Glycolysis steps 6-10 Flashcards
1
Q
What happens in step 6 of glycolysis
A
- Glyceraldehyde 3-phosphate is converted to 1,3-bisphosphate glycerate
- Catalysed by Glyceraldehyde 3-phosphate dehydrogenase
2
Q
Describe the process of converting Glyceraldehyde 3-phosphate (GAP) to 1,3-bisphosphate glycerate (1,3-BPG)
A
- Involves the oxidation and phosphorylation of GAP by NAD+ and Pi
- Aldehyde oxidation- exergonic- drives the synthesis of BPG
- The aldehyde on C1 is oxidised
- Then acyl-phosphate formation (dehydration) takes place
3
Q
What is the equation of NAD to NADH
A
- NAD + H+ + 2e- NADH
2. Forward is reduction backwards is oxidation
4
Q
Describe the thermodynamics of step 6
A
- dG transition state is large
2. big dip between oxidation and acyl-bond formation
5
Q
Describe the structure of Glyceraldehyde-3-phosphate dehydrogenase
A
- Glyceraldehyde-3-phosphate dehydrogenase is a homo-tetramer- is composed of four identical subunits.
- Many of the structures of this enzyme in the PDB have NAD bound in all four active sites, as well as two phosphate or sulfate ions.
- One ion is bound in the site occupied by the phosphate group in the sugar molecule, and the other is thought to correspond to the site that positions the incoming phosphate ion for the reaction.
- A nearby cysteine amino acid will then attack the molecule, forming a bond with one carbon atom.
- The bond is then broken when the phosphate is attached.
- In this structure, the cysteine is changed to a less active serine to allow study. A nearby histidine also assists in the reaction.
6
Q
What happens in steps 6 and 7
A
- Halfway through glycolysis, the cell is finally ready to start extracting some energy.
- In the sixth and seventh steps, the cell will add a new phosphate to each of the molecules, and then use it to make two new ATP molecules.
- Glyceraldehyde-3-phosphate dehydrogenase takes a phosphate ion and connects it to the molecule. In the process, it also extracts two hydrogen atoms using the hydrogen-carrier molecule NAD
- These hydrogen atoms may be used to create even more energy using aerobic pathways, or recycled in several ways back onto the broken sugar molecule.
7
Q
What happens in step 7 of glycolysis
A
- 1,3- bisphosphoglycerate is converted to 3-phosphoglycerate and ATP produced
- Catalysed phosphoglycerate kinase
8
Q
Describe the process of converting 1,3 bisphosphoglycerate to 3-phosphoglycerate
A
- The terminal phosphoryl oxygen of ADP nucleophilically attacks the C1 phosphorus atom of 1,3-BPG to form 3-phosphoglycerate
- Mg2+ cofactor used
9
Q
Describe the structure of phosphoglycerate kinase (PGK)
A
- Similar to hexokinase
- Phosphoglycerate kinase takes 3PG molecules and transfers one of the phosphates to ADP, creating a new ATP molecule.
- As with the first enzyme of glycolysis, this process must be shielded from water to ensure that the phosphate gets transferred correctly.
- Phosphoglycerate kinase uses the same approach taken by hexokinase: it closes around the reaction, protecting it away from interfering water molecules.
- The enzyme is composed of two lobes connected by a flexible linker. The upper lobe binds to ADP and the lower one has a pocket for the glucose fragment.
- Then it hinges close and performs the transfer.
- The PDB entry 3pgk is in the open form with ADP bound
10
Q
Describe the energy involved in step 6 + 7 of glycolysis
A
- GAP + NAD+ +Pi –> 1,3-BPG + NADH dG endergonic
- 1,3 BPG + ADP –> 3PG + ATP dG exergonic
- Overall favourable
11
Q
What happens in step 8 of glycolysis
A
- 3-phosphoglycerate (3PG) is converted to 2-phosphoglycerate (2PG)
- Catalysed by phosphoglycerate mutase
12
Q
Describe the process of converting 3-phosphoglycerate (3PG) to 2-phosphoglycerate (2PG)
A
- The active enzyme has a phosphoryl group at its active site
- It transfers it to the substrate to form a bisphospho intermediate
- This intermediate then rephosphorylates the enzyme to form the produce and regenerate the active phosphoenzyme
13
Q
Describe the structure oh phosphoglycerate mutase
A
- The yeast enzyme is composed of four identical subunits. Our enzyme is similar, but only contains two subunits. Plants and many bacteria build an entirely different type that uses manganese ions for the reaction
- The enzyme in our cells uses a special histidine amino acid.
- This histidine first places a phosphate on the molecule, so that two are attached, then it takes off the other one.
- In order to do this, the enzyme must be charged with this extra phosphate molecule before it can perform its reaction.
- A small intermediate molecule–2,3- bisphosphoglycerate–delivers these reactive phosphates to the enzyme.
- After the enzyme is charged, it remains active for a minute or two (busily performing its reaction many times) before the phosphate falls off and has to be replaced.
14
Q
What happens in stage 9 of glycolysis
A
- 2-phosphoglycerate (2PG) is converted to phosphoenolpyruvate (PEP)
- Catalysed by Enolase
15
Q
Describe the process of converting 2-phosphoglycerate (2PG) to phosphoenolpyruvate (PEP)
A
- Enolase uses two metal ions in its reaction. The first is a magnesium ion
- It anchors the molecule to the enzyme, holding it in the proper place.
- The second ion then binds and assists with the catalysis.
- A perfectly-placed histidine also assists in the reaction.
- The OH on the C3 is eliminated and the H on C2 joins it to form H2O
