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Lecture

BIOL 201 Lecture Notes - Citric Acid, Light-Independent Reactions, Succinyl-Coa


Department
Biology
Course Code
BIOL 201
Professor
Gary Brouhard

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Contents
1 Introduction 3
2 Energy in Biological Systems 3
2.1 MetabolisminE.Coli ........................................ 3
2.2 Equilibrium.............................................. 3
2.3 FreeEnergy.............................................. 3
2.3.1 Standard Free Energy (∆G0) ................................ 4
2.3.2 ∆Ggives an indication of the amount of energy released/consumed . . . . . . . . . . . 4
2.3.3 Standard Free Energy is Additive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.4 Catalysis ............................................... 4
2.4.1 HowEnzymesWork ..................................... 5
2.4.2 EnzymeKinetics ....................................... 5
2.5 Hydrolysis of ATP drives energy consuming processes . . . . . . . . . . . . . . . . . . . . . . 5
2.6 PhototrophsandChemotrophs ................................... 5
2.7 Extraction of Energy from Food . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.8 Electron/Proton Carrier Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
3 Glycolysis 6
3.1 WhyGlucose?............................................. 6
3.2 StepsofGlycolysis .......................................... 6
3.3 MetabolicFateofPyruvate ..................................... 7
4 Photosynthesis 7
4.1 Leaves................................................. 8
4.2 ChloroplastsStructure........................................ 8
4.3 ChloroplastsOrigins ......................................... 8
4.4 Pigments ............................................... 8
4.4.1 AbsorptionSpectrum .................................... 9
4.5 FateofHighEnergyElectrons.................................... 9
4.6 Creation of a Charge Separation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
4.7 Light Harvesting Complexes (LHCs) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
4.8 Purple Sulfur Bacteria as a Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
4.9 Plants ................................................. 11
4.9.1 OxygenEvolvingComplex ................................. 12
4.9.2 TheProtonMotiveForce .................................. 12
4.9.3 Regulation of Light Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
4.10CalvinCycle ............................................. 14
4.11 Adaptations of the Calvin Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
4.11.1 Problems ........................................... 14
4.11.2 Solutions ........................................... 15
4.11.3 Summary ........................................... 16
5 Regulation of Glycolysis and Gluconeogenesis 16
5.1 ThreeIrreversibleSteps...................................... 16
5.2 AllostericRegulation......................................... 16
5.2.1 Hexokinase .......................................... 16
5.2.2 Phosphofructokinase (PFK) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
5.2.3 PyruvateKinase ....................................... 17
5.3 Gluconeogenesis............................................ 17
5.4 Reciprocal regulation of glycolysis and gluconeogenesis . . . . . . . . . . . . . . . . . . . . . . 18
5.5 TheCoriCycle ............................................ 19
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6 Glycogen metabolism 19
6.1 GlycogenStructure.......................................... 19
6.2 Converting Glucose to Glycogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
6.3 Regulation of Glycogen Synthesis and Breakdown . . . . . . . . . . . . . . . . . . . . . . . . . 19
7 The Tricarboxylic acid (TCA) Cycle 20
7.1 PyruvateDehydrogenase....................................... 20
7.1.1 Regulation .......................................... 21
7.2 Steps.................................................. 21
7.3 Regulation............................................... 22
7.4 TCA Cycle is a Source of Biosynthetic Precursor Molecules . . . . . . . . . . . . . . . . . . . 22
8 Metabolism and Physiology 23
9 Membrane Transport 23
10 Biological Redox Reactions 23
11 Oxidative Phosphorylation 23
12 Metabolism and Cancer 23
13 etc. 23
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Lecture 1
2012.01.26
1 Introduction
2 Energy in Biological Systems
2.1 Metabolism in E. Coli
[Incomplete]
E. coli is the first and simplest model used to interrogate metabolic pathways. The way they metabolise is
highly conserved throughout evolutionary history. E. coli multiply and grow in their environment, and in
doing so, require energy. Their major energy source (carbon source) is glucose. The energy extracted from
glucose is used with other inorganic compounds to make building blocks of the cell:
Amino acids
Nucleotides
Lipids
Sugars
Vitamins
Macromolecules
[Skipping the rest of this section]
2.2 Equilibrium
All reactions are reversible to some extent. Equilibrium is the state in which the rate of the forward
reaction is the same as the rate of the reverse reaction.
The forward rate is related to the nature of the reactants and some constant:
rateforward =k1[A][B]
Likewise with the reverse rate:
ratereverse =k2[C][D]
And at equilibrium:
k1[A][B] = k2[C][D]
or
keq =k1
k2
=[C][D]
[A][B]
keq is a property of the reaction.
This tells us how rapidly a reaction is to take place. The feasability of a reaction is determined by the free
energy.
2.3 Free Energy
G=Gproducts Greactants
This equation gives us the change in free energy between two states, which tells us how avidly a reaction
will take place.
G < 0The reaction is spontaneous (Potential energy has to decrease)
G= 0 The reaction is at equilibrium
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