Metabolic pathways Flashcards
(38 cards)
- Explain the difference between anabolic and catabolic processes.
- Know the expression relating change in Gibbs free energy, change in enthalpy and change in entropy.
- Recognize (but not draw) the structures of the key energy transfer molecules ATP, CoA, FADH2/FAD, NADH/NAD+
- Recognize (but not draw) the structure of substrates and products in the preparatory phase of glycolysis.
- Describe what is happening in each step.
Reaction 1: Phosphorylation of Glucose
- Glucose enters cytoplasm of cell where it is phosphorlyated by hexokinase using ATP into glucose-6-phosphate
- The reaction releases free energy and is exergonic and spontaneous because ATP is converted into a more stable molecule ADP in the process
- The conversion of glucose to glucose-6-phosphate is catalysed by HEXOKINASE in most tissues and GLUCOKINASE in the liver.
> THE POINT OF THIS STEP:
- destabilise the glucose to make it more reactive
- By adding the polar component, we trap the glucose in the cell because it cantpass the membrane or use any transport proteins as its structure is different
o First IRREVERSIBLE reaction of GLYCOLYSIS
Reaction 2: Isomerisation of Glucose-6-Phosphate to Fructose-6-Phosphate
- The conversion of glucose-6-phosphate to fructose-6-phosphate catalysed by PHOSPHOHEXOSE ISOMERASE is freely REVERSIBLE
- To produce two identical 3 carbon molecules we have to have symmetry in our molecule
- it is exergonic
Reaction 3: Conversion of Fructose-6-Phosphate to Fructose-1,6-bisphosphate
- Second IRREVERSIBLE reaction of glycolysis and the first COMMITTED step of GLYCOLYSIS (i.e. RATE-LIMITING STEP)
- Exergonic
- Enzyme is phosphofructokinase 1 (PFK-1)
Reaction 4: Cleavage of F-1, 6-bP
- Aldolase cuts the F-1, 6-bisP in the middle, producing DHAP and GA-3-P, each with a single phosphate attached. The enzyme can catalyse the reverse reaction, which is more favourable & is in fact named after the reverse reaction which is an “aldol condensation”
- Produces Dihydroxyacetone phosphate and glyceraldehyde-3-phosphate
- endergonic, free energy absorbed
Reaction 5: Isomerisation of DHAP to Glyceraldehyde-3-Phosphate
- DHAP is an isomer of GAP
- DHAP is converted to GAP by Triose Phosphate Isomerase, which pulls a hydrogen atom off one carbon atom and replaces it on a neighbouring carbon atom. A special glutamate amino acid in the active site (Glu-165) performs the transfer.
- Endergonic
NET RESULT:
- Converted glucose into two 3 carbon molecules (glyceraldehyde 3 phosphate)
- (-2) ATP
- Whenever ΔG′° is shown, interpret the significance ΔG′° and predict how ΔG will be affected by cellular conditions.
- Explain how many ATP are consumed per glucose during the preparatory phase.
- Recognize (but not draw) the structure of substrates and products in the payoff phase of glycolysis.
- Describe what is happening in each step.
Reaction 6: Oxidation of Glyceraldehyde-3-Phosphate to 1,3-Bisphosphoglycerate
- The activity of Glyceraldehyde 3-phosphate Dehydrogenase depends on the turnover of NAD+ in the cytosol of the cell. Rapid turnover of NAD+ is only achieved under anaerobic conditions
- We want to transform a molecule with a relatively low potential to transfer phosphoryl to one that has a higher potential
- The aldehyde loses its H that is replaced by Phosphate
- Endergonic
Reaction 7: Conversion of 1,3-Bisphosphoglycerate to 3-phosphoglycerate
- PGK transfers the phosphate from 1,3-BPG to ADP to form ATP – it’s taken 7 steps, finally ATP is generated!
- exergonic
Reaction 8: Mutase Reaction Converting 3-phosphoglycerate to 2-phosphoglycerate
- Phosphoglycerate Mutase begins the final capture of energy by shifting the phosphate from Carbon-3 of the phosphoglycerate molecule to Carbon-2, priming it for phosphate transfer to ADP
- 3-phosphoglycerate is transferred into a less stable molecule so we can make it more reactive, this is done by bringing the negative charge on oxygen closer to the negative charge on phosphate
- Endergonic process, so it isnt spontaneous under physiological conditions and the product is less stable
Reaction 9: Dehydration of 2-phosphoglycerate to Phosphoenolpyruvate
- Enolase is a Mg2+-dependent enzyme that converts 2-PG (which has a relatively low phosphoryl group transfer potential of -17.6 KJ/mol) to PEP (-61.9 KJ/mol)
- dehydration reaction results in loss of water and converts 2-PG into an enol by shifting hydrogen from carbon 2 to carbon 3 and making a double bond between carbon 2 and carbon 3
- overall reaction 9 is endergonic reaction because product is unstable
- product has very high phosphoryl transfer potential because its trappped in the enol state because the oxygen doesnt have a H but has a phosphoryl group
- the phosphoryl must be donated to ADP and it can transfer to a stable pyruvate molecule in the ketone form with a H bound instead
Reaction 10: Production of ATP from the Conversion of PEP to Pyruvate
- Structure of Pyruvate Kinase tetramer with regulatory molecules (magenta), K+/Mg2+ ions (green) and phosphoenolpyruvate (yellow)
- exergonic because product is more stable
- produces ATP
NET RESULT:
- payoff phase occurs twice for each 3-phosphoglycerates to make 2 pyruvates from the glucose
- Forms 4 ATP total
- Formed 2 ATP molecules in total and 1 NADH, so around 5 ATP in total made
- (1 NADH = 3 ATP)
Describe stage 1 and 2 of glycolysis - AK
STAGE 1 - PREP PHASE
- Traps glucose in cell and destabilises its structure
- breaks down glucose into smaller components
> STEP 1
- Trap glucose in the cytoplasm of the cell by changing the structure of the glucose molecule
- makes it more polar (negative charge of 2) and so membrane transport proteins can’t bind glucose-6-phosphate and move it out of the cell
- IRREVERSIBLE
- to begin destabilise the glucose (polarity makes it unstable and higher in energy/more reactive)
- Requires ATP
- HEXOKINASE is enzyme that adds phosphoryl groups using ATP on HEXOSE sugars
- Hexokinase has two domains that rotate to capture the glucose and requires a divalent metal atom to function (e.g. Mg2+) that interacts with ATP molecule to change conformation of ATP so it can undergo reaction at active site of hexokinase and water is removed from active site so it doesnt react with ATP
> STEP 2:
- The sugar molecule in its cyclic form doesn’t undergo any reaction because the aldehyde group isn’t exposed
- PHOSPHOGLUCOSE ISOMERASE then opens the structure into open chain to expose reactive group and the it converts to fructose-6-phosphate
- converts aldose to ketose
> STEP 3:
- Adds another phosphoryl group using PFK to make fructose 1-6 bisphosphate
- Another ATP used (enzyme is a kinase)
- IRREVERSIBLE
- Commits glucose to undergoing glycolysis because before this step the sugar molecule could have been stored as glycogen still
> STEP 4:
- Take the highly reactive fructose 1-6 bisphosphate and form 2 identical 3C molecules (GAP)
- Two Enzymes - ALDOLASE and TRIOSE PHOSPHATE ISOMERASE
- ALDOLASE breaks down fructose 1-6 bisphosphate into two different 3C molecules GAP and DHAP by first transferring the fructose 1-6 bisphosphate into open chain form so cleavage can occur
- Glucose cant directly be cleaved because it will produce unidentical molecules
> STEP 5:
DHAP is transferred to GAP by TRIOSE PHOSPHATE ISOMERASE
- The active site of the enzyme contains alpha-beta barrels and two catalytic residues (GLU-165 and HIS-95) that catalyse reaction by acid-base reaction respectively
- HIS-95 donates an H to the double bonded ketone carbon on the DHAP molecule GLU-165 removes H from 1st carbon of DHAP
- HIS-95 then removes a H from Oxygen on the other hydroxyl
STAGE 2 - PAYOFF PHASE
- harvests the energy to form ATP molecules and pyruvate
Glycolysis q’s:
1. Where does the oxidation of glucose occur?
2. How many steps are required to oxidise glucose?
3. Where/when is O2 required?
4. How is CO2 produced?
5. How many ATP are produced?
6. What happens when there is no O2 available?
7. Is the reaction reversible?
- Where does the oxidation of glucose occur?
🧪 In the cytoplasm of the cell. - How many steps are required to oxidize glucose?
🧬 Glycolysis has 10 steps.
Further oxidation (in mitochondria) involves many more steps — through the pyruvate dehydrogenase complex, Krebs cycle, and electron transport chain.
- Where/when is O₂ required?
🧾 O₂ is not required during glycolysis.
Glycolysis is anaerobic — it occurs with or without oxygen.
However, O₂ is essential later in aerobic respiration, specifically in the electron transport chain (ETC) in the mitochondria, where it acts as the final electron acceptor.
Without oxygen, NADH produced in glycolysis cannot be oxidized by the ETC — which becomes a problem
- How is CO₂ produced?
🌬️ CO₂ is not produced in glycolysis.
It is released later:
In the pyruvate dehydrogenase complex (pyruvate → acetyl-CoA): 1 CO₂ per pyruvate.
In the Krebs cycle: 2 CO₂ per acetyl-CoA.
➡️ Total per glucose (2 pyruvate):
2 CO₂ from pyruvate → acetyl-CoA
4 CO₂ from Krebs cycle
→ 6 CO₂ total per glucose molecule during full oxidation.
- How many ATP are produced?
💥 From glycolysis alone:
2 ATP used
4 ATP made
Net = 2 ATP per glucose
➕ Also: 2 NADH made → each can yield ~2.5 ATP later in the ETC (if O₂ is present).
🧮 Total ATP yield from full aerobic oxidation (including mitochondria):
~30–32 ATP per glucose
- What happens when there is no O₂ available?
🧪 The cell switches to anaerobic metabolism:
Glycolysis continues (since it doesn’t need oxygen).
NADH made in glycolysis must be reoxidized to NAD⁺, or glycolysis stops.
✅ This is done by fermentation:
In muscle: pyruvate → lactate
In yeast: pyruvate → ethanol + CO₂
➡️ Fermentation regenerates NAD⁺, allowing glycolysis to continue — but no more ATP is made beyond the 2 from glycolysis.
- Is the reaction reversible?
🔁 Parts of glycolysis are reversible, others are not.
Reversible steps: Most of the intermediate steps (like isomerizations, phosphorylations, etc.).
Irreversible steps: Three key regulated, exergonic steps:
Hexokinase (glucose → glucose-6-phosphate)
Phosphofructokinase-1 (F6P → F1,6BP)
Pyruvate kinase (PEP → pyruvate)
🧬 These irreversible steps are bypassed by different enzymes in gluconeogenesis (the reverse pathway that makes glucose from pyruvate).
- Whenever ΔG′° is shown, interpret the significance ΔG′° and predict how ΔG will be affected by initial conditions.
- Explain how many ATP are produced per glucose during the payoff glycolysis.
- State the Warburg hypothesis and explain how this has influenced chemotherapeutic treatments for cancer.
- Recognize (but not draw) the structure of substrates and products in gluconeogenesis.
- Describe what is happening in each step of gluconeogenesis.
> Gluconeogenesis is the process that gives the ability of certain body cells to produce glucose from non-carb precursor molecules - pyruvate, lactate, glycerol, and amino acids
- ONLY SPECIFIC BODY CELLS CAN DO THIS - LIVER (hepatocytes) and KIDNEYS (cuz they regulate glucose levels)
1. When there isnt enough glucose in the body, we can take pyruvate and reverse steps of glycolysis apart from the IRREVERISBLE steps which have to be bypassed
2. if we exercise vigorously, our skeletal muscles produce ATP for contraction and we run out of oxygen, so rate of glycolysis > oxidative phosphorylation so we begin lactic acid fermentation where skeletal muscle cells produce lactic acid that dissociate into H+ ions and lactate, Lactate enters blood plasma and the liver where glucose can be created by lactate dehydrogenase, lactate doesnt enter gluconeogenesis - its transferred into pyruvate first
3. Glycerol (component of triglycerides in adipose/fat cells) - fatty acids cant form glucose, but glycerol can (glycerol kinase and glycerol phosphate dehydrogenase) eventually form DHAP that enters gluconeogenesis
4. Amino acids by breakdown of proteins in skeletal muscles - can either enter glucneogenesis by pyruvate or DHAP
GLUCONEOGENESIS IS NOT SIMPLY THE REVERSE OF GLYCOLYSIS:
- Because glycolysis is a very exergonic process and occurs spontaneously and irreversibly
- It doesnt simply follow the reverse steps of glycolysis or it would be too expensive for the cell - require too much energy
- STEP 1/3/10 are VERY exergonic and make up majority of free energy released during glycolysis
STEPS:
> The 3 irreversible steps of Glycolysis are catalysed by different enzymes in GNG:
STEP 1:
- Occurs in a matrix of mitochondria
- Conversion of pyruvate to oxaloacetate intermediate by pyruvate carboxylase
- hydrolyses an ATP molecule, which can drive carboxylation (attach CO2) of pyruvate into oxaloacetate
- Pyruvate Carboxylase is a mitochondrial enzyme that adds a carboxylic acid to pyruvate to form oxaloacetate using BIOTIN (vitamin B7) as a cofactor
- oxaloacetate is reduced to malate by malate dehydrogenase so it can move to cytosol and this is reversed once it enters cytosol
- Phosphoenolpyruvate Carboxykinase phosphorylateds oxaloacetate and also dereacts oxaloacetate with GTP to generate PEP
- GDP is important as it suppresses protein metabolism, if we’re producing lots of GDP it signals protein metabolism
STEP 2:
- Conversion of F-1, 6-bisP to F-6-P is catalysed by Fructose 1,6 Biphosphatase
STEP 3:
- Conversion of G-6-P to Glucose occurs In the ER lumen using Glucose-6-Phosphatase
Pyruvate Carboxylase:
- Pyruvate Carboxylase is a mitochondrial enzyme that adds a carboxylic acid to pyruvate to form oxaloacetate using BIOTIN (vitamin B7) as a cofactor
Phosphoenolpyruvate Carboxykinase reacts oxaloacetate with GTP to generate PEP
- GDP is important as it suppresses protein metabolism, if we’re producing lots of GDP it signals protein metabolism
Fructose-1, 6-Bisphosphatase is converted to Fructose-6-phosphate by Fructose-1,6-Bisphosphatase a reaction that occurs in the cytosol
Glucose-6-Phosphatase
- Conversion of glucose-6-phosphate to glucose by glucose-6-phosphatase occurs in the lumen of the Endoplasmic Reticulum in hepatocytes of the Liver and in the cortex of the Kidney
- Whenever ΔG′° is shown, interpret the significance ΔG′° and predict how ΔG will be affected by initial conditions
- Compare Gluconeogenesis and Glycolysis highlighting the differences in subcellular location, substrate(s), cofactor(s), product(s) and enzymes used.
- Recognize (but not draw) the structure of substrates and products for the Cori cycle. Explain the importance of the roles of each enzyme.
- Explain why is lactate dehydrogenase important during anaerobic glycolysis.
- Describe the metabolic fate of lactate produced in the muscle and how this is linked to metabolism in the liver.
- Recognize (but not draw) the structure of substrates and products for glycogenolysis and glycogenesis. Explain the importance of the roles of each enzyme.
- Describe the structure of glycogen; and why it is stored in the liver and muscle.
- Explain how glycogenolysis and glycogenesis are linked to glycolysis and gluconeogenesis.
