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BIS103(001)

Abel

Biological Sciences BIS103-001 Winter Quarter 2007(CRN 35498)

Lectures: Tuesday/Thursday 3:10 – 4:30 p.m. (Social Sciences 1100)

Lectures will be recorded as MP3 files and uploaded to the class website (podcast). Media Equipment Service (2-3553).

Instructor: Dr. Steffen Abel, Associate Professor Phone: 752-5549 Email: sabel@ucdavis.edu Office Hours: Fridays (9-11 am),

Location: 210 Asmundson Hall (Office); for larger groups of students, 242 Asmundson Hall (Conference Room).

Other appointments are available upon request. Teaching Rebecca Shipman Email: rlshipman@ucdavis.edu Assistants: Office Hours: Tuesdays (2-3 pm) and Wednesdays (9:30-10:30 am)

Location: Asmundson Hall (Conference Room Annex, 2. Floor). Stephen Abreu Email: sabreu@ucdavis.edu Office Hours: Tuesdays (12-1 pm) and Thursdays (12-1 pm) Location: 139 Hunt Hall

Text: One of these three textbooks is REQUIRED:

• Biochemistry by Garrett & Grisham • Principles of Biochemistry by Lehninger, Nelson & Cox • Fundamentals of Biochemistry by Voet, Voet & Pratt

Booklet: A collection of visual aids specifically prepared for this class is avail-able for purchase at Campus Books, which you need to bring to every lecture. However, this booklet does not substitute for one of the required textbooks!

Class Websites: MyUCDavis (BIS103-001) Go to The “Real” BIS103 Website (http://www.plantsciences.ucdavis.edu/bis103) Exams: Your final grade will be calculated based on your performance in three

examinations: Midterm 1 (33.3%), Midterm 2 (33.3%), and the final test (33.3 %). Parts of the final exam will be cumulative. Regrade requests for midterms must be submitted in writing within one week after return of the tests and will only be considered if you have used permanent ink during the exam. Exams will be given at the assigned times only! No early finals will be given! Exceptions may be granted to students with documented verifi-cation of personal loss or sickness and if the instructor was contacted before the exam.

MIDTERM 1 Tentative: Thursday, January 25 (in class) MIDTERM 2 Tentative: Thursday, February 22 (in class) FINAL EXAM Tuesday, March 20, 8:00 - 10:00 a.m.

Class Context Class Context

General and General and Organic ChemistryOrganic Chemistry

BIS 102BIS 102 ““StructuralStructural”” BiochemistryBiochemistry (carbohydrates,proteins, lipids, nucleic acids, enzymology)

BIS 103BIS 103 ““FunctionalFunctional”” BiochemistryBiochemistry (intermediaryor primary metabolism)

Thermodynamics, redox reactions, nucleophiles, electrophiles, major organic compound classes,chemistry of carbonyls

Nutrition, Microbiology, Human Physiology, Neurobiology, Exercise Biology, Plant Biology, Pharmacology, Cell Biology,

etc.

• How is chemical energy stored?

• Why is there a need for metabolism?

• Directionality of metabolism

Gibb’s Free Energy (ΔG)

Reduction Potential (ΔE)

Lecture 1 TopicsLecture 1 Topics

One Reaction

Fuel or Food + O2 CO2 + H2O + ΔU

John Candy’s Metabolism

Many Reactions

Regeneration ReproductionCarbon Chemistry

Food

Action

Fuel Energy

Energy

Fossil FuelsFossil Fuels

Exhaust (COExhaust (CO22, H, H22O)O)

ΔU = q (Heat) + work (PΔV)

ΔU

HydrogenHydrogen

Chemical(Potential)

Energy

Chemical(Potential)

Energy Food Food

COCO22, H, H22O O

ΔΔU = q (Heat) U = q (Heat) + work (P+ work (PΔΔV)V) = = ΔΔH (Enthalpy)H (Enthalpy)

ΔΔH H ““trappedtrapped”” as ATPas ATP

In intact cells, P and V are assumed to be constant In intact cells, P and V are assumed to be constant

IntermediatesIntermediates

What is the purpose of metabolism?What is the purpose of metabolism?

• Provides building blocksbuilding blocks for regeneration/growth

• Energy conversion compatiblecompatible with C-based life

• Provides energyenergy (motion, transport, syntheses, heat)

All life forms areAll life forms arelikely based onlikely based oncarbon chemistrycarbon chemistry

Energy required to break a bond ((++ΔΔHH)

Energy released during bond formation ((––ΔΔHH)

X Y X Y+ΔH

–ΔH

How is energy stored? In chemical bonds.How is energy stored? In chemical bonds.

Bond Energy ~ Bond StrengthBond Energy ~ Bond Strength

The strength of a chemical bond depends on:

• relative electronegativitieselectronegativities (affinity for electrons)• distance of electrons from nuclei• number of electrons shared• nuclear charge

Table 1: Table 1: ElectronegativitiesElectronegativities of Biologically Important Elementsof Biologically Important Elements

Hydrogen (H) 2.22.2 (P) Phosphorus

Carbon (C) 2.62.6 (S) Sulfur

Nitrogen (N) 3.0

Oxygen (O) 3.4

p. 2

HH HH

HH OO

HH HH

HH OO

+ 436 kJ/mol

+ 463463 kJ/mol

– 436 kJ/mol

– 463463 kJ/mol

Bond

kJ/mol Bond kJ/mol Bond kJ/mol Bonds kJ/mol

C-H 413 C-S 259 C-N 293 C=N 615 C≡N 891 C-C 348 C=C 614 C≡C 839 C-O 358 C=O 799 C≡O 1,072 O=C=O 1,598 H-H 436 H-O 463 H-O-H 926 N-H 391 N-N 163 N=N 418 N≡N 941 N-O 201 N=O 607 S-H 339 S-S 266 S=S 418 S-O S=O 523 O-O 146 O=O 495 P-O 599

p. 2

Table 2: Bonds of Life (Enthalpies of Chemical Bonds)Table 2: Bonds of Life (Enthalpies of Chemical Bonds)

ΔΔHH of a reaction is the sum of bond energies sum of bond energies

consumedconsumed during breaking of all reactant bonds

andand of bond energies

releasedreleased during formation of all product bonds.

If ΔΔH > 0H > 0: EndoEndothermic thermic reactionIf ΔΔH < 0H < 0: ExoExothermicthermic reaction

A + 2B A + 2B 3C + D + 2E 3C + D + 2E

Example: Ethanol combustion/oxidationExample: Ethanol combustion/oxidation

C2H5OH + 3O2 2CO2 + 3H2O

O=C=O

O=C=O

O-H-OO-H-OO-H-O

O=OO=O

O=OH-C-C-O-H

H H

H H

ΔH = –1,255 kJ/mol (exothermic)

Cracking all bonds (+Cracking all bonds (+ΔΔH)H)(kJ/mol)(kJ/mol)

3,2343,234 1,4851,485

4,7194,719

Forming all Forming all newnew bonds (bonds (––ΔΔH)H)(kJ/mol)(kJ/mol)

–– 3,1963,196 –– 2,7782,778

–– 5,9745,974

Other ExamplesOther Examples

ΔH = – 2,639 kJ/mol

C6H12O6 + 6O2 6CO2 + 6H2O

GlucoseGlucose

2H2O

ΔH = – 485 kJ/mol

2H2 + O2

H HH H O O HHHH OO

HHHH OO

““Fuel ValuesFuel Values”” of some foods and fuels (kJ/g)of some foods and fuels (kJ/g)

CarbohydratesCarbohydrates 1717

ProteinsProteins 1717

LipidsLipids 3838

WoodWood 1818

CoalCoal 3232

Crude OilCrude Oil 4545

Hydrogen Hydrogen 142142

Good molecules for storing energy:Good molecules for storing energy:

carbon polymers, hydrocarbons, hydrogencarbon polymers, hydrocarbons, hydrogen

-C—C—C—C-

HHHH HH HH

HH HHHHHH

“Harvest” hydrogen and transportas a “biologically safe” form

NADNAD——HH ++ HH++

O=OO=O

HH22OO CCOO22

Most Most ––ΔΔHH(ATP)(ATP)

CarbohydratesCarbohydratesProteinsProteinsLipidsLipids

Metabolic OxidationMetabolic Oxidation

““High EnergyHigh Energy””SubstratesSubstrates

“Low Energy”Products

CatabolismCatabolism

CellularCellularMacromoleculesMacromolecules

AnabolismAnabolism

IntermediatesIntermediatesPrecursor MoleculesPrecursor Molecules

ΔΔHH(ATP)(ATP)

ΔΔHH(ATP)(ATP)

MotionTransport

Heat

FOODFOOD

Waste

• How is chemical energy stored?

• Why is there a need for metabolism?

• Directionality of metabolismDirectionality of metabolism

Gibb’s Free Energy (ΔG)

Reduction Potential (ΔE)

Lecture 1 TopicsLecture 1 Topics

Gibbs Free Energy (Gibbs Free Energy (ΔΔG)G)• ΔΔGG = = ΔΔH H ––TTΔΔSS

If ΔG = 0: System is at equilibrium

If ΔG < 0: Exergonic (“downhill” process)

If ΔG > 0: Endergonic (“uphill” process)

• Process can be driven by ––ΔΔHH, ++ΔΔSS, or both

7 Molecules7 Molecules 12 Molecules12 Molecules

ΔΔH: H: ––2,639 kJ mol2,639 kJ mol--11

ΔΔS: positiveS: positive(more disorder, fragmentation)

Example:Example:

C6H12O6 + 6O2 6CO2 + 6H2O

ΔΔG: G: –– 2,840 kJ mol2,840 kJ mol--11

See p. 5

Glucose + 6O2

6CO2 + 6H2O

OneStep

Glucose + 6O2

6CO2 + 6H2O

John Candy’s Metabolism

•• Alternative way to calculate Alternative way to calculate ΔΔGG

ΔΔG:G: Measure for the displacement of a reaction from its equilibrium (EQ)

See p. 5

Reactants [R] Reactants [R] Products [P]Products [P]Reversible ReactionsReversible Reactions

If ΔG = 0: Reaction is (already) at EQ

If ΔG < 0: Not (yet) at EQ: Forward reaction is favored

If ΔG > 0: Not (yet) at EQ: Reverse reaction is favored

ΔΔGGoo’’ determined at ““Standard ConditionsStandard Conditions””

• 25 oC (298 K)• 1 M (or 1 atm ) of R and P; or equimolar concentrations

• pH 7 (10-7 M H+)• 55.5 M H2O• 1 mM Mg2+ (if part of the reaction)

ΔΔG = G = RTlnRTlnQQ –– RTlnRTlnKKeqeq

–– RTlnRTlnKKeqeq = = ΔΔGGoo’’

See p. 5

ΔΔG = G = ΔΔGGoo’’ + + RTlnRTlnQQ

KKeqeq = [P]eqeq/[R]eq

QQ = [P]initialinitial/[R]initialinitial

oo

’’

Question: Under standard conditionsstandard conditions, how far areequimolarequimolar concentrations from equilibrium (ΔΔGGoo’’) ?

At thermodynamic equilibriumAt thermodynamic equilibrium

See p. 5

RRR PPP??

If Keq > 1 ΔGo’ < 0

If Keq < 1 ΔGo’ > 0

R

RRRR

If Keq = 1 ΔGo’ = 0 RRR PPP

PPPPP

PP

1,0001001010.10.010.001

KKeqeq

- 17.1- 11.4- 5.7

05.711.417.1

ΔΔGGoo’’ (kJmol(kJmol--11))

C2H5OH + 3O2 2CO2 + 3H2O ΔΔGGoo’’ = = ~~1,300 kJ mol1,300 kJ mol--11 KKeqeq = 10= 10220220

C6H12O6 + 6O2 6CO2 + 6H2O ΔΔGGoo’’ = = ––2,840 kJ mol2,840 kJ mol--1 1 KKeqeq = 10= 10500500

ΔΔGGoo’’ = = –– RT RT lnlnKKeqeq

ΔΔGGoo’’: useful as a general guidegeneral guide to predict directiondirectionof a process (reaction)

However, real conditions in cells often differfrom standard conditions!

•• Temperature: 37 Temperature: 37 ooCC (310 K)(310 K)

•• Cellular or initial concentrations of R and PCellular or initial concentrations of R and P(they are unlikely to be at equilibrium)

ΔΔGG:: ΔΔG = G = ΔΔGGoo’’ ++ RRTTlnlnQQ

See p. 5

QQ = [P]initialinitial/[R]initialinitial

ΔΔGGoo’’ = –RTlnKeqKeq

If QQ = KKeqeq Reaction is already at EQ ΔΔG = 0G = 0(initial P/R ratio equalsequals P/R ratio at equilibrium)

ΔΔG = RT G = RT lnlnQQ –– RT RT lnlnKKeqeq = RT = RT lnln QQ//KKeqeq

If QQ < KKeqeq Reaction is NOT yet at EQ ΔΔG < 0G < 0(relatively more Rmore R or less Pless P,

PP formation favored)

If QQ > KKeqeq Reaction is NOT yet at EQ ΔΔG > 0G > 0(relatively less Rless R or more Pmore P,R R formation favored)

See p. 5

Reduction Potential (Reduction Potential (ΔΔE)E)…… yet another way to express yet another way to express ΔΔGG……

• Metabolic reactions are often redoxredox reactions, involving transfer of electronstransfer of electrons from a donor to an acceptor

1. Direct transfer (ee--)2. Transfer of hydrogen (HH, or ee-- + HH++)3. Transfer of the hydride anion (HH——H, or HH-- ++ HH++)4. Direct combination with oxygen (X X + O=O 2O X)

• Electronegativities can predict direction of e- transfer

• Redox reactions can be written as two “half-reactions”(by conventionconvention: each is written in the direction of the reductiondirection of the reduction!)

AAoxidizedoxidized ++ BBreducedreduced AAreducedreduced ++ BBoxidizedoxidized

1. 1. AAoxidizedoxidized + e+ e-- AAreducedreduced

2. 2. BBoxidizedoxidized + e+ e-- BBreducedreduced

See p. 6

Question: Which “half-reaction” has the higher affinity for electrons at standard conditionsstandard conditions ?

By convention:

If e- flow from reference to test (“test” is stronger e- acceptor): EEoo > 0 (+V)> 0 (+V)

If e- flow from test to reference (“test” is weaker e- acceptor): EEoo < 0 (< 0 (-- V)V)

See p. 6

Reference H+ + e- H2 “half-reaction” (1M each)Electrode: (Eo= 0.00 V)

Test A+ + e- A “half-reaction” (1M each)Electrode: (Eo’= ??? V)

Table 3: Standard Reduction PotentialsTable 3: Standard Reduction Potentials

See p. 3

Excited (Chlorophyll a)Excited (Chlorophyll a)22** ~ ~ -- 1.001.00

Acetate + 2H+ + 2e- Acetaldehyde + H2O - 0.58

NAD+ + 2H+ + 2e- NADH + H+ - 0.32

Pyruvate + 2H+ + 2e- Lactate - 0.18

2H2H++ + 2e+ 2e-- HH22 (at standard conditions, 1M each, pH 0) 0.00(at standard conditions, 1M each, pH 0) 0.00

NO3- + 2H+ +2e- NO2- + H2O + 0.42

O2 + 4H+ + 4e- 2H2O + 0.82

(Chlorophyll a)(Chlorophyll a)22.+.+ + e+ e-- (Chlorophyll a)(Chlorophyll a)22 + 1.10+ 1.10

HalfHalf--reaction (written as reduction by convention)reaction (written as reduction by convention) EEoo (V)(V)

ee-- flowflow

Reduction Potential E for each Reduction Potential E for each ““HalfHalf--ReactionReaction”” (Nernst Equation)(Nernst Equation)

ΔE = EOxidant (A) – EReductant (B)

ΔΔE of E of RedoxRedox ReactionReaction ((AAoxox + B+ Bredred AAredred + B+ Boxox))

RTnFE = Eo’ + ln [e- Acceptor, Aox]

[e- Donor, Ared]

RTnFE = Eo’ + ln [e- Acceptor, Box]

[e- Donor, Bred]

1. Aoxidized + e- Areduced

2. Boxidized + e- Breduced

Relationship between ΔE and ΔG

ΔΔGG = – n F ΔΔE E ΔΔGGoo’’ = – n F ΔΔEEoo’’

ΔΔE E = = –– ΔΔGG//nFnF ΔΔEEoo’’ = = –– ΔΔGGoo’’/nF/nFSee p. 6