Important Biochemistry Concepts Flashcards
Glycolysis, 3 major steps?
Hexokinase converts glucose to glucose-6-p (ATP cost)
Phosofructase(PFK) converts fructose-6-P to fructose-1,6-P2 (ATP cost) (COMMITTED STEP)
Pyruvate kinase converts PEP to pyruvate, produces 2 ATP
Glycolysis, anaerobic or aerobic
Anaerobic
Glycolysis, full chemical reaction?
Glucose -> Glucose-6-Phosphate -> Fructose-6-Phosphate -> Fructose-1,6-biphosphate (COMMITTED)
-> Glyceraldehyde-3-Phosphate-> 1,3-Bisphosphoglycerate -> 3-Phosphoglycerate -> 2-Phosphoglycerate -> PhosphoenolPyruvate -> Pyruvate
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Glycolysis, overall reactants and products?
Reactants: Glucose, 2NAD+, and 2ADP,Pi
Products: 2 Pyruvate, 2NADH, and 2ATP, 2H+
Glycolysis, location?
Cytosol
Fermentation, purpose?
Oxidizes NADH to regenerate NAD+ while reducing pyruvate to lactic acid (or ethanol, yeast)
Pyruvate dehydrogenase complex, definition?
Where oxidative decarboxylation of pyruvate occurs to regenerate acetyl-CoA
Pyruvate dehydrogenase complex, location?
Mitochondrial matrix
Pyruvate dehydrogenase complex, overall reactants and products?
Uses up CoA, NAD+, pyruvate
Creates NADH, CO2, Acetyl-CoA
Importance of thiamine
TPP is a prosethetic group that helps with decarboxylation of pyruvate, it is derived from Thiamine (Vitamin B)
Pyruvate Decarboxylation Complex
Pyruvate dehydrogenase complex, allosteric inhibition?
ATP and fatty acids inhibit oxidative decarboxylation of pyruvate by the pyruvate dehydrogenase complex, s_ince acetyl-CoA goes to fatty acid and ATP synthesis_
Pyruvate dehydrogenase also creates NADH and Acetyl CoA, high levels of those inhibit the function
Krebs Cycle, purpose?
Production of 3 NADH and 1 FADH2 for the electron transport chain
Also produces 2 ATP
Krebs Cycle, location?
Mitochondrial Matrix
Krebs Cycle, overall reactants and products?
Per 1 turn:
Reactants: Acetyl-CoA (from pyruvate), OAA from previous cycle
Products: 2 CO2, 3 NADH, 1 GTP, 1 FADH2
each glycose does 2 turns
Krebs Cycle, regulation methods?
Substrate availability - amino acids can be converted to alpha-ketoglutarate to speed up cycle
Substrates inhibit their enzymes - citrate inhibits citrate synthase; succinyl-CoA inhibits aKG dehydrogenase
Allosteric regulation - ATP, NADH inhibit TCA cycle
Krebs Cycle, full chemical reaction?
-> Citrate -> Isocitrate -> alpha-Ketaglutorate -> Succinyl-CoA -> Succinate -> Fumarate -> L-Malate -> OAA -> Citrate
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Kreb Cycle, steps that produce NADH?
Isocitrate dehydrogenase - Isocitrate to alpha-ketoglutarate
aKG dehydrogenase - alpha-keto glutarate to succinyl CoA
Malate dehydrogenase - malate to OAA
3 per turn, 6 per glucose
Pyruvate Dehydrogenase complex also produces an NADH
Krebs Cycle, steps that produce FADH2
Succinate dehydrogenase - Succinate to fumarate
1 per turn, 2 per glucose
Krebs Cycle, steps that produce GTP?
Succinyl-CoA synthetase - succinyl-CoA to succinate
What is oxidative phosphorylation?
The electron transport chain (Empty electron carriers) + chemiosmosis (ATP production)
Electron transport chain, location?
inner Mitochondrial Membrane. (Protons are pumped into the intermembrane space from the matrix)
Electron transport chain, purpose?
To create a proton gradient as NADH and FADH2 are oxidized
Electron transport chain, location?
Inner mitochondrial membrane
Electron transport chain, pathway?
Complex 1 - NADH dehydrogenase enzyme, pumps hydrogen into intermembrane space and transfers electrons from NADH
Complex 2 - Succinate dehydrogenase enzyme, transfers electrons from FADH2, no H+ pumped
Ubinquinone (Q) - Transfers electrons from Complex 1 and 2 to Complex 3
Complex 3 - Cytochrome C reductase enzyme, carries electrons to complex 4, pumps protons into intermembrane space
Cytochrome C - Transfers electrons from Complex 3 to Complex 4
Complex 4 - Cytochrome C oxidase enzyme, oxygen is converted to water, pumps protons into intermembrane space
Onward to Chemiosmosis
Electron transport chain, definition of prosthetic groups?
A prosthetic group is a non-protein molecule required for the activity of a protein
Electron Transport chain, overall reactants and products?
Reactants: Hydrogen ions, oxygen, NADH, FADH2
Products: Water, ATP
ATP yield, value of NADH?
2.5 ATP
ATP yield, value of FADH2?
1.5 ATP
ATP yield, total eukaryotic and prokaryotic?
Eukaryotic = ~30 ATP
Prokaryotic = ~ 32 ATP
Gluconeogenesis, purpose?
Produces glucose from pyruvate with ATP when glucose is low (fasting) and ATP is high
Gluconeogenesis, overall reactants and products?
Reactants: 4 ATP, 2 GTP, 2 NADH, 2 pyruvic acid, 6H2O, 2H+
Products: Glucose, 4 ADP, 2 GDP, 2 NAD+, 6HPO42-, 6H+
(Reverse of Glycolysis)
Gluconeogensis, location?
Mainly liver, also kidneys
Gluconeogenesis, how does glucose production differ from glycolysis?
Irreversible
Formation of glucose, fructose-6-P, and PEP are irreversible steps that push equilibrium to favor gluconeogenesis
Gluconeogensis, what is the alternative mean of raising blood glucose levels?
Degradation of glycogen, stored in the liver
Gluconeogenesis, pathway and important enzymes?
Reverse path of glycolysis, with alternatives for glycolysis’s irreversible steps 1, 3 and 10.
Alternative enzymes:
Pyruvate carboxylase to convert pyruvate to OAA
PEP carboxykinase to convert OAA to PEP
(OAA is unique intermediate, glycolysis has direct transition from pyruvate to PEP)
Fructose-1,6-bisphosphatase to convert Fructose-1,6-bisphosphate to Fructose-6-Phosphate
Glucose-6-phosphatase to convert Glucose-6-Phosphate to Glucose
Gluconeogenesis, enzymes that require ATP
Pyruvate carboxylase (unique), pyruvate to OAA
PEP carboxykinase (unique), OAA to PEP
Phosphoglycerate kinase (also glycolysis), 3-phosphoglycerate to 1,3-bisphosphoglycerate
6 total per glucose
Steps 10(x2) and 7 of glycolysis, and steps 1 and 5 of gluconeogenesis)
Gluconeogenesis, steps that require NADH?
1,2-biphosphoglycerate to glyceraldehyde-3-P
2 total per glucose
(Step 4 of glycolysis)
Gluconeogenesis, possible starting material?
Lactate, pyruvate, glycerol (enters through dihydroxyacetone phosphate), amino acids (enters through pyruvate), any Krebs cycle intermediates (enters through OAA)
Glycogenesis, purpose and regulation?
Production of glycogen from glycose to store in skeletal muscle and/or liver
Stimulated by insulin and high glucose levels
Glycogenesis, enzymes?
Hexokinase, phophoglucomutase, glycogen synthase
Glycogenolysis, purpose?
Breaking down glycogen into glucose to provide immediate energy and to maintain blood glucose levels during fasting
Glycogenolysis, regulation?
Stimulated hormonally by glucagon and epinephrine
Inhibited hormonally by insulin
Hormonal regulation through cAMP/pKA signalling
Inhibited allosterically by ATP and and glucose
Glycogenolysis, enzymes?
Glycogen phosphorylase catalyzes the sequential phosphorolysis/breaking down of glycogen (no ATP required)
Other enzymes include phosphoglucomutaseandglu-6-phosphatase
Pentose phosphate pathway, purpose and products?
2 phase alternative process to glycolysis, glucose oxidation
Produces 2 NADPHs (reducing power in fatty acid synthesis, eliminating free radicals)
and ribose-5-phosphate (nucleotide precursor)
Pentose phosphate pathway, location?
Cytosol
Pentose phosphate pathway, oxidative phase?
Glucose-6-phosphate is converted to ribulose-5-P with glucose-6-phosphate dehydrogenase
Pentose phosphate pathway, nonoxidative phase?
Ribulose-5-phosphate is converted to ribose-5-phosphate and 2 glycolysis intermediates
Fatty acid/beta oxidation, purpose?
Breaking down fatty acids into NADH, FADH2, and acetyl CoA (for use in Krebs cycle)
Huge source of ATP
Fatty acid/beta oxidation, location?
Mitochondria for eukarytotic cells
Cytosol for prokaryotic cells
Fatty acid/beta oxidation, process?
2 carbons removed from fatty acid chain with each round of oxidation, which produce single molecules of acetyl-CoA
Cycle repeats until fatty acid is 2 or 3 carbons long
Fatty acid/beta oxidation, enzymes?
For saturated fatty acids - dehydrogenase
For unsaturated fatty acids - isomerase
Fatty acid/beta oxidation, requirements?
ATP to activate, FAD and NAD+ for each 2C to produce FADH2 and NADH
Fatty acid/beta oxidation, precursor/enzyme for metabolism?
Before oxidation, fatty acids must be activated by addition of S-CoA to carboxylic end (in cytoplasm)
Lipase is an enzyme that breaks down triglycerides
Fatty acid ketogenesis, purpose?
Under metabolic conditions associated with high rate of fatty acid oxidation (starvation, keto), the liver produces ketone bodies from acetyl-CoA as a source of energy.
These ketone bodies can enter brain or other organisms to be reconverted to acetyl-CoA
Fatty acid ketogenesis, ketone bodies?
Acetone, Acetoacetate, 3-hydroxybutyrate
(Acetoacetate can split to form the other two)
Fatty acid ketogenesis, regulation?
Triggered by low blood glucose and low glycogen
OR
Triggered by high blood glucose and low insulin
Fatty acid synthesis, purpose and precursor molecules?
Creation of fatty acids from activated acetyl-COA and malonyl-CoA
Fatty acid synthesis, location?
Cytosol
Fatty acid synthesis, process?
Acetyl-CoA and Malonyl-CoA are activated by ACP (acyl carrier protein) to acetyl-_ACP_ and Malonyl-_ACP_
Acetyl-CoA is converted to Acetyl-FAS (fatty acid attached)
Fatty acid synthase combines malonyl-ACP with acetyl
2 NADPH’s used (per round) to remove ketone and double bond
Cycle repeats, adding activated malonyl-CoA to create fatty acid chain (typically around 16 carbons)
Protein catabolism, 3 endpoints?
Can be used to construct other proteins
Amino end can be used for nucleotides or urea
Remaining carbon skeleton can be converted to acetyl-CoA or glucose (glycolytic or ketogenic pathways)
Protein catabolism, process?
Hydrolysis breaks peptide bond to detach amino acid from peptide chain
Amino acid deamination utilizes NAD+ and produces NADH
Insulin and Glucagon regulation
- Insulin helps the cells absorb glucose, promotes
- Glucagon instructs the liver to release stored glucose, promotes
