Lec14-16 - Metabolism, Glycolysis and the Citric Acid Cycle Flashcards
Name and define the two main classes of metabolic pathways
Catabolic (breakdown of complex molecules into simple ones to release energy) and Anabolic (build-up of complex molecules from simple ones)
What is the advantage of a multistep pathway rather than a single step one?
In a single step pathway, all the energy would be released at once, mostly in the form of heat, which would be quite inefficient. A multistep pathway (with one enzyme per step) allows the energy to be released in smaller units cells can use.
It also allows activation and inhibition of each step
What are the general characteristics of metabolic pathways?
Highly regulated (to allow response to environmental changes and avoid futile steps); often irreversible, no backing up (with a few exceptions)
Define feedback inhibition
When the product of a pathway controls its own synthesis by inhibiting an earlier step (usually the first “committed” step)
Define feed-forward activation
When a metabolite early in a pathway activates an enzyme further down the pathway
What is meant by “coupled reactions”?
Sometimes, enzyme-catalysed reactions can be the sum of two coupled reactions - one endergonic and the other exergonic, to give an overall negative delta-G
Describe the “interconversion” function of adenylate kinase
It interconverts adenine nucleotides at near equilibrium (ATP + AMP <-> 2ADP):
1. when ATP is hydrolysed rapidly in the cell, ADP levels increase; the eqb reaction will convert some ADP back into ATP
2. As the reaction moves to the left, AMP concentration increases
3. AMP acts as a metabolic signal to increase rate of some catabolic reactions
What do Nucleoside Diphosphate Kinases (NDKs) do?
They convert ATP to any other NTP (ATP + NDP <-> NTP + ADP)
How do enzymes respond to different NTPs (e.g., CTP, TTP, etc.)
They are non-specific, and work on all NTPs. NTPs participate in nucleic acid synthesis and several cellular phosphorylation reactions, and are energetically equivalent to ATP.
Free 5/5 :)
Cheers
State the net outcomes of glycolysis
(Per glucose molecule)
- TWO molecules of pyruvate produced
- TWO molecules of ATP produced
- TWO molecules of NAD+ reduced to NADH
- FOUR electrons transferred from glucose to two molecules of NAD+
Name the products/intermediates of each step of glycolysis
Glucose -> G-6-Phosphate -> Fructose-6-Phosphate -> Fructose-1,6-Bisphosphate -> Glyceraldehyde-3-Phosphate (2) -> 1,3-bisphosphoglycerate -> 3-phosphoglycerate -> 2-phosphoglycerate -> phosphoenolpyruvate -> PYRUVATE
Name the first two steps in glycolysis (reactants, products, enzymes, etc.)
- Glucose -> G-6-Phosphate (transfer of a phosphoryl group from ATP to glucose; HEXOKINASE< GLUCOKINASE)
- G-6-Phosphate -> Fructose-6-Phosphate (Isomerisation; PHOSPHOGLYCOSE ISOMERASE)
Name the third and fourth steps in glycolysis (reactants, products, enzymes, etc.) *after phosphorylation + isomerisation
- F-6-Phosphate -> F-1,6-Bisphosphate (transfer of a second phosphoryl group from ATP to F-6-P; PHOSPHOFRUCTOKINASE/PFK)
- F-1,6-Bisphosphate -> 2 Dihydroxyacetone phosphate//Glyceraldehyde-3-Phosphate (rapid interconversion of triose phosphates (FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE, then TRIOSE PHOSPHATE ISOMERASE)
Name the fifth and sixth steps in glycolysis (reactants, products, enzymes, etc.) *after split + interconversion
- Glyceraldehyde-3-phosphate -> 1,3-bisphosphoglycerate (Oxidation and phosphorylation; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE/GAPDH)
- 1,3-bisphosphate -> 3-phosphoglycerate (substrate-level phosphorylation; PHOSPHOGLYCERATE KINASE)
Final 3 steps of glycolysis (reactants, products, enzymes, etc.) *after S-L phosphorylation
- 3-phosphoglycerate -> 2-phosphoglycerate (PHOSPHOGLYCERATE MUTASE)
- 2-phosphoglycerate -> phosphoenolpyruvate (removal of water; ENOLASE)
- Phosphoenolpyruvate -> Pyruvate (substrate level phosphorylation; PYRUVATE KINASE)
Name all 10 steps of glycolysis (short version)
- ATP hydrolysis
- Isomerisation
- ATP hydrolysis
- Cleavage/split
- Rapid interconversion of triose phosphates
- Oxidation + Phosphorylation by NAD+ + Pi
- S-L phosphorylation
- Isomerisation
- Removal of H2O
- S-L phosphorylation
What are the three possibilities for further metabolism of pyruvate (and where/when do each of these occur)?
- Aerobic Conditions - Oxidised to Acetyl CoA (Link Reaction) then Citric Acid Cycle + ETC
- Anaerobic Conditions - converted to Ethanol (microorganisms; fermentation)
- Anaerobic Conditions - converted to Lactate (muscles, red blood cells)
Name the two steps of further metabolism of pyruvate in Yeasts (alcoholic fermentation)
- Pyruvate -> Acetaldehyde (PYRUVATE DECARBOXYLASE)
- Acetaldehyde -> Ethanol (ALCOHOL DEHYDROGENASE)
State the OVERALL reaction of respiration in yeasts, and state what this shows about net redox
Glucose + 2ADP + 2Pi + 2H+ -> 2Ethanol + 2ATP + 2CO2 + 2H2O
(no NAD+ or NADH appear in overall reaction - no net oxidation or reduction)
Describe the further metabolism of pyruvate in anaerobic conditions in cells of higher organisms
Pyruvate -> Lactate (dehydrogenation; LACTATE DEHYDROGENASE)
State the OVERALL reaction of anaerobic respiration in higher organisms, and state what this shows about net redox
Glucose + 2ADP + 2Pi -> 2Lactate + 2ATP + 2H2O
Name the three steps of glycolysis that involve a free energy change (number, reactants/products)
- Glucose + ATP -> Glucose-6-Phosphate + ADP (HEXOKINASE)
- Fructose-6-Phosphate + ATP -> Fructose-1,6-bisphosphate + ADP (PHOSPHOFRUCTOKINASE)
- Phosphoenolpyruvate + ADP -> Pyruvate + ATP (PYRUVATE KINASE)
What is the significant difference between the three steps of glycolysis that involve a free energy change, and the seven that do not
These 3 reactions are IRREVERSIBLE and their enzymes are REGULATED
Name the regulators (activators and inhibitors) of the enzymes for steps 1, 3 and 10 of glycolysis
- (Hexokinase) - INHIBITED BY G-6-P (product)
- (Phosphofructokinase) - ACTIVATED BY AMP [AND FRUCTOSE-2,6-BISPHOSPHATE], and INHIBITED BY ATP [AND CITRATE]
- (Pyruvate Kinase) - ACTIVATED BY FRUCTOSE-1,6-BISPHOSPHATE and INHIBITED BY ATP
Why is it significant that ATP and AMP are inhibitor/activator for (PFK-1) step 3 of glycolysis respectively
This allows cells to increase or decrease rates of glycolysis in response to energy requirements
Where in the body are there alternative regulators of PFK-1 and what are these regulators?
In the liver - citrate = inhibitor; F-2,6-bisphosphate = activator
Describe the Link Reaction (reactants, products, enzymes, etc.)
Pyruvate Decarboxylation: Pyruvate + CoA-SH + NAD+ -> Acetyl-CoA + CO2 + NADH
Catalysed by Pyruvate Dehydrogenase Complex (PDC)
(Requires Thyamine Pyrophosphate [TPP]; Flavin Adenine Dinocleotide [FAD]; Lipoate)
Describe the role of each enzyme in the Pyruvate Dehydrogenase Complex (PDC) and how many subunits of each
24 x E1 - Pyruvate Oxidative Decarboxylation
24 x E2 - Transfer of Acetyl Group to CoA
12 x E3 - Cofactor Regeneration
Where is the Pyruvate Dehydrogenase Complex (PDC) located in eukaryotes, and how does pyruvate get to it?
In the mitochondrial matrix; Pyruvate Translocase (PT) is found in the inner mitochondrial membrane - it is a Pyruvate/H+ symporter
go over citric acid cycle in full, it’s too complex for a flashcard lol
goes over citric acid cycle in full
What is the first step once Acetyl Co-A enters the citric acid cycle?
Condensation reaction:
Acetyl CoA + Oxaloacetate -> Citrate (6C) ; loss of CoA-SH ; catalysed by citrate synthase
What is the first step of the citric acid cycle in which NADH is actually formed?
Isocitrate + NAD+ -> alpha-keotglutarate + CO2 + NADH (oxidative decarboxylation) ; catalysed by isocitrate dehydrogenase
Which step in the citric acid cycle produces ATP or GTP?
Succinyl CoA -> Succinate + CoA-SH (SL-phosphorylation) ; catalysed by succinyl-CoA synthase
Which step of the citric acid cycle forms FADH2?
Succinate + FAD -> Fumerate + FADH2 (dehydrogenation) ; catalysed by succinate dehydrogenase
What is the third step of the citric acid cycle that produces NADH?
Malate + NAD+ -> Oxaloacetate + NADH (dehydrogenation) ; catalysed by malate dehydrogenase
What is the second step of the citric acid cycle that produces NADH?
alpha-ketoglutarate + CoA-SH + NAD+ -> Succinyl CoA + CO2 + NADH (oxidative decarboxylation) ; catalysed by alpha-ketoglutarate dehydrogenase complex
What are the four outcomes for each Acetyl CoA that enters the Citric Acid Cycle
- Two molecules of CO2 are released
- 3NAD+ and 1FAD are reduced to 3NADH and 1FADH2
- One GDP/ADP is phosphorylated to GTP/ATP
- Initial molecule (oxaloacetate) is reformed
How much ATP is produced on average per NADH, per FADH2, and per Acetyl CoA?
Each NADH = 2.5 ATP
Each FADH2 = 1.5 ATP
Each Acetyl CoA = (3 x 2.5) + (1 x 1.5) + 1 = 10 ATP!
Why do the 2NADH from glycolysis produce EITHER 3 OR 5 ATP?
It is formed in the cytosol and cannot cross mitochondrial membranes, so it reduces another molecule that can carry the electrons across the membranes (a mitochondrial shuttle). 1.5 or 2.5 ATP per NADH DEPENDING ON WHICH SHUTTLE
What are the two mitochondrial shuttles and how much ATP is produced when each one is used?
Malate-aspartate shuttle: more common and more efficient, each NADH converts into 2.5 ATP
Glycerol-phosphate shuttle: brown adipose tissue; each NADH converts into 1.5 ATP
Which enzyme is regulated to control entry into the citric acid cycle (and why is regulation of this reaction so significant)?
Pyruvate Dehydrogenase Complex (PDC) -> the Link Reaction is an irreversible step, and commits carbon atoms either to oxidation to CO2 or incorporation into Lipid
What three things can inhibit or inactivate Pyruvate Dehydrogenase Complex (and which subunit does each of these act on)?
- High levels of Acetyl CoA inhibit E2 [inhibits]
- High levels of NADH inhibit E3 [inhibits]
- Phosphorylation of E1 by pyruvate dehydrogenase kinase [INACTIVATES]
What two things can activate Pyruvate Dehydrogenase Complex?
- Allosteric activation by Fructose-1,6-bisphosphate
- Feed-forward activation by high levels of NAD+
Which two enzymes the citric acid cycle are key regulatory steps (and which extra one in bacteria)?
- Isocitrate dehydrogenase
- a-ketoglutarate dehydrogenase
(Citrate synthase / 1st step)
