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Lecture 7
metabolism and glycolysis 1
51
Biochemistry
Undergraduate 4
11/19/2014

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Term
metabolism
Definition
1. how cells exrtact energy and reducing power from the environment
2. how cell synthesize the building blocks of macromolecules
Term
free energy uses
Definition
1. perform mechanical work
2. active transport of molecules and ions
3. synthesis of macromolecules and other biomolecules form precursors
Term
catabolism
Definition
1. reactions that transform fuel into cellular energy
2. taking fuel such as carbohydrates and fats and turning them into useful energy
Term
biosynthetic vs. degradative pathways
Definition
1. almost always distinct, not just the reverse of one another
Term
2 criteria for metabolic pathways
Definition
1. each reaction will yield only one particular product from reactants
2. the overall pathway must be energetically favorable
Term
what determines the overall energy of a reaction?
Definition
the sum of the free energy changes of the individual steps
Term
ATP
Definition
1. contains two high energy phosphoanhydride bonds
2. non-covalent bond to Mg2+ for physiological purposes
Term
ATP hydrolysis energy release
Definition
1. -30.5 kj
2. Used in coupling reactions where one reaction is unfavorable, making the unfavorable one possible
Term
why does ATP have a high phosphoryl transfer potential?
Definition
ATP is an unfavorable structure compared to ADP and Pi
Term
ATP vs ADP and PI---Resonance
Definition
1. ATP and ADP have sucky resonance structures due to the slightly positive charges on phosphate and oxygen
2. Pi has a way better resonance structure with a double-bond characteristics on all oxygens--good stabilization
Term
ATP vs ADP and Pi--Electrostatic repulsion
Definition
1. at pH 7, ATP has 4 formal negative charges
2. If you went to ADP you would loose atleast 1
Term
ATP vs ADP--Stabilization
Definition
1. Water stabilizes negative charges, through H-bonds
2. 1 H2O can interact with the last phosphate on ATP, but ADP can be stabilized by two H2Os
3. Pi can also be stabilized by H20.
Term
why don't we use molecules with higher phosphoryl transfer energy?
Definition
1. ATP is intermediate in terms of the energy it can release
2. Phosphenolpyruvate and 1,3 bi-phosphate have even more unfavorable structures
3. Using them would provide no way of regenerating the energy
Term
what process do we follow when we break down molecules in our body?
Definition
1. oxidize them to CO2, essentially taking all the protons off molecules until all we have is CO2
2. The more C-H bonds you have, the more energy you can take from your molecule, via oxidation
Term
what type of fatty acids have the most harvestable energy?
Definition
1. saturated fatty acids because of all the C-H bonds
Term
3 stages to extract energy from food
Definition
1st--fats, polysaccharides, and proteins enter glycolysis
2nd--they will be broken down into Acetyl coA
3rd--Acetyl CoA enters the citric acid cycle
4th--oxidative phosphorylation
Term
important structural component of acetyl CoA
Definition
1. S-CoA
2. concerned about what's attached to the Sulphur
Term
common carriers
Definition
1. Nad+, accepts 2 electrons and 1 proton
2. FAD--accepts 2 electrons and 2 protons
Term
oxidation-reduction
Definition
transfer of electrons
Term
ligation (requiring ATP cleavage)
Definition
forms covalent bonds with free energy from ATP hydrolysis
Term
isomerization
Definition
particular atoms are re-arranged in a molecule
Term
Group transfer reactions
Definition
transfer of a functional group from one molecule to another
Term
hydrolytic
Definition
cleavage of bonds by the addition of water
Term
addition or removal of functional groups
Definition
addition of functional groups to double bond
Term
2 stages of glycolysis
Definition
1. first four steps that take glycolysis froma 6 carbon molecule and turns it into two 3-carbon fragments. It is the step where you invest ATP and trap glucose inside the cell.
2. Last 5 steps, oxidation of the 3 carbon fragments into pyruvate. You harvest 4 ATP, and net 2.
Term
Reaction 1
Definition
Enzyme: Hexokinase
Reaction: Group Transfer (Phosphoryl)
Substrates: Glucose and ATP
Products: Glucose 6-phosphate, ADP and H+
Reactions transfers the terminal phosphate from ATP to C6
Term
Reaction 1--notable results
Definition
phosphorylation of glucose traps it in the cell. Glucose transporters work both ways, in and out. Phosphorylating keeps the transporters from recognizing it and moving it out of the cell.
By adding phosphate group, we’ve added 2 formal negative charges. This will destabilize the glucose facilitating it for further metabolism.
Term
hexokinase--what type of enzymatic reaction?
Definition
sequential ordered
1. ATP is bound, not much change in shape occurs
2. Glucose is bound--substrate-induced closing of cleft
3. closing of cleft keeps water out, avoiding ATP hydrolysis
4. creates the ideal environment for the C6 of glucose to attack the terminal phosphate of ATP.
Term
Reaction 2
Definition
Enzyme: Phosphoglucose isomerase
Reaction type: Isomerization
Substrate: Glucose 6-Phosphate
Product: Fructose 6-Phosphate
Term
Reaction 2 notes
Definition
Reaction converts the aldehyde at C1 into a fructose ketone at C2. Remember in solutions glucose prefers to be in circular form. To facilitate the reaction, glucose must be linearized. The reaction proceeds by linearizing glucose before the isomerization. Then, the product is first forms in linear form, then circularized.
Term
Reaction 3
Definition
Enzyme: Phosphofructokinase
Reaction: Phosphoryl group transfer
Substrate: Fructose 6-phosphate
Product: Fructose 1,6-bisphosphate
Transfering the terminal phophate group from ATP to CI of fructose 6-phosphate. Note the name: 1,6 bisphosphate, you added the carbon to C1.
Term
Reaction 3 notes
Definition
Note: this is the first irreversible step in gycolysis. Any glucose that cell consumes that ends up as f-1,6-BP will be destined to go through glycolysis. Up until this point, it could be stored as glycogen after being trapped in the cell.
Term
Reaction 4
Definition
Enzyme: Aldolase
Reaction type: Aldol cleavage (says would be one of those catch-all reactions, but going to refer to it as aldol cleavage.)
Substrate: Fructose 1,6 bisphosphate
Products: DHAP and GAP
Term
Reaction 4 notes
Definition
GAP is the next substrate in glycolysis pathway, but DHAP is not used in glycolysis. DHAP must be converted to GAP.
Term
Reaction 5
Definition
enzyme: Triose phosphate isomerase
reactiontype: isomerization
substrate: DHAP
Product: GAP
Term
Reaction 5 notes
Definition
H and OH group are switched. Reaction is rapidly reversible. 96% exists as DHAP and 4% GAP, but will always continue regenerating GAP. Since GAP is readily consumed by the rest of glycolysis, the reaction constantly generates GAP to maintain equilibrium.
Term
DRAW TPI Mechanism
Definition
Term
TPI structure
Definition
an αβ barrel: a central core of 8 parallel β strands, surrounded by 8 α helices, with a loop that closes off the active site upon substrate binding
Term
TPI mechanism--catalysis
Definition
The only thing that slows down the reaction is the enzyme running into the substrate. Essentially only limited by the diffusion rate of the enzyme and the substrate interacting. Catalysis occurs every time the ensyme and substrate meet. Diffusion is the rate limiting step.
Term
TPI mechanism--specificity
Definition

1. Uses a loop structure that covers the active site to prevent formation of enediol intermediate in step 1.  The loop structure holds the substrate in place until the desired product, GAP, is formed. 

2.  The enediol intermediate would degrade to methyl glyoxal, becuase a Pi group would want to dissociate to remove a formal negative charge.

3.  Because methyl glyoxal is not an intermediate in glycolysis. The body would just end up loosing 3 carbons

Term
Reaction 6
Definition
Enzyme: Glyceraldehyde3-phosphate dehydrogenase
Reaction type: phosphorylation coupled to oxidation
substrate: GAP
Product: 1,3 BPG
Term
reaction 6 notes
Definition

Reaction occurs in two couples steps.

1. inital oxidation where GAP is oxidized and NAD+ is reduced in the presence of water. This is a highly favorable reaction.

2. The second step, acyl-phosphate formation, is unfavorable. The two reactions are coupled and the energy released from the first is used to drive the second.

Term
reaction 7
Definition
Enzyme: Phosphoglycerate kinase
Reaction type: Phosphoryltransfer
substrate: 1,3 BPG
Product: 3-phosphoglycerate
Term
reaction 7 notes
Definition
1. ATP is harvested.  Gain back the 2 ATP spent in stage 1. 2.  Reaction is known as substrate-level phosphorylation because no O2 is consumed. Phosphate is moved straight from a substrate to the ADP.
Term
reaction 8
Definition
Enzyme: Phosphoglycerate mutase
Reaction type: phosphoryl shift
substrate: 3-Phosphoglycerate
product: 2-phosphoglycerate
Term
reaction 8 notes
Definition
unique about mutase is that it takes phosphate group, and gives it’s own phosphate from the mutase to the product. Its a switch, versus a simple transfer of a phosphate group.
Term
mutase mechanism steps
Definition

1. Mutase: an enzyme that catalyzes the intramolecular shift of a chemical group.

2. Mutase will first act as a kinase, donating a phosphate group to the substrate, forming 2,3 BPG as an intermediate.

3. Mutase will then act as a phosphotase, taking a phosphate from 2,3 BPG, forming the product 2-phosphoglycerate.

4. Mutase then resonstitutes itself with the phosphate group from 3-phosphoglycerate.

5. If you radio-labelled the phosphate group from the substrate, after formation of the product, the enzyme would be radio-labelled.

Term
reaction 9
Definition
Enzyme: Enolase
Reaction type: Dehydration
Substrate: 2-phosphoglycerate
Product: Phosphophenolpyruvate
Term
reaction 9 notes
Definition
Dehydration reaction introduces a double bond. Elevates the transfer potential of the phosphoryl group, setting the stage fot the generation of ATP. The enol state of phosphoenol pyruvate is relatively more unstable than 2-phosphoglycerate.
Term
reaction 10
Definition
Enzyme: Pyruvate kinase
Reaction type: phosphoryltransfer
substrate: phosphophenolpyruvate (PEP)
product: pyruvate in enol form then pyruvate
Term
reaction 10 notes
Definition
PEP has high phosphoryl transfer because the phosphoryl group traps PEP into its unstable enol form. Once the phosphate group is transferred to ATP, the enol converts to a more stable ketone.
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