Biochem Exam 3
STEP 7 GLYCOLYSIS
(2) 1,3-bisphosphglycerate to (2) 3-phosphoglycerate Enzyme: phosphoglycerate kinase Releases ATP REVERSIBLE STEP => has a ∆G<0, but is coupled to step 6 of glycolysis, and becomes a reversible step
STEP 9 GLYCOLYSIS
(2) 2-phosphoglycerate to (2) phosphoenolpyruvate (PEP) Enzyme: enolase Releases H20 REVERSIBLE STEP
STEP 8 GLYCOLYSIS
(2) 3-phosphoglycerate to (2) 2-phosphoglycerate Enzyme: phosphoglycerate mutase REVERSIBLE STEP
STEP 6 GLYCOLYSIS
(2) GAP to (2) 1,3-bisphosphoglycerate Enzyme: GAPDH (glyceraldehyde-3-phosphate dehydrogenase) Releases (2) NADH REVERSIBLE STEP => has a high ∆G, but is coupled to the next reaction in order to occur
STEP 10 GLYCOLYSIS
(2) Phosphoenolpyruvate (PEP) to (2) pyruvate Enzyme: pyruvate kinase Releases (2) ATP IRREVERSIBLE STEP
What is the position emission topography (PET)?
Can use PET (position emission topography) to analyze the amount of glucose the different areas of our brain are using Helps with detecting brain tumors
STEP 5 GLYCOLYSIS
Dihydroxyacetone phosphate (DHAP) to glyceraldehyde-3-phosphate (GAP) Enzyme: triose phosphate isomerase REVERSIBLE STEP
Provide a summary of carbohydrate metabolism in plants
Carbohydrate metabolism = photosynthesis Photosynthesis can be divided into 2 parts (occurs in the chloroplast) - Light reactions (occurs in thylakoid of chloroplast) => Using light energy, NADPH and ATP are produced Dark reactions (occurs in stroma of chloroplast) - ATP used to reduce CO2 into trioses (sugars), which are converted into hexoses and pentoses (used in gluconeogenesis and pentose phosphate pathway)
How is energy charge a regulation parameter?
Cells try to maintain a stable [ATP]:[AMP] ratio When ATP is depleted by 10%, ATP levels go down a bit, ADP remains constant, but AMP goes up 600% -> AMP level is a very sensitive parameter to sense the energy charge of the cell! As energy charge decreases, the cell wants to do less and less catabolic pathways (vice versa for anabolic pathways)
Which metabolic pathways occur in the mitochondria?
Citric acid cycle Electron transport Oxidative phosphorylation Fatty acid oxidation Amino acid breakdown
Define catabolism
Conversion of energy containing nutrients into energy depleted end products Produces ATP
Define anabolism
Conversion of precursor molecules into macromolecules Requires ATP
What is NADPH a precursor molecule for?
Fatty acids and sterols
STEP 4 GLYCOLYSIS
Fructose-1,6-bisphosphate to glyceraldehyde-3-phosphate (GAP) + dihydroxyacetone phosphate (DHAP) Enzyme: aldolase REVERSIBLE STEP
STEP 3 GLYCOLYSIS
Fructose-6-phosphate to fructose-1,6-bisphosphate THE COMMITTED STEP Enzyme: phosphofructokinase-1 (PFK-1) Requires ATP IRREVERSIBLE STEP
What are the guidelines for metabolic regulation?
Fuel efficiency - Use ATP responsibly (e.g. don't run glycolysis and gluconeogenesis in parallel) Partitioning - Divert the flow from a common intermediate such that the product in demand is favored Slow down pathway when product accumulates (i.e. there is little demand for product)
What is ribose-5-phosphate a precursor molecule for?
Nucleic acids (DNA and DNA), coenzymes, nucleotides
What happens during the non-oxidative phase of the pentose phosphate pathway?
Occurs when we need NADPH When demand for NADPH is higher than the demand for ribose 5-phoshpate, the ribulose 5-phosphate is recycled to reform glucose 6-phosphate Involves a series of transfer reactions involving transketolase and transaldolase
What is the formula for finding the rate of a reaction?
Rate of reaction (Vo) = (Kcat x [Et] x [S]) ÷ (Km + [S])
Step 1 gluconeogenesis
(2) Pyruvate to (2) phosphoenolpyruvate (PEP) Occurs in the mitochondria and cytosol via malate shuttle Pyruvate from cytosol transported into mitochondria 1) Pyruvate to oxaloacetate - Enzyme: pyruvate carboxylase 2) Oxaloacetate to malate - Enzyme: mitochondrial malate dehydrogenase - Produces NAD+ 3) Malate transported out of mitochondria into the cytosol 4) Malate to oxaloacetate - Enzyme: cytosol malate dehydrogenase 5) Oxaloacetate to PEP - Enzyme: cytosol PEP carboxykinase
What is the energy conversion of FADH2?
1 FADH2 = 1.5 ATP
What is the energy conversion of NADH?
1 NADH = 2.5 ATP
What are the 5 general principles of metabolic pathways?
1) Metabolic pathways are irreversible 2) Catabolic and anabolic pathways must differ 3) Every metabolic pathway has a committed step 4) All metabolic pathways are heavily regulated 5) Metabolic pathways in eukaryotic cells occur in specific compartments
What is the overall reaction for gluconeogenesis?
2 pyruvate + 4 ATP + 2 GTP + 2 NADH + 2 H+ + 4 H20 → glucose + 6 Pi + 4 ADP + 2 GDP + 2 NAD+
What is the energy currency of the cell?
ATP
What are the fates of pyruvate?
Aerobic conditions - Conversion to Acetyl-CoA via release of CO2. Acetyl-CoA enters citric acid cycle Anaerobic conditions - Ethanol fermentation - Lactate fermentation Gluconeogenesis (pyruvate back to PEP)
What are the main points of regulation of glycolysis?
All of the irreversible steps Step 1 Step 3 Step 10
Why do cancer cells heavily rely on glycolysis?
Almost always, there aren't enough capillaries surrounding the cells to provide nutrients and energy to the cells. Therefore, the only way the cell can produce energy is through anaerobic glycolysis Mechanism: Hypoxia → induces Hypoxia-inducible transcription factors → increase expression of several glycolytic enzymes - HIP-1 is the major hypoxia-inducible transcription factors. If amount of HIP-1 increases, there is more protein binding glycolytic enzymes. With more glycolytic enzymes, you can convert more glucose into pyruvate Cancer cells often have fewer mitochondria - Glycolysis occurs in the cytosol, so it can function in cells without mitochondria. Krebs cycle and oxidative phosphorylation occur in mitochondria, and without mitochondria these energy producing pathways can't occur
Why does it take three rounds to make one glyceraldehyde-3-phosphate in the Calvin Cycle?
GAP is a 3-carbon compound and so you need 3 CO2 molecules to build it. So, for simplicity we run the cycle starting with not 1 CO2, but 3 CO2 (and 3 ribulose 1,5-bisphosphate). Another way of saying it is you run the cycle thrice, each time with one CO2 molecule. Different ways of conveying the simple concept that it takes 3 CO2 molecules to build one GAP.
How does gluconoegenesis differ from glycolysis?
Gluconeogenesis is the reverse reaction of glycolysis, converting 2 pyruvate molecules into a single glucose molecule Gluconeogenesis avoids the irreversible steps of glycolysis (Steps 1,3,10) by using different enzymes 3 points of regulation for glycolysis 2 points of regulation for gluconeogenesis Glycolysis primarily occurs in muscles and the brain Gluconeogenesis primarily occurs in the liver (and kidney)
Summarize the reactants of products of glycolysis
Glucose + 2 Pi + 2 ADP + 2 NAD+ → 2 pyruvate + 2 ATP + 2 NADH + 2 H+ + 2 H2O
STEP 1 GLYCOLYSIS
Glucose to glucose-6-phosphate Enzyme: hexokinase Requires ATP - ATP bound Mg2+ facilitates reaction by shielding negative charges on ATP IRREVERSIBLE STEP
Why can't we regulate the last step of gluconeogenesis (aka the first step of glycolysis)?
Glucose to glucose-6-phosphate requires ATP. The reverse reaction would mean producing ATP from glucose-6-phosphate However, the phosphate transfer potential of glucose-6-phosphate is insufficient to actually transfer the phosphate group to ADP to make ATP - Therefore, there is no reversal of glycolysis possible at this step Glucose-6-phosphatase will converte glucose-6-phosphate to glucose at a rate depending on concentration that can't be controlled
What happens during the oxidative phase of the pentose phosphate pathway?
Glucose to glucose-6-phosphate via hexokinase (requires ATP) Glucose-6-phosphate to 6-phosphoglucono-d-lactone - Enzyme: glucose-6-phosphate dehydrogenase - Produces NADPH 6-phosphoglucono-d-lactone to 6-phoshogluconate - Enzyme: lactonase - Requires H20 6-phoshogluconate to ribulose-5-phosphate - Enzyme: phosphogluconate dehydrogenase - Produces NADPH Ribulose-5-phosphate to ribose-5-phosphate - Enzyme: phosphopentose isomerase
STEP 2 GLYCOLYSIS
Glucose-6-phosphate to fructose-6-phoshpate Enzyme: phosphohexose isomerase REVERSIBLE STEP
Which metabolic pathways occur in the cytosol?
Glycolysis Pentose phosphate pathway Fatty acid biosynthesis Gluconeogenesis
What is the summary of glucose regulation?
If glucose is high: - Dephosphorylation of enzymes → increases glycolysis, increases glycogen synthesis, decreases gluconeogenesis, decreases glycogen breakdown If glucose is low: - Phosphorylation of enzymes → decreases glycolysis, decreases glycogen synthesis, increases gluconeogenesis, increases glycogen breakdown
What are the differences between an irreversible reaction and a reversible reaction?
Irreversible reactions - Highly exergonic (∆G<0) - Once product formed, unable to reform reactant Reversible reactions - ∆G≥0 - Are driven forward by depleting products (low product concentration)
What is a shortcut that occurs in gluconeogenesis that is unique to muscle cells and erythrocytes?
Lactate present in these cells can be converted directly to pyruvate via lactate dehydrogenase (reversible reaction), simultaneously converting NAD+ to NADH Pyruvate then transported to mitochondria from cytosol Pyruvate to oxaloacetate - Enzyme: pyruvate carboxylase - Requires CO2 Oxaloacetate to PEP - Mitochondrial PEP carboxykinase - Produces CO2
Which metabolic pathways occur in the smooth ER?
Lipid and steroid biosynthesis
Where does glycogen synthesis occur?
Muscles and liver
Define homeostasis
Organisms maintain homeostasis by keeping the concentrations of most metabolites at steady state Steady state means the rate of synthesis of a metabolite is equal to the rate of breakdown of the same metabolite
Which metabolic pathways occur in the rough ER?
Protein synthesis
What happens during ethanol fermentation?
Pyruvate => acetaldehyde => ethanol Step 1 enzyme: pyruvate decarboxylase (prosthetic groups TPP, Mg2+) Step 2 enzyme: alcohol dehydrogenase Pyruvate to acetaldehyde releases CO2 Acetaldehyde to ethanol produces NAD+
What happens during lactate fermentation?
Pyruvate => lactate Enzyme: lactate dehydrogenase Regenerates 2 NAD+ molecules to be used in glycolysis
How is step 3 of glycolysis regulated?
Reaction: fructose-6-phosphate to fructose-1,6-bisphosphate Enzymes involved: PFK-1 (glycolysis) and FBPase-1 (gluconeogenesis) Low blood glucose increases glucagon activity. Glucagon activates cAMP protein dependent kinase (via ATP), which activates FBPase-2 and inactivates PFK-2. FBPase-2 inhibits PFK-1 and activates FBPase-1, thus promoting gluconeogenesis to make more glucose High blood glucose increases insulin activity. Insulin activates phosphoprotein phosphatase (via water), which activates PFK-2 and inactivates FBPase-2. Increased activity of PFK-2 and decreased activity of FBPase-2 increased activity of PFK-1, promoting glycolysis to breakdown glucose Remember: dephosphorylation means glycolysis. When FBPase-2 is phosphorylated, it's activated and thus promotes gluconeogenesis. When FBPase-2 is dephosphorylated, it is inactivated and glycolysis is promoted
How is step 1 of glycolysis regulated?
Reaction: glucose to glucose-6-phosphate Regulated mainly by substrate inhibition Hexokinase regulation (hexokinase 1,2,3,4) - Hexokinase 1,2,3 have a high affinity for glucose - Hexokinase 4 has a low affinity for glucose - Hexokinase 2 is allosterically inhibited by glucose-6-phosphate - Hexokinase 4 is allosterically regulated by fructose-6-phosphate Reasoning: if we are producing a lot of glucose-6-phosphate and fructose-6-phosphate, negative feedback regulation onto hexokinase 2,4
How is step 10 of glycolysis regulated?
Reaction: phosphoenolpyruvate (PEP) to pyruvate Regulation of pyruvate kinase - In high energy state (ATP high), ATP will phosphorylate pyruvate kinase, inactivating it and inhibiting reaction - In low energy state (low ATP), water with help dephosphorylate pyruvate kinase, activating it, promoting glycolysis to make ATP - Fructose-1,6-bisphosphate promotes pyruvate kinase activity (helps keep pass of glycolysis) Pyruvate (enol form) tautomerizes to form pyruvate (keto form), the more stable tautomer
Step 7 gluconeogenesis
Regulation through dephosphorylation of FBPase-2, which activates FBPase-1 and inactivates PFK-1, promoting gluconeogenesis when glucose levels are low
What happens during glycogen synthesis?
Starting point: glucose-6-phosphate 1) Glucose-6-phosphate to glucose-1-phosphate - Enzyme: phosphoglucomutase 2) Glucose-1-phosphate to UDP-glucose - Enzyme: UDP-glucose phosphorylase - Attachment of a nucleotide to glucose-1-phosphate via a phosphodiester bond - Formation is metabolically irreversible 3) Chain extension - Glycogen synthase adds UDP-glucose units to non-reducing ends of glycogen chain of at least 4 glucose residues - Release of UDP during attachment 4) Priming - Formation of new glycogen molecules catalyzed by glycogenin - Glycogenin side chains are glycosylated, allowing for UDP-glucose to be added by glycogen synthase - Glycogenin remains in the core of the glycogen molecule
What are the 3 stages of the Calvin Cycle?
Step 1 = CO2 Fixation - Ribulose-1,5-bisphosphate to (2) 3-phosphoglycerate (3-PG) - Enzyme: Rubisco (takes a 5 carbon sugar, captures CO2, and forms 2 molecules of 3-PG) Step 2 = Reduction - (2) 3-phosphoglycerate (3-PG) to (2) glyceraldehyde-3-phosphate (GAP) - Enzyme: GAPDH - Requires NADPH Step 3 = Regeneration - (1) GAP to (1) Ribulose-5-phosphate - The other GAP goes into glycolysis
Name the 4 pathways of glucose utilization
Storage (glycogen) Glycolysis Pentose phosphate pathway Synthesis of structural polymers
How can the rate of metabolic regulation be altered?
The availability of substrate The concentration of enzyme [Et] - Changing the location of the enzyme - Changing the steady-state of the enzyme (translation, degradation) - Changing the steady-state level of the mRNA encoding the enzyme) The specific activity of the enzyme - Binding of inhibitor or activator (allosteric or non-allosteric) - Covalent modification (e.g. phosphorylation)
What is the Calvin Cycle? It's purpose?
The dark reactions of photosynthesis Purpose => use reducing equivalents of NADPH and energy (ATP), which are generated during light reaction of photosynthesis, to reduce CO2 to carbon intermediates (as part of the biosynthesis of starch, cellulose, lipids, proteins, and other organic molecules NOTE: dark reactions occur at the same time as light reactions because requires products from light reactions The Calvin Cycle requires 3 turns in order to produce 1 glyceraldehyde 3-phosphate (GAP) - 3 CO2 + 9 ATP + 6 NADPH → 1 GAP
Why do you have to run the oxidative/non-oxidative cycle 6 times to oxidize all the carbons in 1 molecule of Glucose-6-P to 6x CO2?
The simple way to think about it is that there are 6 carbons in glucose. In each oxidative phase, only one of those carbons can be released as CO2. So, to get all the 6 carbons from one single glucose 6-phosphate, you will have to do this 6 times. However remember that running the oxidative phase 6 times will consume 6 glucose 6-phosphate molecules, but at the same time, running the non-oxidative phase 6 times will regenerate 5 glucose 6-phosphate molecules. So overall, 1 glucose 6-phosphate goes in and 6 CO2 come out when you run the cycle 6 times.
What is the purpose of the pentose phosphate pathway?
To produce NADPH and ribose-5-phosphate, both of which are key biomolecule precursors NOTE: pentose phosphate pathway does not produce energy
