Biochemistry I Exam 5 Flashcards
Autotroph
use CO2 from the atmosphere as their sole source of carbon
Heterotroph
cannot use atmospheric CO2 and must obtain carbon from their environment
Metabolites
series of intermediates through which precursors are converted to product
Intermediary Metabolism
the combines activities of all the metabolic pathways that interconvert precursors, metabolites, and products of low molecular weights
Catabolism
the degradative phase of metabolism; releases energy
Anabolism (biosynthesis)
the building phase of metabolism; requires energy
Energy Transduction
changes of one form into another
Free Energy
expresses the amount of energy capable of doing work during a reaction at constant temperature and pressure
Enthalpy
the heat content of the reacting system
Entropy
a quantitative expression for the randomness or disorder in a system
Free Energy Change Equation
delta G=delta H-T delta S
Exergonic
energy-releasing reaction
Endergonic
requires energy input
Exothermic
releases heat
Endothermic
takes up heat
Understand the relationship between Keq and DG
-Keq>1.0=negative delta G (reaction proceeds forward)
-Keq=1.0=zero delta G (reaction is at equilibrium)
-Keq<1.0=positive delta G (reaction proceeds in reverse)
Heterolytic Cleavage
cleavage of a covalent bond where each atom leaves the bond as a radical, carrying one unpaired electron
Nucleophile
functional groups rich in and capable of donating electrons; combine with and give up electrons to electrophiles
Electrophiles
electron-deficient functional groups that seek electrons
Kinase
transfer a phosphoryl group from ATP to an acceptor molecule; catalyzes a phosphorylation reaction
Phosphorylases
catalyze a displacement reaction where phosphate attacks and becomes covalently attached at the point of bond breakage; catalyze a phosphorolysis reaction
Phosphateses
catalyze the removal of a phosphoryl group from a phosphate ester; catalyze dephosphorylation reactions
Synthase
catalyze condensation reactions in which no nucleotide triphosphate is required
Synthetases
catalyze condensation reactions that require a nucleotide triphosphate
Oxidases
catalyze biological reactions where oxygen is the electron acceptor and oxygen does not appear in the oxidized product
Oxygenases
catalyze biological oxidation reactions where oxygen is the electron acceptor and oxygen does appear in the oxidized product
Dehydrogenase
-catalyze oxidation-reductase reactions in which NAD+ is the electron acceptor and molecular oxygen is not involved
-Electron acceptor is NAD+
What is the relationship between electron donors/acceptors and oxidation/reduction?
-NAD going to NADH
-NADH is the reduced form
-NAD is the oxidized form
-If something is getting reduced, something else has to get oxidized
What metal ion does ATP associate with and why does hydrolysis of a phosphate lead to energy release?
-Magnesium (Mg2+)
-Phosphate groups are negatively charged and thus repel one another when they are arranged in series
What is phosphocreatine used for and how does it’s DG compare with ATP?
-Phosphocreatine is used to serve in the maintanence and recycling of adenosine triphosphate (ATP) for muscular activity like contractions
- Phosphocreatine Delta G is -12.8 kJ/mol and ATP is -30.5 kJ/mol
What compounds are considered high energy and what is the DG cutoff for high energy?
-High energy compounds have a DG cutoff of more than -25 kJ/mol
-High Energy Compounds: Adenosine, 1,3-Bisphosphoglycerate, Phosphoenolpyruvate, Phosphocreatine
Transphosphorylation
the other nucleoside triphosphates (GTP,UTP,and CTP) and all deoxynucleotide triphosphates (dATP, dGTP, dTTP, and dCTP) are energetically equivalent to ATP
What do nucleoside diphosphate kinases do?
carries phosphoryl groups from ATP to other nucleotides
-high [ATP]/[ADP] ratio normally drives the reaction forward
What is the electron motive force?
-force proportional to the difference in electron affinity between chemical species
-drives electron flow spontaneously through a circuit
-Biological Circut: electrons from glucose flow through a series of electron-carrier intermediates to another chemical species, such as O2
What are the universal electron carriers? How many electrons can they carry?
-NAD, NADP, FMN, and FAD
-They can carry 2 e-
What vitamin is used to make nicotinamide?
Niacin: forms NAD and NADP
What vitamin is used to make FMN and FAD?
Vitamin B2 (riboflavin)
What are the 10 factors affecting enzyme activity and what effects do they have?
-1. Extracellular Signals
2. Transcription of Specific Genes
3. mRNA degradation
4. mRNA translation on a ribosome
5. Protein degradation
6. Enzyme sequestered in subcellular organelle
7. Enzyme Binds Substrate
8. Enzyme Binds Ligand
9. Enzyme undergoes phosphorylation/dephosphorylation
10. Enzyme combines with regulatory pathway
How does substrate concentration correlate with enzyme kinetics?
-Activity drops with lower substrate concentration
-When [S] is greater than Km the reaction rate is linearly dependent on [S]
Why would a reaction that is far from equilibrium serve as a regulation point?
??
Why is AMP a more sensitive indicator than ATP?
-The relative change of AMP is 600%
-The relative change of ATP is 10%
What are the 10 steps of glycolysis?
-Step 1: Phosphorylation of Glucose
-Step 2: Conversion of Glucose 6-Phosphate to Fructose 6-Phosphate
-Step 3: Phosphorylation of Fructose 6-Phosphate to Fructose 1,6-Bisphosphate
-Step 4: Cleavage of Fructose 1,6-Bisphosphate
-Step 5: Interconversion of the Triose Phosphates
-Step 6: Oxidation of Glyceraldehyde 3-Phosphate to 1,3-Bisphosphoglycerate
-Step 7: Phosphoryl Transfer from 1,3-Bispphoglycerate to ADP
-Step 8: Conversion of 3-Phosphoglycerate to 2-Phosphoglycerate
-Step 9: Dehydration of 2-Phosphoglycerate to Phosphoenolpyruvate
-Step 10: Transfer of the Phosphoryl Group from Phosphoenolpyruvate to ADP
Which steps of glycolysis are irreversible?
-Step 1: Phosphorylation of Glucose
-Step 3: Phosphorylation of Fructose 6-Phosphate to Fructose 1,6-Bisphosphate
-Step 10: Transfer of the Phosphoryl Group from Phosphoenolpyruvate to ADP
Which steps of glycolysis use ATP?
-Step 1
-Step 3
-Step 10
Which steps of glyclolysis use ATP?
-Step 1
-Step 3
-Step 10
Which steps of glycolysis produce ATP or NADH?
-Step 6
-Step 7
-Step 10
What are the key products of glycolysis from the prep phase?
glyceraldehyde-3-phosphate and dihydroxyacetone phosphate
What are the key products of glycolysis from the payoff phase?
energy conserved as 2 ATP, 2 pyruvate, and 2 NADH
How do glycogen, galactose, and fructose feed the glycolytic pathway?
What is galactosemia?
-Galactosemia: caused by a genetic defect in enzymes controlling dietary galactose; treatment involves carefully controlling dietary galactose
What are the “fates” of pyruvate? Which ones apply to humans?
-Under aerobic conditions, pyruvate is oxidized to acetyl CoA
-Under anaerobic conditions, pyruvate is reduced to lactate or ethanol
-These apply to humans
-Fermentation: general term for processes that extract energy (as ATP) but do not consume oxygen or change the concentrations of NAD+ or NADH
-Lactic Acid Fermentation: pyruvate accepts electrons from NADH and is reduced to lactate while regenerating the NAD+ necessary for glycolysis
-Ethanol (alcohol) fermentation: pyruvate is further catabolized to ethanol
What happens to lactate?
What is thiamine pyrophosphate and what is it involved in?
-Thiamine Pyrophosphate (TPP): coenzyme derived from vitamin B1; thiazolium ring plays an important role in the cleavage of bonds adjacent to a carbonyl group
-Reactions: ethanol fermentation, synthesis of acetyl-CoA in the citric acid cycle, carbon-assimilation reactions of the pentose phosphate pathway
What is gluconeogenesis?
-Gluconeogenesis: pathway that converts pyruvate and related three-and four-carbon compounds to glucose
How does gluconeogenesis overcome the irreversible steps of glycolysis?
-They are bypassed with exergonic reactions?
What two enzymes and reactions are required to convert pyruvate to PEP?
-Reaction 1: pyruvate is converted to oxaloacetate
-Enzyme 1: pyruvate carboxylase (requires coenzyme biotin)
-Reaction 2: oxaloacetate to PEP
-Enzyme 2: phosphoenolpyruvate carboxykinase (requires Mg and GTP)
What enzymes are needed to convert fructose-1,6-bisphosphate to fructose-6-phosphate and glucose-6-phosphate to glucose?
-fructose 1,6-bisphosphatase (FBPase-1): converts fructose 1,6-bisphosphate to fructose-6-phosphate
-glucose 6-phosphatase: catalyzes the hydrolysis of glucose 6-phosphate to glucose
What are glucogenic amino acids?
-gluconeogenic amino acids: able to undergo net conversion to glucose
-intermediates of the citric acid cycle can also undergo oxidation to oxaloacetate
What factors are regulating glycolysis and gluconeogenesis?
-Promoting Glycolysis/Inhibiting Gluconeogenesis: Hexokinase, Phosphofructokinase, Fructose-2,6-bisphosphate, AMP, pyruvate kinase, fructose-1,6-bisphosphate
-Inhibiting Glycolysis/Promoting Gluconeogenesis: Glucose-6–phosphatase, fructose-1,6-bisphosphatase, citrate, phosphoenolpyruvate carboxylkinase, Acetyl-CoA, pyruvate carboxylase
How are phosphofructokinase-1 and fructose-1,6-bisphosphatase regulated?
-ATP inhibits PFK-1 by binding to an allosteric site
-ADP and AMP allosterically relieve this inhibition by ATP
-FBPase-1 is allosterically inhibited by AMP
-high [AMP], which corresponds to low ATP, inhibits FBPase (slows glucose synthesis
-High [ATP] slows glycolysis and speeds gluconeogenesis
What effects do glucagon and insulin have on fructose-2,6-bisphosphate levels?
-Glucagon: lowers [fructose 2,6-bisphosphate]; inhibits glycolysis and stimulates gluconeogenesis
-Insulin: increases [fructose 2,6-bisphosphate]; stimulates glycolysis and inhibits gluconenogenesis
What does xylulose-5-phosphate do that affects F-2,6-BP levels?
-Xylulose 5-phosphate: an intermediate of the pentose phosphate pathway that activates phophoprotein phosphatase 2A; causes an increase in [fructose 2,6-bisphosphate]
What effects do glucagon and insulin have on gluconeogenesis and glycolysis?
-Glucagon: hormone that signals the liver to produce and release more glucose and to stop consuming it; released when blood glucose level decrease; inhibits glycolysis and stimulates gluconenogenesis
-Insulin: hormone that signals the liver to use glucose as a fuel and as a precursor for the storage of glycogen and triaglycerol; released when blood glucose level increases; stimulates glycolysis and inhibits gluconeogenesis
What factors regulate pyruvate kinase activity?
-Inhibited by ATP, acetyl-CoA, and long chain fatty acids
Name three examples of genes regulated by insulin and what roles do the proteins made by those genes serve?
-Hexokinase II, Hexokinase IV, Pyruvate kinase
-Essential for glycolysis, which consumes glucose for energy
-I may have misunderstood this question, IDK
What is the purpose of the pentose phosphate pathway?
-Purpose is to oxidize glucose 6-phosphate, producing pentose phosphates and NADPH
What are some primary products of the pentose phosphate pathway and during which phase are they produced?
-Primary Products: NADPH and ribulose 5-phosphate
-Produced in the oxidative phase
What is a transketolase reaction?
-Transketolase Reaction: catalyzes the transfer of a two-carbon fragment from a ketose donor to an aldose acceptor
-First reaction yields sedoheptulose 7-phosphate
-Second reaction forms fructose 6-phosphate and glyceraldehyde 3-phosphate from erythose 4-phosphate and xylulose 5-phosphate
What is a transaldolase reaction?
-Transaldolase Reaction: catlayzes the condensation of a three-carbon fragment from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate, forming fructose 6-phosphate and the tetrose erythrose 4-phosphate
