1. Section 6 5. Pentose phosphate pathway Krebs cycle Carbohydrate catabolism: control, dental aspects
10/28/05

2. Pentose phosphate pathway
alternate catabolism of glucose 6-P
energy channeled into reducing potential (high-energy e–s), not ATP
cytosol of most cells, especially adipose tissue, liver
functions: synthesis of pentoses, supply e–s for fat synthesis
coenzyme: NADP
NAD with a phosphoryl group on a 2' ribose
e– carrier used in reductive biosynthesis (e.g., fatty acid synthesis)
stoichiometry varies with specific cell, situation
stoichiometry of version that maximizes making NADPH:
glc 6-P + 12 NADP+ + 7 H2O → 6 CO NADPH + 12 H+ + Pi
Similar but different enzyme, NADP, a wide variety of version of this pathway, and this is just showing one, one glucose, 6 carbons converted to 6 CO2 and energy is being harnessed in this form, that can be used to make fat, something that is prominent when high carbs in the diet are converted to fat 1

3. Pentose phosphate pathway: first 2 steps, control
Control of the pentose phosphate pathway: glc 6-P DHase rate controlled by [NADP+]
6-P gluconate DHase
Two of the steps of the pathway, two oxidations, how electrons end up as NADPH. One of the substrates regulates the pathway, the NADP+. The pathway gets its name because you get 5 carbon sugar which can be used to make ribose phosphate for nucleotide synthesis
¯ ribose-P, other sugars 2

4. Overview of catabolism
FATS
POLYSACCHARIDES
PROTEINS
Stage 1
glucose, other sugars
fatty acids, glycerol
amino acids
pyruvate
Stage 2
acetyl CoA
CoA
H2O O2
Shows what we’ve covered here, now we have to take a look at Kreb’s cycle
Stage 3
e– CO2
Krebs cycle
oxidative phosphorylation v v
ATP ADP + Pi
adapted from Fig

5. The Krebs Cycle
aka the citric acid cycle; the tricarboxylic acid (TCA) cycle; the final common pathway for fuel oxidation
location: mitochondrial matrix
function: acetyl group → 2 CO2 ATP production
aerobic
O2 not used directly
NADH & FADH2 transfer e– pairs to e– transport chain
transfer required to regenerate e– carriers
ATP made by oxidative phosphorylation
Krebs cycle takes place in mitochondrial matrix, generates most of the electrons in the form of NADH which eventually produces lots of ATP, AcetylCOA comes in, two decarboxylations, back to C4, and the other steps generate high energy phosphate, more oxidation that takes place. A lot of electrons are being transferred to these electron carries which go to electron transport chain and that’s how you make a lot of ATP 3

6. The Krebs Cycle (steps 1-4)
step enzyme reaction type
1 citrate synthase* condensation (Claisen)
2,3 aconitase isomerization via dehydration-hydration
4 isocitrate DHase† oxidative decarboxylation
*inh by ATP
†inh by NADH, ATP; activ by ADP
Rather than go through all the steps, the first step is the condensation, where acetyl COA is condensed, one of the places where the pathway is controlled, unidirectional arrow. One of the steps that goes in only one direction, makes the cycle as a whole unidirectional although some of the individual steps can go backwards. The other place where control is exerted is step 4, oxidative decarboxylation so isocitrate is both oxidized, electron carrier taking electron, and loses a carbon dioxide. In the second half of the pathway 4

7. The Krebs Cycle (steps 5-9)
step enzyme reaction type
5 a-ketoglutarate DHase oxid. decarb.
6 succinyl thiokinase phosphorylation driven by thioester hydrolysis 7 succinate DHase oxid.-reduction (complex II)
8 fumarase hydration
9 malate DHase oxid.-reduction
5 carbon intermediate goes under another decarboxylation. GTP is made and another oxidation, this time electrons go to FAD and this succinate dehydrogenase is complex II, embedded in the matrix side of mitochondrial inner membrane. Then the last couple of step are hydration and one final oxidation producing more NADPH. This table lists the types of reactions going on 5

8. Connection to electron transport chain
most e–s enter e– chain via NADH
transferred from NADH via 3 complexes (I, III, IV) to O2
end up in H2O via transfer to O2 (the final electron acceptor)
stoichiometry: NADH + H+ + ½ O2 → NAD+ + H2O (2.5 ATP made)
some e–s enter via FADH2 enzymes (enter e– chain at Q) stoichiometry: FADH2 + ½ O2 → FAD + H2O (1.5 ATP made)
NADH → complx I → Q → complx III → cyt c → complx IV
from ↑ ↓
mal-asp shuttle FADH2 enzymes: O2
pyr DHase succinate DHase (complex II)
Krebs cycle DHases GOP DHase
hydroxyacyl CoA DHase* acyl CoA DHase*
others others
Lehninger 3ed Fig 19-8
Connect to electron transport chain. Arrows show the path of electrons. Various pathways and processes generated. Here are some of the named pathways that generate NADH and you’ve seen that the krebs cycle generates lots of NADH, eventually 2 ATP are made. Complex II generate electrons as FADH2, lower energetic level, get 1.5 ATP made for each pair of electrons. As you continue, several places where both of the electron carriers are generated
* fatty acid catabolism (Section 7) 6

9. Stoichiometries ATP Krebs cycle (steps 1-9): yield
2FAD + 6NAD+ + 2acetyl CoA + 6H2O → FADH2 + 6NADH + 6H+ + 2CoA + 4CO
oxidative phosphorylation:
2FADH2 + 6NADH + 6H+ + 4O2 → 2FAD + 6NAD+ + 8H2O 18
stage III: 2acetyl CoA + 4O2 → 4CO2 + 2H2O + 2CoA 20
add in stages I & II: glucose + 2O2 + 2CoA → 2acetyl CoA + 2CO2 + 4H2O
complete oxidation of glc:
glucose + 6 O2 → 6 CO2 + 6 H2O
9 steps, 2 ATP or GTP, ATP equivalents, feed electrons to carriers, hgue number of ATP generated. This is where if you start from glucose about 2/3 of the ATP from glucose comes from this final common pathway, this Krebs cycle. Stage three adds up in this fashion, so this sums of up Krebs cycle itself plus the transfer of electrons. Now we add stage 1 and 2 and find that we get the complete oxidation of one glucose producing this number of ATP
10-12
30-32 7

10. Replenishing (anaplerotic) reactions
cycle intermediates used to make other biomolecules
e.g., succinyl CoA → heme oxaloacetate → aspartate
cycle itself results in no net change of [intermediates] (slide 7: Stage III)
other reactions needed to ↑ [intermediates]
example of a replenishing reaction:
CH3COCOO– + HCO3– → –OOCCH2COCOO–
pyruvate oxaloacetate
driven by being coupled to ATP hydrolysis
enzyme: pyruvate carboxylase (coenzyme: biotin)
allosterically activated by acetyl CoA
same reaction as gluconeogenesis: step 10'a (S6L4,slide4)
Krebs doesn't produce or consume those intermediates, some used for other purposes. Reaction to replenish oxaloaccetate. Cant elaborate any further, Krebs cycle intermediates need to be maintained at minimal level. )occasionally when there is not enough oxygen, krebs cycle slows , and Acetyl co A is used to make ATP. Generates acetic acid. 8

11. Krebs cycle: anaerobic conditions
Krebs cycle is the same in microorganisms as in eukaryotes
cycle is aerobic (linked to electron transport chain)
to regenerate e– carriers (e.g., NAD+), e– transfer to O2 must occur
under anaerobic conditions, some microorganisms produce acids from cycle “backup”
examples: acetyl CoA + ADP + Pi → ATP + acetic acid + CoA succinate → CO2 + propionic acid (CH3CH2COOH)
these acid products are membrane-permeant
by acidifying local regions, products can damage tissues e.g., in caries & periodontal disease, they are among the numerous substances that cause damage
Other acids produced that contribute to carries and other dental problems. One final mention of control of all these pathways feedback inhibition as one general mechanism, ATP is by fat the most important feedback inhibitor of catabolic pathways. Feed forward activation AMP and ADP, signals that ATP is depleted, signals for the activation of catabolic pathways, and this is what this looks like. .. 9

12. Control of metabolic pathways
feedback inhibition usually an early step (committed step) of a pathway is inhibited by a pathway product
example: a pathway functioning to produce F:
A → B → C → D → E → F
F will often allosterically inhibit step A → B or B → C
in catabolism, main product is ATP, so ATP common allosteric inhibitor
feedforward activation
usually a precursor: of the pathway’s product or of a related pathway’s product
example: AMP & ADP as precursors of ATP 10

13. Control of carbohydrate catabolism
glycogen
AMP, ADP 
glucose 6-P
fructose 6-P
AMP, ADP  
fructose 1,6 bisP
pyruvate
AMP  
 acetylCoA
oxaloacetate citrate
isocitrate
ADP  
-ketoglutarate ATP
NADH ↑ox phos
ADP + Pi
GLYCOGEN- OLYSIS ×
pentoseP ? pathway
GLYCOLYSIS 
Each of these steps has either AMP or ADP as an activator, see also that just about all of these pathways have ATP as inhibitors, or was to put the metabolic breaks on the pathway. One other time not here, pentose phosphate pathway, what it is that regulates its activity.
KREBS CYCLE 11

14. Dental aspects of carb metabolism: summary
sucrose
source of fermentable monosaccharides
an activated precursor of plaque polysaccharides
plaque polysaccharides (mutans, dextrans, levans)
synthesis catalyzed by bacteria-secreted sucrases
adhesion, fuel, anaerobic conditions for microorganisms
anaerobic conditions (fermentation)
glycolysis lactic acid
Krebs cycle acetic acid, propionic acid, others
low pH
solubilizes enamel hydroxyapatite (caries)
damages supporting tissue proteins, cells (gingivitis, periodontal disease, pulpitis)
Not going to say much about this because I already said it, puts in all the dental or oral aspects and how they are affecting 12

15. Web links Stryer site: Chapter 19 (Glycolysis)
see also Chapters 18, 20, 22 at that site
Carbohydrate Structure and Metabolism from the University of Kansas Medical Biochemistry Center. This site is essentially an online course in carbohydrates and many biochemical pathways.

16. Next section: 7. Lipid Metabolism Next exam (#6): Monday, Nov. 7 at 8 a.m.