Elements of Biochemistry I

Transcription

1 Elements f Bichemistry I CHEM 2770 & MBIO 2770 Je O Neil Tel: Parker Building Je.ONeil@umanitba.ca Office Hurs: Open Lectures: Mn, Wed, Fri, 12:30-1:20 in EITC Tetbk: "Principles f Bichemistry, 5th editin" by: Mran et al. Available in the Bkstre and als used fr CHEM / MBIO Curse www site: Cntains ld eams. Curse ntes will be psted there. 1

2 Labratry: The labratry manual is available in the bkstre. Lab cats and safety glasses are required. Mnday Afternn Lab please reprt t any Bichemistry lab in Parker (406, 416, 422). Tuesday Mrning Lab please reprt t either rm 416 r 422 Parker. Friday Afternn Lab please reprt t rm 406 Parker. Evaluatin: Labratry: 25% Mid-Term Eam Tues. Octber 25 6:00 7:00 PM: 25% Final Eam Set by Student Recrds: 50% All lecture material is eaminable. Study the ld eams. Read and Study! 2

3 Yu will find sme advice n studying in the fllwing article: Retrieval Practice Prduces Mre Learning than Elabrative Studying with Cncept Mapping Jeffrey D. Karpicke, et al. Science 331, 772 (2011); The article suggests that memrizing is an effective way t learn. See als Malcm Gladwell s bk Outliers that prmtes the 10,000-hur rule. Fig. 1 Results f Eperiment 1. J D Karpicke, J R Blunt Science 2011;331: Published by AAAS 3

4 IN THE CASE OF A FIRE ALARM: REMAIN CALM IF IT IS SAFE, EVACUATE THE CLASSROOM OR LAB GO TO THE CLOSEST FIRE EXIT DO NOT USE THE ELEVATORS IF YOU NEED ASSISTANCE TO EVACUATE THE BUILDING, INFORM YOUR PROFESSOR OR INSTRUCTOR NOW!!! IF DURING A BUILDING EVACUATION YOU NEED TO REPORT AN INCIDENT OR A PERSON LEFT BEHIND: Ø CONTACT ONE OF THE BUILDING FIRE WARDENS OR Ø CALL SECURITY SERVICES DO NOT REENTER THE BUILDING UNTIL THE ALL CLEAR IS DECLARED BY A FIRE WARDEN, SECURITY SERVICES OR THE FIRE DEPARTMENT Student Accessibility Services Vlunteer Nte-takers Needed! If yu wuld like t vlunteer, and receive a reference leaer fr yur Bme, please lgin t JUMP and click n the Student Accessibility Services link. Vlunteering is nw easier than ever, yu can uplad ntes directly t JUMP in the Student Accessibility Services scheduler. Thank yu! 4

5 Chapter 1 The nature and structure f cells. Unifying principles f Bichemistry fr yu t review. Animal Cell Plant Cell We will address what is knwn and hw we knw it. The latter is ne purpse f ur labratry. Rat muscle cell actin. Human endthelial cell micrtubules. 5

6 Bichemistry Bis = life Greek al kimya = the transmutatin Arabic Chemistry eplains change using atms. All chemical change invlves rearrangements f electrns. Bichemistry eplains life in terms f the atmic structures f bilgical mlecules and their reactins. What is the scale f life? Where d we fit in the universe? Size Universe m Redwd Tree Human 110 m 2 m Ant m Human Skin m Red Bld Cell m Largest Virus Cell Membrane Thickness f DNA Water Mlecule C-atm Atmic nucleus Prtn m 10-8 m m m m m m Electrn m Plank Length m scaleftheuniverse.cm 6

7 The Bichemical Peridic Table: Lynda Ellis and Larry Wackett,University f Minnesta, Bimlecule % in E. cli Prtein 15 Nucleic Acid 7 Carbhydrate 3 Lipid 2 Water 70 Other 3 The Bisphere cntains abut different species ranging frm single cells t cmple animals. 7

8 New Species f Mammal Discvered in 2013 Giant Sundew (Drsera magnifica). A carnivrus plant All life uses the same types f bimlecules and all share sme cmmn metablic features. This suggests a cmmn ancient ancestr. Variatins n a Theme Change = Chemical Reactins Synthesis and degradatin f bimlecules and ther transfrmatins assciated with life. 8

9 Metablism: An rganized netwrk f reactins ccurring in cells. E. cli cntains abut 1000 metablites intercnverted by abut 2000 enzymes. Catablism: Reactins that degrade nutrient mlecules yielding energy. Anablism: Reactins in which cell cmpnents are assembled frm small mlecules and energy. There are 5 different types f bichemical transfrmatin invlving bnd frmatin r breakage: 1. Grup Transfer 2. Internal Rearrangement 3. Cleavage 4. Cndensatin 5. Oidatin-Reductin Bnd strength depends n the prperties f the atms including: 9

10 Electrnegativity: A measure f the ability f an atm in a mlecule t attract electrns t itself. H 2.1 C 2.5 N 3.0 O 3.5 P 2.1 S 2.5 Saturated Hydrcarbns mlecules with mstly C H and C C bnds. They are als called aliphatic. They are nn-plar r nly slightly plar because they share electrns equally. In cntrast, the cvalent C O bnd is plar. δ + C O δ - Recall that cvalent bnds invlve sharing pairs f electrns. Bimlecule reactivity is fund in functinal grups that have plar bnds. C=O Carbnyl, Carbyl H S Thil = Sulfhydryl H O Alchl, Hydryl P O Phsphate, phsphryl H N Amin 10

11 Bichemical Functinal Grups Nuclephiles: Bichemical Functinal Grups Electrphiles: 11

12 Nuclephile Reactivity Nuclephiles: Electrphile Reactivity Electrphiles: 12

13 A lt f bichemistry happens when nuclephiles meet electrphiles. Arrw Pushing Nuclephilic Additin This is a Grup Transfer. 13

14 Nuclephilic Substitutin Anther Grup Transfer. Cndensatin 14

15 Thermdynamics All living rganisms require a surce f energy t live and grw. 1 st Law f Thermdynamics: The energy f the universe is cnstant. Energy is the capacity f a system t d wrk r release heat. The units fr energy are Jules. There are many frms f energy: Kinetic Energy is the energy an bject has wing t its mtin. Ptential Energy is the energy an bject has wing t its psitin in a field; e.g. gravity, electric, magnetic. H is enthalpy, the heat energy f material at cnstant pressure. Heat is the transfer f energy frm a regin f high temperature t a regin f lw temperature and assciated with the mtins f atms r mlecules. 15

16 Even thugh energy cannt be created r destryed, during a physical r chemical change, energy may change its frm. In the picture belw, the ball at rest has zer kinetic energy and lts f gravitatinal ptential energy. The falling ball cnverts its ptential energy int kinetic energy. When it strikes the grund, the ball cnverts its kinetic energy int heat, warming the ball and the grund and the air arund it. It might als d wrk e.g. squish a bug. At rest, all the ptential energy and kinetic energy have been lst as heat. The ttal energy in the whle system (ball, air, bug, table, grund, etc.) is unchanged but it can intercnvert frm ne frm t anther. PE + KE = cnstant. 16

17 2 nd Law f Thermdynamics: The entrpy f the universe increases. Entrpy S, is a measure f the disrder f a system. It is the tendency f energy t spread ut ver time. Units are Jules/Kelvin. A ht frying pan spntaneusly cls when placed in cld water, and the water heats up. This is because the heat is mre randmly distributed between the frying pan and the water afterwards. Anther eample: At rm temperature, ice spntaneusly melts, beying all the Laws f thermdynamics. H 1 < H 2 ice liq water Energy Level Diagram H 2 H H 1 Reactin ΔH = H 2 H 1 ~ +6 kj / mle Clearly, ΔH is nt a gd predictr f spntaneity. 17

18 Cnsider a spntaneus change in which ΔH = 0. The gases mi spntaneusly and irreversibly but there is n change in the energy f the atms. The degree f disrder, entrpy increases spntaneusly. By cmbining the 1 st and 2 nd Laws we can predict spntaneus change. G = H TS Gibb s Free Energy, G, is the energy available t d wrk at cnstant temperature and pressure. Think f H as the ttal energy f the system and TS as the wasted energy then ΔG is the useful energy. The greater is H, the mre wrk can be dne. The smaller is S, the greater is the rder, the mre wrk can be dne. Hw much wrk is available in transfrming a system frm G 1, H 1, S 1 t G 2, H 2, S 2? 18

19 e.g. glucse à water and carbn diide G 2 G 1 = H 2 H 1 T (S 2 S 1 ) ΔG = ΔH T ΔS In a chemical change: ΔH = H C + H D (H A + H B ) If ΔH is +, heat is absrbed Endthermic. If ΔH is, heat is evlved Ethermic. (ice melts) (glucse idatin) ΔS = S C + S D (S A + S B ) If ΔS is +, disrder has increased. If ΔS is, rder has increased. ΔG = G C + G D (G A + G B ) If ΔG is +, free energy is absrbed: Endergnic. G must have been added t the system. This will nt ccur spntaneusly. If ΔG is, free energy is released: Eergnic. The reactin is spntaneus. 19

20 ΔG = ΔH T ΔS ΔH ΔS ΔG + spnt. + + nn-spnt. + +???? The 2 nd Law states that ΔS universe > 0 But, as cells grw ΔS cell < 0 D living cells defy the laws f thermdynamics????? N! Cells remve G frm sunlight / nutrients in their surrundings, decreasing the rder in their surrundings, increasing the rder within themselves. S all laws are beyed. ΔS univ = ΔS cell + ΔS surr > 0 But where is the energy in glucse? Mlecules cntain internal energy. This includes kinetic energy f vibratins, rtatins, and translatins f the mlecules and the ptential energy f the electrns in chemical bnds. 20

21 Fr the reactin in a clsed system, the reactin will prceed until equilibrium is reached, after which, n change will ccur. This is the Law f Mass Actin. Equilibrium can be described by the equilibrium cnstant. K eq = [C] [D] [A] [B] The reactants and prducts are driven t equilibrium by free energy changes. They spntaneusly fall dwn the free energy hill tward equilibrium which is their lwest free energy state. The relatinship between free energy change and equilibrium is given by: ΔG = R T ln e (K eq ) R = Gas Cnstant = 8.31 J / ml. K. T = Temp in K. If K eq = 19 at 25 C then, R T ln(k ' eq) = (8.315 J/ml K)(298 K)(ln19) = 7,296 J/ml = 7.3 kj/ml We will discuss this realtinship again later in the curse. 21