Term
|
Definition
1. how cells exrtact energy and reducing power from the environment
2. how cell synthesize the building blocks of macromolecules |
|
|
Term
|
Definition
1. perform mechanical work
2. active transport of molecules and ions
3. synthesis of macromolecules and other biomolecules form precursors |
|
|
Term
|
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
|
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
|
Definition
1. Nad+, accepts 2 electrons and 1 proton
2. FAD--accepts 2 electrons and 2 protons |
|
|
Term
|
Definition
|
|
Term
| ligation (requiring ATP cleavage) |
|
Definition
| forms covalent bonds with free energy from ATP hydrolysis |
|
|
Term
|
Definition
| particular atoms are re-arranged in a molecule |
|
|
Term
|
Definition
| transfer of a functional group from one molecule to another |
|
|
Term
|
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
|
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
|
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
|
Definition
Enzyme: Phosphoglucose isomerase
Reaction type: Isomerization
Substrate: Glucose 6-Phosphate
Product: Fructose 6-Phosphate |
|
|
Term
|
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
|
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
|
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
|
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
|
Definition
| GAP is the next substrate in glycolysis pathway, but DHAP is not used in glycolysis. DHAP must be converted to GAP. |
|
|
Term
|
Definition
enzyme: Triose phosphate isomerase
reactiontype: isomerization
substrate: DHAP
Product: GAP |
|
|
Term
|
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
|
Definition
|
|
Term
|
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
|
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
|
Definition
Enzyme: Glyceraldehyde3-phosphate dehydrogenase
Reaction type: phosphorylation coupled to oxidation
substrate: GAP
Product: 1,3 BPG |
|
|
Term
|
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
|
Definition
Enzyme: Phosphoglycerate kinase
Reaction type: Phosphoryltransfer
substrate: 1,3 BPG
Product: 3-phosphoglycerate |
|
|
Term
|
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
|
Definition
Enzyme: Phosphoglycerate mutase
Reaction type: phosphoryl shift
substrate: 3-Phosphoglycerate
product: 2-phosphoglycerate |
|
|
Term
|
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
|
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
|
Definition
Enzyme: Enolase
Reaction type: Dehydration
Substrate: 2-phosphoglycerate
Product: Phosphophenolpyruvate |
|
|
Term
|
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
|
Definition
Enzyme: Pyruvate kinase
Reaction type: phosphoryltransfer
substrate: phosphophenolpyruvate (PEP)
product: pyruvate in enol form then pyruvate |
|
|
Term
|
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. |
|
|
