown on the below: Finally, Lcarboxypeptid_e di_;estioh + "

. • . liberated free metliignine. Given this ihformation, what is the amino atilt sequenceofthe_e? Usetheone,.letter code to report your answer -_Z'VC k^ " " " "" " +'

. . , , • , , . . + •

" ' "Amino acid composition of trypsin fragments: - Amino acid corriposition ofchymotrypsin fragmenN: + + "+"

7+ - . - C..P-P-oS 1:J. .. c cb. ..i. _,LYff'Tyr o0 ;4tcsZ.L_l,+ . - + " .+ i.,I_ys, M+t, Glu-_ - _ + + Ip_ ++I + _+ . yq_+ .+ r+.u, Met ' ii. Phe, Ser"., -. .. • .

':" iii. Ser, Arg rphe. _-'_(" t-_.15_,._'+_, "_u: ,',,Z_, ": iii. Ai'g;Tyr, .::'. :. .. -. • ..-; ..-+ . x " . .... "

-'%. .,q',',+lo :' + -"+` " "-- ,1 ,t:, r

: " 23: The element nitrogen.is located in which row and column of the' periodic table? Use the blank periocli_ table" ' "-." . . . below to hel[_ you answer:. Example: If I were to ask where,in the periodic table, the element neon'is, located,, y9u . -,"" + would write the answer "R2C 1g" to indicate that the element neon is located in row 2 and c'olunm 18. _ + ° '

"" "+ .+. - . . - • , - . "- .. I 2 3 4 .5 6 "+T 8..'9 1011 12 i3 14 15 16 17 18."

. ,% •

ft" " 6 "__ ': "

"1- ++: "' _ "_ "7 "+ . ++

_" ._..11 ,_ '0 : _,.... " " I m " " " )' + "+" _:% _ .: 'i= ' ' ''11"_ 1" '4',:., _+_) ' " _ " + + , : + , _ " _ . K ' " +" : : " i+_ ++1) " :+ ]'#_ _'' +"1 d+k++ I+ _+ _ I + I_l ++'++" + + I + _< _ l . + "+ + " ++ ++? + + ++ I+++++ + $ + I _ -- + + + _ l I + i _ I + + + .+ I I+ + + I + + " i + " + I _+ _ + +_ + _+ +

f _t' • , o *

' : _. _,,' ". ,24. The codin_ strand of a segment of double-hefical DNA contains the seq'uen_:_ TGGTAC(_AGGAC _

"; [f the strand that is complementary to the above coding strand (i.e._ the template . . -..strand) .'#as transcribed to InRNA and the mRNA was,translated produce a peptide, F_r,,_,,,rof_,no,_S',,d_

"l Second letter

• of ¢odon .

what :,vould.be theamino acid sequence of the resulting peptide? Assume that ' _ c .A _G •lati fi RNA beg (i e'th od I. trans o of the m ms with the fit:st codon .e., assum at a start c on "_uc ¢0_o_ .............. _ .... -......

- . . is n'ot required to begin translation) Also, assume'that if a stop cod6n is'. _."" . u -,_ "_"..................1

ncohnte ed p r t ching the end t'th tmnsiation _tops and d n ..........._........r rio o rea o emRNA, oes ot . uuG_;_7ucw._,, _tz,,._: ,o_,-,,._,CUU'_L_u, CCU_7_P_ CAUt'_'HI_ CGU_Ar_

• ._ ' .-. resume, in which case you shodld enter the sequenc6 o c o ated • ¢ueg_tei_¢cc._,_r*c_c_Hu c_r.,.^_,i/ato the peptide prior to encountering the stop c0don. Use the adjacent genetic code ¢ CUA-'t.o',_o,,".................

_. , .. o he u. t your nswer using the one-letter code of amino acids: , : ", . . . .." " " " " . - • "^utff_!'._i ACU;>rn_ AAU;_,^m ^_u,,:st*

" * 'AUG [Met AC_3,3Tht AA_x_,.LY_ AGI_Arq

• , - GUU;]_Val I GCUi I_Ala _x,u_,Ast_ _GC_UC=_dV

C nid th pi sh [ pi _spo-. 25. o s er es nstates own below Which'of theses nsstatesco e rids. - • . _ . _,"

to the Fe(IIl :on in ox_6globin? . " , " - . •-.--• _ t /\

C) both I and II are reasonable . . " _ • .°• [9pregentations of the.spin state .:, "' _ . " - : " - " r

": ."-ofoxyh_moglobin .... _[ " _ _ ,_ "'_ ,:"t_. ""• - D) neither I nor II corresponds to the , -- m . ." -

; "'.'- spin state'ofoxyhemoglobin • " . . ', .

7

- 26.-If binding curve 3 r_/presents the binding cur,)e of oxygen to maternal hemoglobin, which cur4e would be_t " ". - repi'esent the binding of oxygen to'fetal hemoglobin? I_

C) Curve 3

.... - - -D)'Cdi've 4 ,. : )' -.._

- ° " r_'f .... " '..

:" " - "¢Ov"_-'/ " ' * _ " "" " -."

- 27. In the beta-cham of hemoglobm.._(HbS ) there is a {_oc_l)o_w residue substituted in _lace" of a. residue that ends up on the _xtaLft f.t of the protein. . "" _ ' "• __O ..,

U ."

_,.charged, surface " - •

• '" ': ._R_ n_np01_nterior_,_z --'-"'---'-- - " " " "" : " "_npbiar, charged, surface " _ . .,.. "

:.. D).nonpolar, charged, interior " " "_:" ; . - '- "i ". -_ :... F_'etrarged, polar, interior ; - . ... "_ -..". _ : . _ . - "

._lilr, nonpolar, surface .... . -..'(_glpt:tl_ harg d

, . , c e , interior .:. .°: :

" .C . ' . • , -... -

_ . ,, •., _ - . -

:., 28, What factor(s) influence(s) the binding of oxygen to myoglobin., --, - ", -.

: _tion of,bicarbonate ioh _HCO3- -: - '" : " :. , , , . . . . •

_l_epartialpr_s r fo genlpsu e o xy 02 J ....___oncentration ofhemoelobino___present.. '- • " " : " - " ," " " "

'.l_)=l_"efncentration of2.3-BPG. •. " . * , ; - " " --, E_Re_,,^._ ,,m,,. ._,,r-,,, " ....

/ ,_l-,_Ltaes _ z auu tl . " : . -

fisid he folio " " "- . 29.,Co eft wing reactions, which occur at 25 °C: . , - '. " f_h

: _" - " " " " " ' _I'_A•+B<-->C+'D.A{'__', ,._ "_ Ikcd.,.t/:45

'-" - " . "'- 2) C.D<-->E+F£'cq"-,rt _ ,, '_:- • ' " "

. .... . -. 'Net:A'+B<-->E+F. o " ' '_ _" ' ""

'": "i' ,,',":' :' -. - '.".::: _CI =l;l_ .k_V_dr. " ,'! ." " ,.• " -.' "" "AG for the first i'eaction is "-3.1 kcal/mol, arid AG°' for tti6 seCond rea_e_orl is 4.2 kcal/m01.'Given this ihforination, +' "":

•what is tile value of K/q' for the net reaction9 Report your answer to two significantfigures . "' ',"' 'i' '" "

d*

- . . .: 0[: - ,_._ . . - . \ .. : . ": •

. , . . , ° ""

n e. ,1

• _,""?-"/... new.,,_-=c°mp°und.......... is discovered and. is foundto.contam.two.. _-- Carbox_ups and a,_gruan oup (1 ke .the side .. _'_- _" cnamo_.'._gmme):The respectwe pK_s ofthese groups are 2 1,4.2-and 123 If 100mLofa0 1 Msolution ofthis '

- - - compound is at a pH'of I 1.9, what fraction " " _ " • " " " •....• of this compound (expressed as a percent) will carry a net charge of-2? _"-- -.....:EnterSyour answer to two signific_mt figures. " ","" "" ,--" - ". - " - " - ".... _ "'

.-. .... :. , .. . ,< . ._ .., • , ?. , ,..

, ,. " .' '. • .t 'it/, z11.4-1_.3. ; + . . • -,'IT: tt_"'-'" "/C-g3 .- . ,..". ,-._;'t/.t ,,_h_',- . - , -.--. " --, ..r -. --_ - .. -

'. . oi.... ;.. .-.. ' "--J

L-

CHEM 3653 Fall 2009 Exam !i Versfiin -2.,, _ ; . NameTID:

Instructions: ,. .:

1 Write me ( '_" ID onthis " sheet the " "" -- ) your na legibly) and your stu,_e.t cover and on answer sheet•

_, . 2) you should have a-working (i.e., new,batteries) non-progrfimmable, scientific calculatdr (i.e., no'grapffifigcalculators) and.your student ID. You will not be allowed to '"borrow" another student's calcillator. Any students who .

. . do so (both the.borrower and the lender) will receive an F on this e:_am _nd will be cha_ged withacademic ''misconduct.__________".... " _: " " -.... ' ::. " _: " " " " . ' . ..

" .3) No cell phones o'r any other electronic communication devices such as p'agers,FM receivers, headphones etc.. will ,..be allowed• Any students who are observed having such.a device will receive anF fol: this exam an_l will be charged;with academic miscond_ict subject t_ sanctioi/s in accordance with thg Norman Campus A6ademic MisconductCode:I•ro6tinely recommend "F" for the course and expulsion from the-University for any such violations.' :.... " " '

4) You will ri_cord yolir answers to the exam.questions h_;:1) writing your answers on the elimand.2) w_fing.your answers on the answer sheet. ]l'he answers on the answer sheet will be graded, b'ut the Work that led to the

"" answers (whicli you will recor d on tlie exam) may be checked as well.Any discrepancies between the work - :shown on the exam and the answers written on the answer sheet Will be counted as incorrect.- Make sure that

• .., the work you record on the exam does in.fact lead to the answer that you record on the answer sheet• A,ny "patterns of inconsistencies w!ll be grounds for academic misc0nduct as discussed above in #3. r " .-." " -

" . • _ _ Fold your.answer sheet vertically down the center suchthat your answers are not visible.:Keep your answer -

. sheet folded in this manner at all times except when you are recording an answer. •

5) When you are done witli the exam, turn in to the TA the completed exam and the completed answer sheet• Also,show theTA your student.ID. Any students who do not follow these instructions will receive an F.for this exam and

'_ " will be chargec[ with acadel_ic misconduct,as discussedabove.

%/

: _ement magnesium is located in which row and cohimn of the p_eriodic'table? Use the blank perio_lictable below" ,J/to help you "answer. Example:If I wore }o ask where iiathe periodic table the element neon, is Iocated,'you would write the,

. _ . " answer "R2C 18" to indicate that the element neon is located in roiv 2 ahd column 18_ ' "

-" -. I 2 3 44 5 6 7 S 9 10 II 12 13 14"15 16'17" 18

• " • "- I , L

: I " -I,t

. . . . - . 7 '," • . •

° 2. Use thefigure on the right to help you decide which of the following

" st_ttement,4 is/a_List the letters adjacent to all true statementsm v_ . ",,, ._ .,' i:il '

_;,"!:"ali_habefical order toindicateyour answefillT.,_" For example, if you felt that-the, i" _ " :_" -'

-.:_._"_statements]adjacent to. etters A; C; and E were the ohly correct ones then,you i, i -: ,would enter ACE for your answer.. .... _ ....

- "I-A) Curve l'represents the,activity ofa non-allostenc enzyme. - - _ ..... " ,;" ;': _Curve 2 represents the activity ot'a monomerie enzyme. . • " " " ' - "

"' C) Curve 3-could represent the aiztrvlty of an allosteric enzyme in the absence of :.7,_•' ; ?'_ an•_'llosteric'activator,,_, and could 2 i:ould, represent the activity bfthe.. same. ._ ' :' :i

, • ,." allostei'ic enzyme but in the presence of an allosteric activator. " ' ' - _

":l_kCurve 3 could repregent the activity of an allosteric t_nzyme in the absence of, _lr_ '" ". ' .: '_- an allosterie aetix,ator, and could 4 could represent the acti'0ity of the same •

" . \ allostenc enzyme but m the presence of an allostenc actwator, " ' ' . " :. - . :" 2

, • .,_urve 3 couid represent the actrv_ty ofan,allostenc enzyme m the.absence of an allostenc inhibitor,,and could'2 could . . -.... ,: /,represent thd activity of the'same allosteric enzyme but in the presence of an allostei'ie inhibitor- . " .... " . " . .

F) Curve 3 could represent the acti_,ity of an al osteric enzynie in the absence of an a 16ste/ic inhibitor, andcould _1could -._ "_/_':Cepresent.tlie ao_. , ,... etivity, of tilesame., , • allosteric, enzyme• but in the. p_:esence of_in allosteric inhibitor. . ,.

: 3. Which enzyme m the adjacent Lmeweaver-Burke plothas,the "..........

_" , :._..hwhest _____Vmax/gra9 '. . " " ' "Nc_'l%'_ _ _'.-",lt-" .... : ....... " - _ -: "

_.. - A) Enzymel(El)' • , . . . ',' , ' . ,' . . . • .

" D)Notenoughinformationtotell :-:.._ _. ,.: , ... _ . :_.'L /

4. Consider, the data shown below. On the bas_s of these data, whmh - . -

- enzymes are operating at mother nature's speed_hmit (i.e., di_ ? . _. _/ts] :.: -_ '_.

_jme.,Bpnly - Enzyme .Kin • k=t - • -: ....",. " ..'_.Efizy_ne C on13} '" A . ° .0.3 mM 5000 s-!, _]:7'i'tO _ "

_dB. : B'xI%%" .10rim ' 2s -_ _'_w "_ " . ' " '' _sAandC C xaec5 2pM. 850S-" _lo

-"" @z_ynaes B'and C_ " . . ., /4._ ? "- -. e

- ' •

5 ConsidertheWasomecbanismshownonthorightTbisenzyme •, . . " 2, 3, Cyclk nuclooltlde

. . has a _l_ata_1.t_fa_ (log of the rate of the reaction x_ersus • " .,_ . , . o

pH) such thht the highest rate occurs at near ph_H, and _.-,-_-c., .- , ., ___

- i c, i.

the rate declines _ the pH is increased or decreased above or below• • I, f'-:N_/ . H:° .

this optimum_ Given this information, what is the best explanaiion - ' I .' ,. -o-p o_. _ i

for the decline in activity as thepH is increased abovd its antimum9- " " - . I . 'fr-L i o-_>...._. $3.: .

- , .,r_ "o-!-o. i _2,4. -_''A'9_ 12 I_ecomes deproionated and it can no longer act as a .i,,:,i_.'! !. "/ . _ •

genei'gl-basecatalytic Lresidue " " " ' " " _" . "-i'7 : _""' Q_Iis 119 becomes deprotonated and it'can no longeract as a2

general-acid catalytic-residue . " " " "," " " "_ " _ ' __ " " ]'.5 , 2-

_is 12 becomes protonatedand can no longer act as a general- " " ' ""*":b_'_ catalytic residue .*" - _ , • "- .: ; .

.:_.His 119 becomes proti_nated and it can no longer act as a general- :./ ' *'_._a.-h'_,:_v_"_q_'_"_' _/_;."' acid'catalytie"r_idue. -- -- " " " _ " .,' ;' _ "E) None of the above provides a reasonable explanation

"fo•

: -- nsider the kinetic mechan Sm (shown'below affdto tlac right) " " ' " , ' .. . • ' :

_; i/anci_dedide which of the following'statements is/_eN&ja:l_List the " " C " "i : "*- letfers adjacent to all true Statements in alphabetical order to'indic_ite"':"- youraqswlef.l_or ekample, if you felt that tl{e s}atemenis adjacent to letters _ ." " "-_ " " .._ "

• ' A,'C, and E were the only correct ones then .you fvould enter ACE for ....

j your answer: _. kl /5,3

Al£l'he stead!,'-state assumption t'oi-this reaction holds that the ES E .+ S _ ES. _ .E + P "coin'plex forms' more rapidly ihan-it breaks down. .' " . " _"k2' c .. .

• "" • A catalytically perfect enzyme would have k3 << k_. , . . - "-,tg,._The mechanism as-drav,;fi is valid when" [P] = [S] at the'i;tart_of the reaction.. - : .... _ _ - ", _ -: " '

• " D_)..Thereaction is essential y zero order when [S] >> K_ :-. " " " , _ • - - : ,_ -:, ,E) None of theabove s a true statement " ,, * "-

_ . , • . . -'* . .

•. 7_'What is the,c6rrect order 6f ste'ps involved ir_permanent waving of hair?- - ..- " ' " __ L-- ": " "J""-- =-•-

.'." % _h'emigal_reduction, shape remodeling, cheml_aloxidaiion -.:-""i"_=E_=ai_l reduction; chemical oxidation_ shape remodelin'g_ " -" " "" '_....': ":" -*- "",_ .'e')L-C-l_aieal 0xidation,:shape remodeling, chemical reduction " "" " . " • ', '_.-

:: '_emodeling,, . . chemical oxidation, chemical... reduction : -- . __ .- - ...._modeling, chemical reduction, chemical oxidation ,. ' , . - : .... .......

. " 8. During muscle contraction hydrolysis _/l"ATP _,,_i_;,.'o ,4,_,.g e ih the: '_ ' "

" 7_):emnfomiation of actin - , • : "lil).slxucture Ofthe sarcoplasmic reticulum." " ", : ! - "" "

" :,_tructureofthe myofibrils. • - - -.._[l,]_nformation of myosin: _. _ ,-_ " " _',

• ture ofthe Z isk * -: ..,

" 9. Select the statement that best matches the'following: Nctin, . _')Z _13_,.g_.ct v'_-1. "" •, .• r,

" forrhfo _ fth Yto•... e nohmuscle- rms that are part o e,e skeleton " _°

' *_r,_vlajorcomponent'0fthe thin filament ofthd_yofibrilJ , -" ' , ,;'_L_Jtn-_mponent of the "chickfilamenliof the m_/ofibril. - " • . - -. "

"DyetlC_ical energy sourcefor muscle contractigr _", , -.- _.,• _o/ial unit of the myo.fibril. "- . . . . "-,.

:_ difig p " .. . - alcium bin rotein. - _. .... . :

. ,: . , : 2••.

10. The "catalytic triad" in the protease subtilisin consists of:

A) three aniino acids: SER, HIS, and GLU :.- ,,l_)=e_yme, substrate, and metal-ion cofactor •- -:

. "C) three amino acids: CYS, HIS, andASP

_.._'.D']3threeamino acids: SER, HIS, and ASP " " "ti:J::l;_te, transition state, and product

11. Enzymes accelerate biochemical re_actions by

:_"-'_)-decreasing the AG fortl_e'reactions

-;w,.,_-_ncreasing the AG for the l:eactions " " " ".:._promoting reaction pathways associated with a positive AG

: ._moting reaction pattiways associated with a negative AG •• £_iding a more favorable pathway for,the reactions • _.

_hing a 'closed system' foreach reaction

12. Consider Figures 1 and 2 (shown to the right) 1. 2.and decide which of the following statements is/are

._ List the letters adjacent to all true statements in " " "

, alphabetical order to indicate your answer• For " _-2-__"_;"_/'_'

Reaclanls - -example,-if.you felt that the statements adjacent to Free Free .,• - energy energ_letters A, C, andrE Were the only correct ones then (G) (G)' - ' Pmauetsyou would enter ACE for your ?nswer.

.... _ " ._) Products Reactarltse formation of products from reactants is . ...• spontaneous in Figure'l but it is nonspontaneous in

Figure 2. - Reactionco0rdlnate . . . . Reactioncooralnaie

"C_fhe formation of roductsfro - rants_has a loweractivationbarrier in Figure I versusFigure 2:"69_i_e position of AG for the reaction in Figure. I indicates that this reaction is fast. . .--_9:NDne'of the above staten_ents is true. " " .

J

13. If you add enzyme to a solution containing only theproduct(s) of a reaction, would you expect any substrate to form?.

because the enzyme lowers the transition state energy barrier.•" _:_o, because prodtict inhibits the enzyme. • , -

C'y'N_, because enzymes catalyze only the forward reactibn.

D) Yes, because" the enzyme reduces the standard free'energy change for the reaction.•_es, because the reaction proceeds backwards until equilibrium is reached.

"14. For the reaetioia: _----_ B, which of the following statements is true9 List the letters adjacent.to all true •statements in alphabetical order to indicate your answer. For example if you felt that the statements adjacent to letters'A,C, and E were the only correct ones then you would enter ACE f0r yo_.answer.

"AT"Tti_eaction is first order overall ._)_-_._<_)The reaction is second order overall " - "-:C:,-)--_hereaction is unimolecular

(_g'he l:eaction is bimolecular .. . ._----Fg--Wa_r,4teconstant has units of reciprocal time only.

,_--_"_m.. te constant has unit_ of reciprocal eoncentrati0n only .. .. _rate constant has units of reciprocal time and reciProcal concentration - " " -

f -* o,

, 15.Tind kc_, fora'reaction ' in which Vm_ is 7.0 × "10-_ mol.s -1 andthe reaction mixture contams one microgra',m 6genzyme .

(t_te m01ee--'_uar weight ofthe enzyme,is 25,000)'. ___(: _ ,_!0"_ v'_o ;B_ I_)-L_9 }_,0)., ". l_×l _

C)3.57 × 10_ sq •

D) 1.75 x 10-9 s -I ..; "" ' = " - _" ,,"

E) 1.75 X ]09 s-I -. . . ' _ " " _. ", " ._ "m _

k

. _.In the.side cha_z)'ofa glutamine atpH = 2 how many carbons;'hydro_ens, n trogens, and "oxygens" are '" :"" "- -:;_redominantly'6resent?___, _ .. I=-r---- : , - . ,,

i .

,a_)-4--e_bons,.6 hydrogens, 2 nitrogens, and 1 oxygen . ¢ ,_, " : ..

• _¢,. -B)4-e_bons,5 hydrogens, 2'niti'ogens,,and 2 oxygens :, " ;-

L_- C) 3' carbons;,5 hydrog-eris, 1 niir_gen, and I roxygen ' " : .... : '

- -D_..3 carbons, 6 hydrogens, 1 nitrogen, and 1 oxygen - ' . - -. .E)_neoftheab6ve " - -i ' " . , !" '?/'_ :." .' _'

"-iw. ...... ......... . _ch of the followmg IS all appropriate name for the'phospholipid shown below? ; . . " ,': " • _ - ]- "

- hatidylserine - ' " - .:. - . ", H-AA _ A' A_.: :A..,:, ,'_B)_Phosphatid_,lcholine . " . • ' " O H2c----LO C_ v "-_, V -, .

C_'Yh0splaatidylethan °lamine " _c--o ',_ u - _: .. ": ' "

_ldyhnoslto _ . " . " o .... ' .-."_-)-,_l_it]_s!ne " ): " • " " !1 ". "+ "- " ; .

,..'_rol . _ _ _.... -

• ],_ O- ." .: "-- -

g - . ,. -

18. What wa's the fatt 3) acid that was esterified to C1 bfthe glycerol backb'6ne of the phospholipid in # 1_'79 "

' .almitie acid : " " " "

ff_a_. -'_:t:?!^:^ acid ..... '- "C) Stearie acid " _' " ' ' " ".... _ "

, _ricacid "." " " ' " _ " " ":" " " ":( " "" .acid, - ". ."- " . -" .."-,'- .... . .- "'

• ' ,_inolenic acid " _'"_ela{dicacid ". - " " "'" .' : - " "

l_).Whati th opri t sh rth hdzi tatio tth fatty idthat ifi dt C2 ofth glycer I '"s eappr ae o a o ntorepresen e ac was'ester e o e: o

" backboneof thephosph01ipidshown in #'17? , , "" -- , . - . "

-. ,, • , "- .. , . . -

: (,_9) _ , .- .. . - . _.."

! (k . ,.- . , "_

. . _ . . ,

. • . * . • , •

k

20. Which of the t:ollowing best describes the funct oning of the non-voltage gated pot_sium channel?• -. . • -- • • . • - •

•.'_otassium ions readily pass throiJgh in.hydrated form but'not larger', hydrated sodium.ions " : - -

._tassiuni flows through the channel as an ionic compound withchloride ions. - . .-.,,.._ince the' channel is iarge enougl_ to allow the passage of potassium ions it necessarily allows-the passage of the d"

_--__smaller sodium ions almost as readily as pdtasiium ions• : " -' _. ,_ -" . " • "A,, D)_of_assium•ions must give up their sphere of hydration'to pas_ through the channe but compensating interactions _""' ;

: within the_.ehannel more than offset the energetic cost" of dehydrating the potassium ions .... • " " • "n ...... - . _=_otassium Ions must give up their sphere of hydrati0n toi_ass through the channi_l, b t sothum ions are small enough to_

-'_"-pass through with their sphere of I_ycl'ration intact. - _

2 1.'Whichof the following is true about compehtwe m 9 ':

- _ompetitive inhibitors lower the_ of th6 enzyme/ " ..... . °_ "

- "-_-Competitive inhibfiors structurally resemble the substrate and s6 they bind to thg active siti_mid _cbnie-_ " " ;, ,-attach_l to the enzyme .... . . . - \::

(,_ransition state analogs often make better competitive inhibitors than do substrate analogs. " - - .•.- D) P/and C are both true.: " - "_ " •

E) A,B andC are all hue. . : ._ "- " ' """ " '" 'r.

22. Why are glyeerophospholipids callable of spontaneously as_semblihg into the bilayer structure found.in biologicalmemb/anes but triacylglycerols ar6 not? ....... . - "L.-

A) Glycerophospholipids are amphipathic and aggregate into bilayers that can interact.with water on both faces." -".

B)Glycerophospholipids have two acyl chains that align eas!ly side-by-side to form a_bilayer. "" , • _ : -C) Triaeylglyeei'ols are not amphipi_thi c (amphiphilic). ""

- - .LD._Both A andB are true. " ' "_=': - _, :_ _ .• , B and e are true .. _ • - -.. . _-

. , . .o.,. •23: Consider an enzyme that obek,s Michaelis-Menten kinetics• What fraction o_v_ (expressed as a percent3 .would be _.obtained when the substrate concentration was 45 times Kin9Re'port your answer to twoflgures. •' -

• , •

%

h _

. ° ° ... l . , -4

. .- . - . . ... , • j

- . •k- ,_ ° -

L

- °. . . _ .

" 24. When sodium teti'adecyl sulfate (STS) is added to water each detergent molecule is initial y dissj__o_edin the water AS -more sTs i_ added to the w_iter, a point is reached at which the STS molecules form micelles. This criticalmicelle

• concentration is 2.! mM.'The average m61dcular weight of the micelles (the sum of the constituerlt 5_1"Smolecules) is" " "24.300. Given this information calculate the ttumber of detergent molec.le__ in the average micelle. Use enough figures to

adequately convey your answer: For th {problem, you can assume that the sodium ions are not components of themicelles; thus the MW of an STS molecule (minus the sodium ion) is'293'._ma ". . • . ' . _ ' • / _ ' . , "

• , _./_rc_O!. • ., . :. _.. _-,_,._._-_-----_'._ ..... --w_.'z'_.'::: ........

. ' • ','G"_'_'_ X _:Pl___• " " ---'=_-- " _.z=:"L........................ ::._--__ Z--- - ^:_" • .._.....,/..._,o_ ."\ ._ _--_=._._ ___ ....... . -c4X..... ,., . • , r-, .:2 • '_.' _ . •- -

. ' / ; " .L \ " . . . jc_.:_.,-.:, -, .... .- . : . .>• '' " 7" _ .- _-. "D- ' ' " ' : ._..-.-< .. ¢L_. £LI__C_3J/_;_ . . -. . ..... ,:.._,,

"25."A Hanes-Woolf plot expresses[S]/v as a htnction of IS]. Write the M ch'ae s-Menten e6uati0n and reari:an_- ' ".....algebra cally to express [S]/v asa function of [S]. What.doits they-intercept equal (in terms of V_ax,or Kin) in a Hanes- - "Woolf plot?

A) V_,, - B)-Vm_, C)"K_- . D)-Km E)l/V_x . F)-I/V_, '-'- "

: H)-Km/l(m_, ,_ I) Vma_/ LJ)'-Vma,,/K,,, "'". t . .

V_

-" ."" F_.S-3,..

• " .--:: " .. ' - ' '" " "_ -- _¢W,:--S/_/,,;, :,. := _ ." " " ' , ' _s,_' ' ' _"_-'_ _' i

_: ":: 26.C/resider the peptide sh'own on the right. What is . ._£_"_ - " -

the sequence of this peptide? Use the onb-letter code _p_.X" CH_C_"to convey your answer. ,, . .,'_', _: .-:

oo-I,,. H H

• " -" ' . -: ", ' " . Gi. ',-. --..' :27. Draw theproper curly .arrows.(on.the figur e 0nanswer sheet) to correctly_on,bey flt.C,._xt step of the chemical " -mecnanlsm oi cnymotrypsm. _nown In the tl.gure i_ the first t,_fl'_h,.d,'_rltefmexliate that forms and ,,-,,_ ;_,,_h,o,_,,,o .

should c0nveyXhe movement of electron pairs that results ill the eleaw£_ of the oentide boad_ot'the sub_stra_'_i_ the

-. next step ofthe reaction., , " .... ".. . . '" , . _ - . _.-,., . . ,

. ,...... .. . ., . :..,.',,;, _,_, _.,_

•CHEM 3653 Fall 2009 Exani III • Version 1 " Name/ID: _ .

°, • .

Instructions:

l).Write your name (legibly) and y0ur'student ID on this cover sheet and on theanswer sheet.

• 2) You should have a working (i.e., new batteriesi non-programmable, scientific calculator (i.e., no graphing: 'calculators ) and your student ID. You will not be allowed to "borrow" another student's calculator• Any students who ''

do so(bo[h the borrower and the lender} will receive an F on this exam and will be charged with academicmisconduct. • -_

3) No cell phones or any other electronic communication devices such as pffgers, FM receivers, headphones etc.., will "be allowed. Any students who are observed having such a device will receive an F,for this exam and will be chargedwith academic'misconduct subject to sanctions in accordance with the Norman Campus Academic Misconduct Code..

• I rout!nely recommend "F? for the course and e_pulsion fri_m the University for any such violations• . .'; '

, 4) you will record your answers to the exam questions by: 1) writing your answers on the exam and 2) writing

: " your answeus i_n the answer sheet• The answe_ on the answer sheet will be graded, but the work that led to theanswers (which you will recoed on the exam) inay be checked as well. Any discrepancies between the workshown on the exam and the answers written on the answer sheei will be counted as incorrect. Make sure that

the work you record on the exam does in fact lead to the answer that you record on the answer sheet• Anypatterns of inconsistencies will be grounds for aeadi_mie misconduct, as dise'ussed above in #3.

Fold your answer sheet vertically down the center such that your answers are not visible. Keep your answer

sheet folded in this manner at all times except when you ar_e recoeding an answer• - ....

_- 5) When you are done w!th the exam, turn in to the TA the completed exam and the completed answer sheet• Also,show the TA your student ID. Any students who do not follow these instruction.s will receive an F for this exam andwill be charged with academic misconduct as discussed'above. • . ,_.:

2

•i

I.

,_i ,'_ . '. _ - . . , •

'.' "._.-The element iron is located,in whichrow and column of the periodic table? Use the blank pei-iodic table below to help.? ,:_,you,an.swer. _Example: If I wereto ask where in the periodic ' _ " " , ' ._"" , _" table th6 element neon' is'located, youwouidwrii_thehnsv_r i 2 3 4 s .,6 7 s 910 ii 12 ,3 14 Is 16 ,7 is

and"R2Ccolumnl8" to 18.indicatethat .the element., neon is located in row. 2 ._z "" " " "" ' _;t"F]L"

. - 6 ri ' "

•..... " I'.ll -. ." "_ 7 , • r,

.... " " " l ±LtL J, .• . What Is the sequence of the peptlde shown below. Use theone-letter code to report your.answer. , _, , . ....

, .- - . ' /CHz'. ' :

• . .- . , CHa_\ -, . . CHz • . , -

........ - , • .... "" ':_ 'i " - ; "\ .... -- - • " , : . I " - CH2 ' _ . , ".CH z .

,.,- ' ' J.:.•' ',' ...... , .. _ II ' X-.-' I II ..X: • -3. What would be the predommant net charge ofthts 9eptdeatpH= ', _ _C"_ _,'.N _ _C/_ _C_4C_N"_'C_c_'OH

- 0? Enter your answer to twofigures.. - " "¢_ ./.c. _l . • /_ ' I ' II . ,•- - . . - . / 2 ,xH O "H CH20 HH, " ; 'O ' "

' " "'-': ' L:-"} -'" ,'-CH2 " _'- " " " "_

........ . C--OH '•_ . - - ._ . Ioi

. ,. Use the'sU]ucture of the disaccharide shown below to help you answer qu'esti6ns (4 - 6). ;" - .

"'-. "_ " ; • " . , " - : . '" ' " '. " HO" " ; " -

_, ". {,_fthe disacchari'de w_ hydrolyzed to component monosaccharides and the , : _ "' ' " _ "o OH • • ::• . ,_omponent monosacchandes retained thetr configuratmn (Le., d,d not undergo , . , HO._ . _'_,, HO'_. -

", J'y¢'_ .mutarotat!on) tile composition Wouid bei . ' . -, '._ ' , " " _]. _ _q_._"tTL,.,u - ,,'. o , - , . , _ , , * O ' _jt i

._. . ' . . .. :., -'',, ,r , ; . " - " - " t/H.'.'. \1' -. ""., " , ;;" : ---A-)49r_'m01ecule of_LD;glu_bpyrariose.and one moleculec_¢=l_lg-glucofuratldse . ,.--:> __OH \ yj,,.] ;, " . " " "

. ._3_)49r_t_le_Ltle _lucopyrahose and one molecule;e-f-'_O=_-mannofuranose - .- -' H _ i H -: "

/.__)4_-'616cule _a::_g_alactopyranQse and one molecule ofct-D-fructopyranose _.. .... - ', Id . OH _.....

_<_e molecule ofl3_D:-galactopy_'anose and one moiecule o_'&-D-fructop'yranose - 2 " . ' . . -

_e of 13-D-galactopyranose and one molecule oft3.-DZfructop_ranose . q/b_0_ ' " "• '-.-F)One-mole6ule'of 13_D-galactopyranose'and one molecui_ o_-D:_'fructofuranose _

_ olecule of _-D- fructofuranose .. .... , -', leeule actopyranose and one m . _ . . , -:

. ich arro w in e above gt_re points to reduci en " ' :, ., . , .,,* .- .

: B) arrow2, . • -- .- .,,, :. , " '"• ' C__bothai-ro'd 1:andarrow 2 as'both ends are reducing'ends . : " - .

.. Oeither arrow, as _e disaccharide is a n_)n-re_tucing disaccharide. _ ; . .. .

• - "6. The i_6rr6ct description ofiheglycosidic linkage is: - " ' " " .... . ,.

,, "" A) 13(-1--_2).... ; " . _) • _ _ " " " -: _,'.. _ ' " F) 13(1--_3)13 ...... __ " _. :..... / _

• - . • . . , .. . , . .

"7[What is the path of electrons from NADH tl_rough the eiectron'iransport chain?4" " " . "

'. _- i • _ omplexHI,(_ytC,'ComplexlV, O_..f

"" B) NADH,,Complex I, Q, Complex III, CytB, Complex IV, 02 . ? -_.DH; c'-,_p!,e_x:!,-_, Complex I1 CytC Complex IV, 02 "

[. ) __Complex ill;'CytC, Complex Pc, 02 ": :" ".' .... 't' _ _._ ,'-- "" " ". '2, Corot_lex III, CytC, Complex IV,-02 " - .'

T^r_u r_ r_----i.v Ce_p!°y IH, cTtC, Complex IV, 02. ,- < - " "_@ ..... , M ...... r: v'" I

-_lex I;Q Complex II Q, Complex HI CytC Complex IV 02 : -'-..-: "" " "ta. r_,,m,,lo,, T c,..,o_:.._.....c_^--1.=,r.... IlI,' Q, Cothplex IV, O2 : <" " "

i

• , . • • , - . . . - •

8. Corlsider thefollowirig ii has'l_ 'two half-cells: one half-cell (half-cell A) ini al13_ M each of 1 3-bisphospl_oglycerate (I,3-

BPG) and glyee_aldehyite-3-pliosphate.(GAP); the other, half:cell (half-cell B) initial!y has IM eachgf pyruvate m.ad" " lactate. What .... ,o -- i_ the va ue ofAG (m kcal/mol) when the two half-cells are connected by a salt bridge. To answer this

. question you will need the standard reduction potential of I 3-BPG (-0Q:._.2V) and.you will need the standard reductmn

- potentml of pyruvate (-0.185 V). Both half-cell reactmns mv__ns and two electrons. Faraday.s constant.is -

23.] kcal/V.mol. Report your answer to three figures: (':'2_ciV') i )'_''(-" Iq_'_k/:,o"},_j_Q _f_d(..

Z3 - . " .

/-" ;" -_ " " [" " • '" " - "o_ _. " z,._o_ '"

- . , G°'".

9: If,a sample ofa_ that _s labeled m the car_on of the acetyl group:is allowed to condense with• unlabeled oxaloacetate (OAA) and l_roceed through twotums of the Krebs cycle;,then where will the labeled carbon

. _appear inthe resulting OAA molecules? Use the molecule below for the numberinlz_- scheme. : ..-.:."-:_._:':" . . _. '< . " . • , %;-.. -

".,'A_b'nly in carbon 1 of all isolated OAAs " " t_cxO-" ",. : , 0 0 • ,0..... , , . I " _; - _ .I '! " "

B)'only in carbon 2 ofallisolatedOAAs : C--O , ::,11 II . " rll,C) only in cai'bon 3 of all isolated OAAs. " -o_C--C CH_--_C--o-

in carbon of all isolated OAAs • • C:D) o_ly _4z . ,1.... 2 ' .3.. ',4_,-" •• 2E) in carbon 1 of about halfthdOAAs and'in carbon 2 of the other half. " '_COo_. - 1 :

F) in q_rbon 1'of about half the OAAs and in carbon 3 6f the other half. 0x_: _'(_0A. I _7 _'[)_,3/t.0_)- "_ " "G)in carbon 1 of about half ttie,OAAs and in carbon 4 of the other half. ,:

.- IT) in carbon 2 of about half the OA[As and in carbon 3 of the other half. " • - ' ": 'I) In carboh 2'of abdut half the OAAs and in carl?on 4 of the other half. . .:

.,_n c_bon 3 of about half the O'AAs and in carbon 4 ofthe"other half.. D_) _ _L} I/c_ _'h _-_4-'. '"'._._none of the above; the labeled carbon is lost _ CO2 - "' " - "- ' "

Lt

. a'sample.of lactate.that is labeled in th_ second carbon is'allovded to proceed through'gluconeogenesis as the sole

. 7_, ubstrate of this pathway, theia >vhere will the labeie'd carbon appea£ in the resulting glucose-6-phosphate molecules?The

' bold P in the structhre'belo,_, represents a phosphol:yl grou!b.' ' . , " " "_"" _ _ • ." ", , ,

A) only•incarbon 1Oi'all'isolatecl glucose-6-phosphate molecules .. O " • - _'-.. B) only in caEbon 2 of all isolated g!ucgse-6-phosphate molecuies "Y I - '"L.. • .

C) only in carbbn 3 of all isolated glucose_6-phbsphate molecules - '. • . _ (]-_--H. .D) only.in ca[rb0n 49f allisolat'_e]d glucose-6-phosphate fnolecules " • _ ..__'

• _-- H" _E) 9nly in carbon 5 Of all isolated glucosed6-phosphate molecules H 2 0F)'only _n carbon 6 of a isolated glucose-6-phosph'ate molecu es ..

G) in both carb6n 1 and carbb_n2 of all isolated gludose-6-phosph_lt_ molcdules nO3- " ".HH)'i n both.carbon 1 arid carbon 3 oj_hllisolated glucose-6-phosphate molecules 4 ....

I) in both carbon 1 and carbon 4 of all isolatedglucose-6-phos'pllate molecules" P't-7-- --'T'OH :. • J) in both carbon 1 and carboh 5of all i_olated glucose-6-phbsphate molecules _ • i

• -H :_ _---_-oH'_--K_bot-bc_lrbon l'aiid carboh 6 of all isolated glucose-6-phosphat_ molecules "" " • " ".L_n both carbon_2 and carbon 3 of all isolated glucose_-6-phosphate molecules .... " " "-

M) !n both carbon 2 and carbonA of all isolated glucose-6-phosphate molecules 6 CH20P -,.N) in both carbon 2 and carbon.5ofall isolated glucose-6-phosphate molecules <'_ " ; •O) in botti darboii 3 ' " .... " " ": "_and carbon 4 of all isolated glucose-6-ptiosphate, molecules ..j - ,_.,•,

. 1 . . - . , , .

11; In the reoxidati0n of QH_by_,_,blq,_fi.-.o.-.e-cytoch.i'ome c reduclaZse(Compl6x III)'from tieart muscle, tlae ()verall -.

st6ichiomeiry of the reaction requires_c.yt_hrome-e-per mole of QH 2be-_au'sei ... ' .." "_

1_ is a one-electron accep " " " :oc ome c t'or, whereas QH2.is a two-electron donor• . ,. . . . . .. .,

_.is a two-electron ac,ceptor, whereas QH 2is a one-electron donor• • '- - •-

C) cyloulut?me t; i_ water soluble and operates between the inner and outer mitochondrialme'rnbranes. _)- . . - "-"

• _ - - " high rate o_foxidative metabolism, and therefore requires twice as much.cytochrome c as QI_ for

• " electron transfer to proceed norn]ally. . ' " • - . .

_ ,_cuies of 6ytochrome c must first c()mbine physically before they are catalyticallyactive. - • - • • .....

" 12. Almost all of the oxygen (O2) one consumes in breathing is conve_ed.to: :._'? ., . ._ .

A) acetyl-CoA:, " : " : :

B) carbondioxide (CO., -.-

_on'monoxid dthe .... . • -.e an a to carboh _ioxide, " " " " :c .

E) done of the above. ." "

_I¢3;If the pH'ofthe interrnembrabe space is 1.7 units lower,than that of-the matrix 6f mltochondrm, and ffthe membrane ,./'_ potential is01105 V (intermembrane spacepositive relative to matrix), then what is AG (in'l_cal/moi) for'th6trahspo_tof '" ;

one mol'of prot'onsfrom the intermembr_e spaceto _e maiTix? The tetnperature is 37°C, and $ i_ 23. I kcallV.mol."" ._, Enter youranswer to two significant figures ' _. " ,--,t , -i>" _ _ ' '-.,' ,. " • : _'

• . , .< . . • . : :,,

- "- .' .,..' , . . ' '--<" t 7..,..,: / . .._ ' .. , " .'."., - ,. ..

k

_onsider the conveision ,.,t _P/into _ during the TCA cycle• If the Pi used .in this reaction was. b'uniformly labeled With 180 (see below), then how many of the labeled oxygen atoms wouTd end 'u, o "_ate that is

formed in this reaction?L,

(_ne " 18 /.- O 18

• _ B) one.- . 18 [" r_P--O -C) two H ,-.' ..',' D) three .-. • " ,

E) four . . Is 0

Use the figure below (showing the skeleton of glycolysis) to help you answer questions 15 -" 18."

1)15. The compound shown below should be placed next to which number

1)in the adjacent figure? . _ 2 - .

'"- - _ 3) "0_./0 - . _..

. .,))IH-- 13"---..OPOI- 5)

" H 1 6) -

16. The enzyme'gl cy..£e_ldehycle3-pho_nh_*o ,l_hydrogenase2s_t_ld 7)be placed next to which number in the adja6ent figure? _ "

., . . // 8)'x\ ---

• i 7. The conlpound di--dr, :" etone _ho ._ sh_ be placed // _'_

next to which number in the adjacent figure? _ "9) 1ii _' "' --• h "' Ib__-_t'l' ?4 ,.J

- " 18. The enzyme ph_.hosphoglycerate_iaa_shoul_,b_placed flex! 10) |l

to which number in the adjacent figure? ('14_ ']l 12)

• ('_"_". ,_t_---,Cl ,,>_),_ " " " "' 13) L3_,_,-19. If glucose labeled'witl__._ C-3 and C-4 is functioning as'the sole glycolytic source and is ."_,'_%'2c_v-a4,l "

. completely converted to acetyl-CoA via glycolysis and the pyruvate dehydrogenase complex, - .

then what percentage ofth.e aeetyl-CoA molecules thus formed wall be labeled with C, and m'1 14)

which position of the acetyl moiety will the t4C label be found? _ _-_C_< ' 15) 3-_h0,_,...,

A). ] 00% of the acetyl-CoA will be labeled at C-I (carboxy!). IB) 100% of the acetyI-CoA will be labeled at C-2 (methyl). C_=-O -- _/

C) 50% of the acetyl-CoA will be labeled, all at C-2 (methyl). c,_< " II 16)(_0 .label will be found in the acetyI-CoA molecules. 1_)

E)-Not enough information is given to answer this question.

• ;.. 19)

: I 20)

. . . "21)

:. • .: . ... ": . ,-,:.. ' . ..

' " 4033 . '-"• "' .. - - C _-0 __ . ., ,. :

-"20, Oxaloacetate labeled at CI with 14C is added_a'suspension of respirifig'mitodhondria:-What is the fate of the labeledcarbon,'? - '. - " "

• " _is lost as 14CO2 during the second turn of the'cycle after which it yeas added, " o o : " o.

. "_s lost as 14CO2during the first turn of thecycle when isocitrate'isdonverted into c_- '- -o--C c-'r'cH2--c--6-: . . -_"l_etoglutaratel . " • " - " - .,_ 2 - s" . ,,4" _ "

G) It is lost as;14GO2dur(ng the first tum of the cycle when a-I_etoglutarate is converted into' _ (! G-. -" _• succu{yI-Co-A. . " " " " - .

- D);It shows up at C2 ofoxaloacetate after one turn of the cycle. • ' ' • _:0 z "

... :.E) Nonebfthe above , :, : .... : .... . ..

' _'. Con_ide!'the structure shown below. During t_p of the TCA_@cle-reaction of this suhstrate,'.what happens?cy .

_oxylate.attach6d to the carbon:indicated by ('@" is lost as CO2 .. -"- C-H2COO:• _l_he'car6bxylate attached t6"l.hecarbon:indicatedby "*".is'lost as'C'Ov : . [ " "" _

(3) Th,;,,,,.bc_,.yh,_d ,,_.ached to the.carbon indicated by '_'#"is lost as CO2 - : - :. - " .- H =-C .-_, ,GOO_

D) A base abstracts a proton from the hydroxyl that Is attached to the @ • " . . . ] " • . ;. _ carb( m and a hydride is transferred from this carbon to NAD _,, '" " ' " ." ._ HO:_L_-C.,.-:_-H " - "

_transferred from the * carbon'to,NAD* and a base abstracts'" " • _ . ] . :.-" - a proton from the @ carbon. " " " - -' .... " -- " _"': .... . C007 _ •

- " "• 22. Why. does re-oxida.tion of FADH2 via the electron transport chain ultimately produce fewer molecules of ATP than the"

re-oxidation of NADH? --" ,' . : "

.- _, " mpx[ ....:, H do not pfiss through co le I. , _._-_-= ..... thr0ugh7 ple:_ II_sm_.._._,,o=t...... ....... ,_',,2 do not pass corn . ' " .... , ":

• _.._)--A.aar._fFIt gradient is generated when FADH2 is oxidiz_l compared to that generated by th.e oxidation of N_ADH. - "

L- 'D)_._maller'H+ gradient is genei'a,ted when FADH2 is oxidized compared to that generated by the oxidati0n 0 ,NADH. -EyNone of the above• . " , .. , _ . - " f

{Jse the figure(showing theskeleton of the ;FCA cycle) belo_v to help y9u answer questions 23 - 26.'To hell_ orient you ,• "acetyl-CoA shou!d be placed next to # 1 and oxaloacetate should be placed next to #2 in the....figure. " " " " " "

" 23.,The ewzynie malate dehydrogenase shoul/d_placext next to

_ which'number inthe adjacent figure?" t.._7"_)" " " /0 _ ''...2zi..The _nzymatic step.in'_vhich the'decarbo'X?ffation of . ._c_ctt _, ,_ 4) _i_¥c,t_

"an a-keto acid occurs is indicated / / ,3) . " -"

" "'intheadjacentfigure? _'_ " : "16 "/1" " 1[ +( "25. The enzymatic step in which a GTP is formed'is .,_ _. 7) .." " " . • ",_'"• indicated'bywhich number in the adjacent figure. )_,t _.x_t_ . " - " t . 6) i_._oib¢,d.._it '_ _ • . .... • .

26. The,enzymatic step in which the compound shown " " • 1: 7)is an intei'mediate of the reaction? 15) _-a_C_,'-_"" " _ "

O_c'O- " " :'" 14)"_u-_"a"k¢"_ .... " 8)0,"_._l_,. d|_ "

. . .:.. 3) 5.u_c,_ " . .: CH 2 "_ . , -C--CO0 - " ,'_

• ': HC -CO0 , - " :

'"' .... - ",qc.,aq .... " " " .... " _ 11_': " " .... "'" "'

,27. Consider the following metabolic reaction: " - -.

.... r NA1,3-bisp phohos glyce ate .+ • DH IT _ Glyceraldehyde-3-phosphate • + NAD" + Pi _ -

Which ofth-e following statements is TRUE? , "

. . "-+}--Ttti'g'r_ctionis irreversible ih the cell• _ " " - " "'" , _ "5 <,- _ction is catalyzed by an isomerase.

_s reaction proceedsin the opposite direction during gluconeogenesis. . - : . '." wM.2XL,_isi'eaction is _iredox.reaction. " , . " :. " ' --

• A) i, ii, and iii " - " _ " " -" , "B) ii only .. .....

h

") ale " " " " "-, , ;n . • . -,, .-

", ,j •.,

s bs l ph iphor-jlatior/28.Which bfthe following compounds are used in a u trate-leve o reaction? -

,,,,t2_,.aut_e,puolyt:ztc,.dS'-''_'_.L:-:ph'-s:-'_g':.c:ra.:. " ,. . .. . . .": _-6 phosphate'-" ' •

_hosphoenolpyruvate " "• ,._-4a94-ptaosplaoglycerate . .. ,- .

- ? q v) suecinyl-CoA - -• % _ . *

v). . .

' ." 29. Draw'the curly arrows (on the answer sheetl to indicate the movement.of electron pairs during the next step of the

' "-""_ reaction _ofthe intermediate stiown in the figure.° " , ....

-, 30 Draw.the curly arrows (on the answer sheet) to indicate the movementof electron pairs during the ne:<tstep ofth6 ....

reaction, of,.the compound;._ i ,..,sh°wn_inthe. figure such.•.'ihat the glycolytic., product.:,. is,..produced.r_. ,: .... - -.

. , . . o . ,

y .•o .. . _ • • - ^

1

• - _ . • "7 . . ,

. . ° •

• . ,- .

- : "i _ , - .

• '.[

Matchlng'Questions: Use the following to answer questions I-I0.

Choose the letter adj_tcent to the correct answer from the list below• Some answers may be used more'than once, and some

• answers may not be used at all. Write the letter that is adjacent to the correct answer in the space provided next to eachnumbered statement or question, and enter the same letter into your PRS clicker for the appropriate question.

A. Linus'P ufing '. " ' . ' ' "G. Oswald Avery M: Glycerol" "B. 2*d Law of Thermodynamics : " H. Rosalind Franklin N. Jacques Bardeen ,• ,, ' C. Frederick Sanger . " '" I. Max Pemtz O. Glyceraldeh}de

•, D. I't La w Of Thermodynanl.ics , J. John •Kendrew P. Pyruvate

E. Catabolic Reactions . K. 3'0Law of Thermodynamics . Q. ot-ketoglutarate

F, Francis Crick L. Javier Papeo R. Glycerate

"' ,'1 _/f . : ,.• This scientist obtained the X-ray diffraction data that led to the discovery, of the double helical'nature'of DNA.

2D Th." isconlpoundisthereferencecompound fortheD-L systemofnomenclature.

: ". 3._" Thisscientist(alongwithc0workers)demonstratedthatDNA was responsiblefortransforminga non-virulentstrain.of Staphylococci nto a virulent strain'. - _

i• ' 4. Stat at the tota. entrop3 of a system.plus that of its surroundings 'always increases.. ,_ ) ,

;_._ 5. '_" This scientist was a memberof the team that elucidated the double helical nature of DNA, and he _,ent on to propose"9".- . . that an adaptor molecule should exist to carry aminoacids onto what he called the template but which we now call

mRNA. ..

6' • na1 _

This compouis. an intermediate of the TCA c_'_:le and it is a transamination "'cousin" of the amino acid glutamate.

., 7. ,_ This _ciendst won the firSt,of lais two Nobel, Prizes for his/her effo_s (and that of his/her co-workers) in determining"' tile mnino acid s(_quence of bovine insulin. •

t> itha' 8. States t the total energy of a'system and its surroundings is constant.

• 9. -- This.scientist (along wi_ co-workers) used X-ray crystallography.to determine the structure of myoglobin.

f :nil a p lyhydr y n'atoms. "10. • s compound is o ox alcohol and contains three carbo

Mu|tiple Choice Questions Circle the letter that is adjacent to the response that best answe'rs each qiJesfion,'.and • .

-_ent_r the's_ime letter ifito your PRS clicker for the appropriate question. . ....

• |' - " : ..... • . 2f_.ld_. "

I . Pbospbonc acid _s mbas_c, with pK, s o _j, 6.86 and 12.4. The_.ie_,-m that p_:edominates, at pH _2 is: "'-

"A) H3PO_. -' . : • " . -'

B..--,.__._)

D) P0,3-.E) tione of the above.

,_ 12.. A s_It_¢nce of amino acids m a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably t)art of

L)¢:ca(n): " . . , _ l " " . .b_,_' : " , A) , antiR ,m'allel _ sheet._ .• t B) parallelpsheet. , . . . " "D_ 14 " I_

".B_r,s-heet. '"

E) '[_turn. 7 "-

t .

• _ ..,_. • , . , , .. .' ._ -.:,

13.,Which of the following best describes th_ m:ra_agement of amino acid side chains iti an Mpha helix? ....i

•'A) The side chains point outward away from the helical axis ........ =::. _"5_ _) The stale.chains point nward toward the center of the hehx. /_ -'" - _-

; ('IV r,C) The sidechains point toward the N-terminal _nd of the helix• " ',-

x_. _e side chains point towafci,the G-terminal end of the helix • ,• . . , • _.• E) The side chains point toward the' nearest beta sheet. _ ,: - --

14. Which of the following statements is false?

, , b . . .

'A) Collagen is a protein in which the polypeiitides are mainly ifithe _-helix conformati6n. " " • :"'. :, B)'Disulfide linkages are important for-keratin structure. ... _ " ,

C) Gly residues are particularly abundant incollagen. : . '.-

D) Silk fit) i h th lyp al ly" the I_C fo 'rma " • " ". _ ru!.n, s a protein in-whic e.po eptide is most entire in on tiom _ .: ._. _ --'_-;,E) lyi,i,ad l_ 9 h onfo_m'-' (x-keratin is a protein in'which the po e es are main in e (x- elix c ation. -- , . .

, 15. The'm01ecular geometry (i.e., shape) of a water molecule is , -

D) pyramidal . " " - "E) tetraliedral .

-. 16. Cbargaff's rules state that in typical DN._: . . .... • " " " " "

-- -B)A=.C._- ,:. """ " " _ _.__= [ " " _ "

•- C) A__J-L---_ ...... c_-r C. -:: :o_

17. Side chains of amino acid residuesthat are pali of a _-strand project ", - --, . • * • . ° -

" ., C ,, •

A) in a _nanner parallat4a.tha.tah_e of'the strandB) uniformly abofe_ the plane in the N=to-C direction _ " " - ' " " :"

•C) un.ifo_fily,bel0w.the plane•_n the N-:to-C direction " . " -_•@alt6ruatel _ gb_ve and below tl3e plane of _e strand:E) None oftheabove " ...- .. " . ."

, 18.,Th_ one=letter code for the amino acid Shown on the _ght i_"_"--_ " ' ,

(l", I. )-- ' " "-"

fl--C--OH . :D) Y.., " "'" l " " ".... "• :

" E) None of the'above ;" CH_ . ..

!" j

19. The threeylet_r (:ode for the amino acid shown 6n the right_ ..... •' A, Ser ' , ..... " L.'._!__N - -- -

E) Thr". . ,.. .... o-I_ , . . " ..... •

- i., ....,.- - ._,.., , , . : ...... '_ .... • .... . .-

• : i:20. In the side chain only of a t_pJ.oNa_ at pH =_7. how many carbons, hydrogens, and nitrogens Ere pi'edominaritly present?

_ns,,8 hydrogens, and 1 nitrogen , . " '"•' _L_:_=l_ns, 8 hydrogens; and 2 nitrogens "-, _ [-_-7-_) . . . ,- •

c_ carbons, 8 hydrogens, and 1 nitrogen_ : ..... ':-. -. -- t , ". i i:"D),9 carbons,'8 hydrogens,_ogens • . _ .E) 9 ca[bqns 9 hydrogens, and 1 nitrogen - _ • •F) 9 carbons. 9 hydrogens alJ_)_Irogens -. "'G) None of the above "•

21 - 25. Multiple ei)mpletinns: A question or incomplete 21. Which of.the following compounds is/are vdlid representationsstatement'is followed by four'numbered completions, one or n)ore of the enol form of guanine? .....

_0f ;,vhich are correct. Select, OH .. NH2 -

A) if only # I is correct I) if 2 and 4 are correct . • N N . - _B) if only #2 is correct J} if 3 and 4 are correctC) if only #3 is correct " K)'if 1, 2, and 3 are correct : OH "

t . . •

-', D) if only #4 is correct r .L) ifl, 2. and 4 are correct . 2, < H ' ' •,E) if l and 2 are correct M) ifl. 3, and 4 are correct I. H • ""

OH;" " . tF) if 1 and 3 are correcl N) if 2, 3, and 4 are correct - NH2G) if'l and 4 are correct O) if 1..2, 3, and 4 are correct ' •

- ; It) if 2 and..3 are correct , PI none of the above is correct // " _ " ' _

• . " " " - N H2• " OH.-_ ". 3. H 4. .i .

23 Deamination of cytosine i-esults it[ which of the following _ :• , - 22. Which of the following bases are found in_?" _" compounds? . . .

. I ..... L H -'"1. H . 2. H "" .... .2, '

.. t ..... O - : " - O+0 - "0 . ,_

N NH " - . NH ; NH " ., .

• 0 " _" , -- + "

¢, 3. H: 4 H - - 3., H 4 ," H ,

- t ; .

-24. :Which of the following amino acid(s) have nonpolar side 25. Which _:hoi6e (or choic_es] listed below p)'ovides al) accel_tablech/fins? • description'of the coml_imd shown below? ' -.

. _ ,. " I. It is mi L-araino acid " " " H

"/I_ 0 "" 2. It is a Diamino acid, • 7_O._?00. _- ( 2. isoleucine _ • . .- 3.1t has the R--configuration Hs . - .

3. alanine \ _/ _ 4. It has theS-cofifiguration •

" \ 4. phenylalanind " '..... -. -_,." ' " " " , ' - ""' .s , _-NHz ..

Mixed Bag_ problems, True or False,Short Answer _"

• " " " " '9 * " -I0" 26. _,(ssume that an ethanol molecule (CH3CH2OH) is spherical. What is the thameter of this sphere m A._(I_ A = 10 m; the

" • .rn01ecular weight of ethanol is "46.07: the density of ethanol is 0.7893 g ml_-ti•and the.volume of a st)liere. _is_4m'_/3). Report. -"" : • your answer_to three significant figures."

' 27. True or false. Hydrophobicinteractions p_ii_arily aredue to the thermodynamically favurablg association of noupolar ._.:.molecules with other nonpolar molecules and,not to entropic effects of liberating water molecules to the bulk phase: Write T ."or F_below and enter T or F mto your PR S chcl_er. . _ "_ - • . • ". _-_ _ " :

28. If the reside of a Cubulo cubulous cell contains •7.0 x 10 fructose molecules, what is the molar 6oncerilr_/tio/|of... fructose" in the bell? Assume that aC. cubulous cell is cubical and has sides 1).1 I.tm long. Report your answe¥ to tl@ee significanl

,,,sures. ... -.. . ,.L. . . .o. ,

z .:

•-"29. A weak acid HA is 0.1% ionized (dissociated) in•a 0.2 M solution• What is the pK, of tl_s acid? Report your answer to :• t'_o siguificimt figures..

• 30. A _,eak.acid HA is 0.01% ionized (dissociated) in a 0.2 M solution. Wlaat is the pH of.this solution? Report.yuar answer _ •to two siguificantfigures.- '.... ' - - .

2 31. For _e glycolytic reaction shown below, AG°''is reported to be 0.4 kcal/mol, and AG _s reported t? Ix__ 6 kcal/mol .-, .- Given this |iif6rmation, what is the reaciion quotient Q (i.e., raiid'of t'ruciose-6-phosph_,te to glucoseS-phosphate)in the cell? "

_ . Tbe gas 6on}tant is_1 987 cal/K-mc d. Assume a temperature of 25_*C. Report.your answer to three significant figures. _.....

r _,- -,r--r----_ducose-(i-nhosnh@e""¢_" fructose-'6:phosnhater ' " "

i

q

-i

" " , :32.What is the" approximate molecular weight of a.proteiu cooiaifiiog 350 amino acids? (Assume thei'e are no other protein _modifications.) Report };our answer to five digits.. " •" ' "

• ._• . . . .

: _ ' 33. The t_o PK, s ofalanine are 2.3 and 9.7. At pH 10.0, what percentage of the alanjne moleculesare in the _,witterionic '. .S. _'_._..._f,_r,_,9_..._t:-_'ryour answer to two si,,_ificaW fioures: " ' " "" • • : ' • " ' - . " "

.' peptid " " " _ " ' fthis" a_ pH " ': "....-__ 34 A e has the following sequence: GEDLKA. What isthe predominant net charge o peptide t. ---12? . ' --

L " . t " ,

35. Use the foUowing information to determine the sequence of an oligopeptide. (i) complete hydrolysis in 6 M

HCI at 100 °C followed by amino acid analysis indicated the'preset_ce of Gly; Leu, Phe, and Tyr in a 2:1:1:1 molar

ratio; (ii) treatment of the peptide with Sanger's reagent followed by complete hydrolysis and chrom_itograpliy

indicated the presence of the 2,4-dinitrophenyl derivative of t_crosine, with no free tyrosine detected; (iii) complete

digestion of the peptide with pepsin (cuts at the N-side of Phe, Trp, and Tyr residues in peptides) _,ielded a

• dipeptide cgntaining Phe and Leu, plus a tripeptide containing Tyr and GI3, in a 1:2 ratio. Report your answer usingth'e one-l&ter code• -.

p . .

. . " " " " help answer the following" 36 -_40. Use the accompanying figure of the titration curve for the amino acid glutamate to

question_ (Hint: it will be helpful to ask yourself what glutamate "looks like" at various points along the titration curve.• Drawings may help in this regard.): _"

36. What is.the average net _:harge of ghitffmate at pKt? 10 Glutamate - °_9__.

"" 37. What is the average net charge of glutamate at the' 8 :::- " ' ' ..... :.. _.. :'j(,;i •.• point on the curve midway between pK "and pKa? " :" [ "

• . average -. _--- '58. What is the net charge of glutamate at pKR? pH ./1"

39. What is the average net charge of glutamate at pKz? 4 7pt_7-"--7--_/ -

40. What is the pl of glutamate? Report your answer tO three " 2 ;_ - I .significant figures. ' '. .

0 t .0 2.0 3.0

', ' . , , ; . " . " OH- (equivalents" i,_

41: True or fa!se. The object shown on the right has four-fold rotational symmet_. Write T or F I:)elow, " _

and enter T or F into your PRS clicker.

' 42. ff you wanted to synthesize a peptide that had the sequence GADVH using a solid-phas e approach, which residue would '/you attach or add to the reactive resin to begin your synthesis?use the one-letter code to record your answer.

43. In solid-phase synthesis, which part of the amino acid attachesto the reac'tive resin?Write and enter "C" for 0t-carboxyl,

"N" for ct-amino, or "R "rfor side chain. ..

. 44:'In solid phase synthesis, when a new residue (s to be added, it must have =ts group acUvated. Write and enter, C .1 for (x-carboxyl, "N" for iX-amino, or 'R for side chain. , . t,

451 Tree or false. The Meselson and'Stahl density g/adient-centrifugation experiment demonstrated that DNA replica_tion was"

(:onseryative such that daughter DNA molecules;base-paired'with each other and parental DNA molecules reformed'their" '

• .original base pairs with each other'afier replication. Write T or F below, and enter T or F into your PRS clicker•

46, Tree or false.In the In-stround of Edman'degradation, the C-terminal amino acid is labeled and then released from the

rest of the polypeptide. Write T or F below and enter T or F into your PRSclicker. "- , • . .

- 47. Tree or false. A cross-sectional view of a typical, globular protein (e.g., myoglobin) shows that many of the interior

amino acids are polar or charged. Write T or F below, and enter T or F into your PRS clicker• .

48. True or false. In bothRNA and DNA synthesis the phosphodiester bond is formed when the 5"-hydroxyl at the terminus- ,of the growing chain _ittacks the innermost phosphate of the incoming nu_leoside (or deoxynucleoside) triphosphate. Write T

o_rF below, and enter T or F into your PRS clicker• • .

• , • . . •