September 23, 1997                MAST 634                             Lecture 6: Thermodynamics 
                                                                                              Introduction to Metabolism 

Important Points From Last Lecture  
      PMF in photophosphorylation ("photosynthesis") vs. Oxidative phosphorylation ("respiration") 
      Quantum yield 
      Light absorbance by water: problems for plants 
      Three "solutions" 
            Green 
            Brown 
            Red or blue-green 
      General structure of pigments 
            a. Tetrapyrroles 
                  chla: ring with Mg²⁺, similar to heme 
                  Phycobilin: linear 
            b. Carotenoids 

Energy Flow in Phycobilin - containing algae  
      Groups containing phycobilins (PE, PC, APC) 
            Cyanobacteria 
            Red algae 

Some algae only have PC and APC 

Absorption and fluorescence characteristics 
      Emission of one pigment overlaps with excitation of another 
            Data suggest PE --> PC --> APC --> chl a 
Note: Chl a in reaction centers 

Direction correct, but energy transferred as excitons, not fluorescence 

Phycobilin proteins in phycobilisome 

Another example of energy transfer -- lack there of 
      Normal in plants: fluorescence = < 5% of total Light absorbed 
      Acetone extracted chl a 
            remove chl a from membrane 
            disrupts energy transfer 
            all light energy goes off as fluorescence 
      Because of this, can measure chl a concentration by fluorescence 

Heterotrophy 
      C and energy from organic compounds 
      How? 
            Mostly, we'll talk about catabolism (energy production) and only a little about anabolism             (biosynthesis) 
      Overview of Central Metabolism 
            "Central" = present in most organisms 
            Needed for breaking down glucose 
            Synthesis of monomers for macromolecules 

General comments about what to learn 
          See handouts 
          Web page of central metabolism 
                www.ai.sri.com/ecocyc/ov.html  

How is ATP produced: catabolism 

First, what is ATP? 
      See page 428 of V & V 
      not an energy reserve 
          brain cells have ATP enough for a few seconds; reason why lack of O₂ kills brain rapidly 
      energy transmitter 

What's this mean?           See page 51 of V&V 
      ATP hydrolysis, highly exergonic reaction, drives endergonic reactions 

In general: 

      A + B = C + D     delta G₁ 
      D + E = F + G    delta G₂  
A + B + F = C+F+G delta G₃ 

What's important is delta G₃ <O, not whether delta G₁ or delta G₂ <O 

How is ATP made? 

Two general classes of reactions 
      Substrate - level phosphorylation 
            glycolysis; fermentation 
            Oxidation (and photo-) phosphorylation 

In oxidative phosphorylation (= "respiration") 

                                                      Glycolysis and Kreb cycle 
                                                              | 
                                                              v             PMF 
                                                        NADH + O₂ ------> NAD⁺ 

Summary of Substrate - level (SL) phosphorylation and oxidative phosphorylation (OP) 
 

Bucher 1897 "life in test tube" ---> argument against "vital force", separate from chemistry 

What e^- acceptor? 
e^-donor: C₆H₁₂O₆ ---> 6CO₂ + 24e^- 

e^-acceptor: H⁺ + O₂ + 2e^- ---> H₂O 

How is organic matter catabolized? 
      Usual starting point is glucose, but most material has a high molecular weight 

What's a large molecule? 
      What can't pass through a cell membrane, very roughly >500 Da 

      Large compounds ------------------> monomers, 
                                         extracellular     oligomers 
                                           enzymes              | 
                                                                     v 
                                                        Transported into cell 

True even for higher organisms 
      enzymes excreted into gastro-intestinal tract 

What happens next depends on compound and whether O₂ is present 
      Everything "feeds into" central metabolism 

See diagram 

Let's focus on glucose degradation 

What happens if O₂ not present 
      can't run Kreb cycle (where most of NADHs are synthesized) because NADH would build up 

Anaerobic respiration: e ^- acceptor other than O₂ (next lecture) 

Fermentation: oxidation of NADH 

Most "common" fermentation -- > in your text book 

Name of fermentation ---> endproduct released 

                                                                        LDH 
lactate fermentation: glucose ------>2 pyruvate ------> 2 lactate 

 

      Lactate dehydrogenase (LDH) 

          "old" enzyme ---> used in phylogenetic studies 

Occurs in muscles, but soreness and muscle fatigue due not to lactic acid but other acids. 
         -lactate itself doesn't harm muscle ---> pH decrease does 

Usually, lactate excreted and converted back to glucose in liver ---> in mammals, but not necessary in all organisms 

Effect of switching from aerobic growth to fermentation in yeast 

Observations 
      1. More glucose consumed, very rapidly 
      2. Cells get smaller 

How to explain these observations? 
#1 glycolysis is ~ 100 X faster than respiration 
      "Pasteur effect" -----> 
#2 Fermentation is less efficient 

How to determine efficiency? 
Thermodynamics            pages 48-53 

Consider a general reaction 
      aA + bB = cC + dD 

At equilibrium, i.e. No net change 
      delta G^o = -RT ln Keq. 

            Products [C]^c [D]^d  
Keq. = reactants = [A]^a [B]^b 
 

When not at equilibrium 
      delta G = delta G^o + RTln K 

What's delta G^o?       free energy of formation 
      Delta G^o = Sigma delta G_f^o (products) - sigma delta G_f^o (react.) 

Additional problem 

      STD biochem conditions Delta G' & delta G^o' 

            [H₂O] = 1 ; not [H₂O] = 55.5M 
            [H⁺] = 10^-7 , not [H⁺] = 1; i.e. pH=O 

Example delta G^o' for 
1. Glucose ---> 2 lactate + 2H⁺ 

             Delta G^o = (2* - 526.6)- -917.2 
                           = -116 kJoules/mol 
             Delta G^o= -196 kJ /mol 

      (page 51 on delta G^o----> delta G^o' i.e. taking into account H⁺)  

What's efficiency?  

Lactate fermentation ---> 2 ATP's 

      delta G_f^o' for ATP = -30.5, so 2 ATP, total E harvested is 61 kJ 
                         61 
so, efficiency = 196      31%      Actual eff. > 50%! 

In comparison: 
      Respiration is 41% 
        But many more ATP's released 

   Many types of fermentation 

Note: Problem with all fermentation is acid production 

Drawbacks of fermentation 
      1. Low energy production 
      2. Acid production ---> lower pH 
      3. Other endproducts harmful 

Strategies of invertebrates ( and others) to deal with anoxia 

Many invertebrates can survive long period without O₂