8. Overview of Metabolic Pathways Flashcards
Energy charge Determines Anabolism vs Catabolism
E charge = ([ATP] + ½ [ADP]) / ([ATP] + [ADP] + [AMP])
Note that ATP contains two high energy bonds while ADP contains one
The energy charge has a value ranging from 0 (all AMP) to 1 (all ATP)
Catabolic pathways are inhibited and anabolic pathways are stimulated by a high-energy charge and vice versa for low-E charge
Energy charge, like the pH of a cell, is buffered and ranges from 0.8 (catabolic) to 0.95 (anabolic) for most cells
Energy Charge And Metabolic Pathways
graph- y vs x- relative rate vs E charge (0 – 1 scale)
ATP generating pathway- hyperbolic curve from high to low relative rate as E charge inc
ATP-utilizing pathway- hyperbolic curve from low to high relative rate as E charge inc
Generate and use ATP at same time: energy charge of ~0.9 (both ATP-gen and ATP-utilizing graphs cross)
Three Types of Metabolic Pathways
Converging catabolism- Catabolic pathways=converging pathways bc converge on same endpoint
Diverging anabolism- Anabolic pathways=diverging pathways; start at same point but end differently
Cyclic pathway=partially catabolic, partially anabolic eg TCA (Acetyl CoA to CO2), E-prod
Summary- catabolism vs anabolism
Catabolism- Convergent process End products are simple molecules eg CO2, H2O, ammonia Releases Energy Breaks something down Stimulated by low energy charge
Anabolism- Divergent process End products are complex molecules eg macromolecules Requires Energy Builds something up Stimulated by high energy charge
Metabolic Pathway – An Example
A sequence of individual steps catalyzed by specific enzymes (some reversible)
The product of one enzyme is the substrate for the next enzyme
glycolysis (10 steps): 6C molec broken down to 3C molec
Metabolic Pathways: Interconnected (carb, protein, lipid metabolism)
Key reactions are repeated throughout metabolism
Oxi-red: e- transfer
Ligation req ATP cleavage: form covalent bonds (ie C-C bonds)
Isomerization: rearrangement of atoms to form isomers
Group transfer: transfer of func gp from one molec to another
-involves activated carriers- E rich molecs (Activated carriers come from vitamins)
Hydrolytic- cleavage of bonds by addn of water
Addn/removal of functional gps- addn of functional gps to double bonds or removal to form double bonds
Common themes in metabolic pathways
Irreversibility Committed step Rate-limiting step Regulation Compartmentalization eg within cell or body organ
Why Are Metabolic Pathways Irreversible?
If the reaction sequence for anabolic and catabolic pathways were identical:
1. Their simultaneous operation would be wasteful.
2. They cannot be regulated separately.
Metabolic pathways also have one or more steps that are essentially irreversible under physiological conditions
What Is A Committed Step?
Although metabolic pathways are irreversible, most of the component reactions function close to equilibrium (delta G close to 0) and are readily reversible (based on substrate/product [])
Early in each linear pathway there is usually an irreversible reaction that commits the product of the reaction to continue down that pathway
The committed step is generally the target of regulation
In many instances, but not always, the committed step is also the rate-limiting step
Circular pathways do not have a committed step (though they do have a rate-limiting step)
What Is A Rate-limiting Step?
A rate-limiting step is the slowest reaction in a metabolic pathway
The rate-limiting step generally has the highest activation energy of all the reactions in the pathway
The velocity of that step determines the overall flux of metabolites through the pathway
A rate-limiting step is usually subject to intense regulation, both positive and negative
Branch Points In A Pathway Are Often Regulated
Regulation pathways- branch pathway
Product reg rate of rxn eg B
If want high G, use feedback inhibition of E (allosteric, noncompetitive inhibition)
vs product inhibition of enzyme (very close)
Clicker-
Which enz subject to feedback inhibition by prod E? enz 2 (allosteric enz)
Feedback inhibition- by product farther down pathway
*don’t confuse allosteric vs noncompetitive (in body- allosteric, not noncomp)
How Are Metabolic Pathways Regulated?
Isoforms (diff structures, same func) of enzymes
Substrate concentrations (eg inc substrate, remove end product)
Product inhibition
Allosteric regulation
Covalent modification (of enzyme)- change amt of enzyme []
Changes in enzyme protein concentration
- Induction (gen more enz protein)
- Repression (dec enz protein)
- Sequestration (hide enz away in diff compartment)
- Degradation (inc in enzyme turnover) > more protein degraded faster
Compartmentalization- rxn takes place in small compartment
Isoforms of enzymes
-e.g., Hexokinase (glc G6P) in most tissues, Glucokinase in liver
Substrate concentration
-Normal plasma glucose level on (5 mM): saturating for hexokinase (low Km)
-Higher level in portal blood (20 mM) after a meal: not saturating for glucokinase
-Glucokinase w high Km, not satd, help high enz rate
Product inhibition
-Hexokinase inhibited by G6P (product)
»Glc > G6P by coupling w rxn of (ATP>ADP) in inorganic phosphate, which is transferred to glc
-Prevents depletion of ATP
Allosteric Regulation
Allosteric=other site
Feedback inhibition is an example of allosteric control
Allosteric regulators bind at a site other than the active site
Eg- orange=substrate site; A=activator; I=inhibitor
w bound activator, forms better site for substrate, catalyze conversion of substrate better (modifier=activator)
Allosteric inhibitor binds inhibitory site diff from active site, changes substrate site so that substrate can’t bind
Normal allosteric enzyme- sigmoidal curve eg Hb
Allosteric activator- curves shifts left
Allosteric inhibitor eg BPG- shift to right of enz activity curve
Covalent Modification – An Example
Eg
Glucagon, epinephrine activate protein kinase A which catalyzes pyruvate kinase a (active) -> pyruvate kinase b (inactive, phosphorylated); also ATP -> ADP
Insulin activates phosphoprotein phosphatase (pyr kinase b -> pyr kinase A); also H2O -> Pi
Phosphorylation of (hydroxyamino acids) serine (Ser), threonine (Thr) by protein kinase A (converts pyr kinase a to phosphorylated pyr kinase b [phosphorylated Ser/Thr])
Pyr kinase a= imp in glycolysis/glc metabolism
-Inactive > active: stim glycolysis
Imp in hormonal regulation of met.
By altering lvl of covalent modif of enz, insulin and glucagon have opp effects on metabolic pathway
Amount of an Enzyme
Gene expression
- Rate of transcription (DNA > mRNA) ↑ or ↓
- Rate of translation (mRNA > protein) ↑ or ↓
Sequestration
-e.g., glucokinase (metabolizes glc) located in the nucleus in the absence of glucose
> E-utilizing enz so don’t want it unnecessarily using ATP up; hard to saturate glucokinase so need high conc of glc
Degradation
-e.g., Cholesterol derivatives increase the degradation of HMG-CoA reductase (rate-lim enz for chol syn)
