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137 Cards in this Set
- Front
- Back
Chemotrophs
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obtain chemical energy through oxidation of foodstuffs generated by phototrophs
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Phototrophs
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Use energy of sunlight to convert energy-poor molecules into energy-rich molecules from which energy can be derived.
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Catabolism
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Convert energy into biologically useful fuels (carbohydrates, fats) --> (Carbon dioxide, water, useful energy)
BREAK DOWN |
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Anabolism
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Reactions that require energy
useful energy + small molecules --> complex molecules. BUILD UP |
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Kinases are coupled with:
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Usually Mg2+ (sometimes Mn2+)
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Structural Basis of the high phosphoryl transfer potential of ATP
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1. Resonance Stabilization (ADP and Pi have greater resonance stabilization than ATP)
2. Electostatic Repulsion (fewer resonance structures because positive structure charges are next to each other. Also, at pH 7 there are four negative charges that repel each other) 3. Stabilization due to hydration - h2o can more effectively bind to adp and pi than ATP, stabilizing them. |
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Oxidants
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NAD+ and FAD
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NAD+ (reactive part?)
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nicotinamide ring, a pyridine derivative synthesized by the vitamin niacin
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FAD (reactive part?)
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isoalloxazine ring, a derivative of riboflavin
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Reductant
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NADPH
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NADPH (what is the tag that allows enzymes to distinguish between electrons for reduction and oxidation?)
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the extra-phosphoryl group
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Coenzyme A
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Important carrier of acyl groups; terminal sulfhydral group is the reactive site. Acetyl group linked to CoA by a thioester bond.
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Bronsted - Lowry Acid
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a substance that donates a proton (hydrogen ion, H+)
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Bronsted - Lowry Base
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a substance that accepts a proton (hydrogen ion, H+)
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Lewis Acid
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A substance that accepts an electron Pair
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Lewis Base
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A substance that donates an electron pair.
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Iron sulfur clusters can act as...
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Lewis Acids (Four Iron Atoms - three of which are coordinated to a sulfur and a cysteine - one can coordinate with oxygen).
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Electrophilic Addition Reactions can be used in the synthesis of...
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Terpenes
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Sn1 Reactions
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Proceed through a carbocation intermediate; synthesis of terpenes
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Sn2 reactions
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inversion of stereochemistry; The biosynthesis of epinephrine from norepinephrine occurs by an Sn2 reaction with SAM
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Pyruvate + PAP -->
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Imine
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Conjugate Addition
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Fumarate (plus water) to Malate
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Reactivity of Acyl Groups (from least to most)
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amide
ester thioester acyl phosphate |
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Prochirality
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a molecule that can be converted from achiral to chiral in one step
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ATP is a coenzyme for
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phosphorylation
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Coenzyme A is a coenzyme for
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Acyl Transfers
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NAD+ is a coenzyme for
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oxidation/reduction
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FAD is a coenzyme for
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oxidation/reduction
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Tetrahydrofolate is a coenzyme for
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transfer of C1 units (derived from folic acid)
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Lipoic Acid is a coenzyme for
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acyl transfer
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Thiamine Diphosphate is a coenzyme for
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decarboxylation
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Biotin is a coenzyme for
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carboxylation
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SAM is a coenzyme for
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Methyl Transfer
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Many _____ reactions depend on PLP
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decarboxylation / amination/ deamination / Epimerization
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Net gain of how many ATP in glycolysis
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2
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Net gain of how many NADH in glycolysis
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2
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In glycolysis, glucose is broken down into
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pyruvate
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Glucose --> Glucose 6 phosphate
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catalyzed by hexokinase.
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What is the importance of hexokinase:
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keeps glucose from leaving the cell once it enters.
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What cofactor is required for hexokinase?
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Mg 2+
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Glucose + ___ --> Glucose - 6 - phosphate + ____
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ATP // ADP
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Phosphorylation of Glucose
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- goes through a pentacoordinated intermediate
- inversion of configuration at the phosphorous |
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What residue on hexokinase acts as the base to deprotonate glucose
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Aspartyl
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Induced Fit
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Hexokinase; Substrate induced cleft is a feature of kinases
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G-6P --> F-6P
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isomerization reaction; catalyzed by phosphoglucose isomerase; tautomerization mechanism
Goes from ring structure, to open chain, converted to fructose, closed chain |
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Phosphorylation of F-6P
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Results in F - 1, 6 - BP.
Catalyzed by PFK F-6P is in beta formation; must convert to alpha formation before forming alpha 1,6 BP |
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Phosphofructokinase
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conversion of fructose-6-phosphate to fructose-1,6-bisphosphate.
Mg 2+ required as a cofactor. Critical enzyme in metabolism; one of the rate-limiting enzymes. |
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1,6 BP --> DHAP & GAP
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Catalyzed by Aldolase. its a retro-aldol conversion.
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DHAP v. GAP
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DHAP is much more abundant than GAP, though Le Chatlier's principle drives formation of GAP
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TIM
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8 parallel beta strands form core; 8 alpha helices form outer ring. perfect enzyme (kinetics)
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What residue of TIM is the general acid-base catalyst?
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Glutamate 165
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What residue of TIM protonates the developing tetrahedral oxyanion
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His-95
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GAP --> 1,3 BPG
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oxidation reaction; catalyzed by glyceraldehyde-3-phosphate dehydrogenase; results in the formation of 2 NADH (one for each 3 carbon molecule)
Involves an oxidation (energetically favorable) followed by a dehydration (not energetically favorable). Thioester intermediate |
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1,3 BPG --> 3-glycerate
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Catalyzed by phosphoglycerate kinase. 2 molecules of ATP produced (one for each 3 carbon molecule).
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ADP Phosphorylation from 1,3 BPG to 3-glycerate occurs via
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nucleophilic substitution
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3PG --> 2 PG
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Phsophoglycerate mutase catalyzes this reaction.
In animals and yeast, this reaction involves a histidine residue. |
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2 PG --> phosphoenolpyruvate
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catalyzed by enolase; loss of water.
The base that extracts thhe acidic alpha hydrogen is lysine 345. |
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PEP --> pyruvate
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pyruvate kinase catalyzes this reaction; ATP is formed
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Redox Balancing
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Must regenerate NAD-
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Pyruvate -> ethanol
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Pyruvate --> acetaldehyde catalyzed by Pyruvate decarboxylase (release of CO2)
Acetaldehyde --> ethanol catalyzed by Alcohol dehydrogenase (release of NAD-) |
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Pyruvate Decarboxylase requires what cofactor?
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TPP
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Alcohol Dehydrogenase uses an active site ____ atom to polarize ____ of acetylaldehyde
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zinc; carbonyl
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Pyruvate --> lactate
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catalyzed by lactate dehydrogenase.
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TCA Cycle Dependent on
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the availability of oxygen as the ultimate acceptor of electrons and the electron transport chain to shuttle electrons to oxygen
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Acetyl CoA
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shuttles 2 carbon fragments to the TCA cycle.
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___ (#) decarboxylations occur during the TCA cycle
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2
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TCA cycles occur in
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the mitochondrial matrix
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Pyruvate is ______ to form Acetyl CoA
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decarboxylated
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Pyruvate Carrier
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Pyruvate is exchanged for hydroxide
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Pyruvate Dehydrogenase Complex
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made up of E1, E2, & E3
Three Steps: Decarboxylation, Oxidation, and Transfer to Acetyl CoA |
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CoFactors for pyruvate dehydrogenase complex
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TPP, Lipoic Acid, NAD+, FAD, CoA
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TPP has a pKa of
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10
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Decarboxylation of pyruvate depends on what cofactor:
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TPP; E1
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Acetyl group of the pyruvate is oxidized and transferred to
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lipoic acid; E1
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Acetyl Group Transfered to CoA
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E2; leaves a dihydrolipoamide
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dihydrolipoamide oxidized to ____. Depends on ____ as a cofactor. catalyzed by ___.
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lipoamide. FAD. E3.
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TCA cycle: oxaloacetate to citrate
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oxaloacetate + acetyl CoA --> citryl CoA (aldol condensation)
citryl CoA --> citrate (hydrolysis) catalyzed by citrate synthase. |
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coordinated kinetics
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oxaloacetate binds first; acetyl coA binds second - prevents hydrolysis of acetyl CoA.
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Citrate --> Isocitrate
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Dehydration followed by a hydration. Catalyzed by Aconitase, an Fe-S protein.
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Isocitrate --> alpha-ketoglutarate
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oxidation reaction, catalyzed by isocitrate dehydrogenase.
isocitrate --> oxalosuccinate --> alpha-ketoglutarate NAD+ is reduced to NADH; CO2 is released. |
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alpha-ketoglutarate --> succinyl coA
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oxidative decarboxylation, results in release of CO2 and NADH
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succinyl CoA --> Succinate
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GTP is synthesized from GDP and Pi. CoA is released
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Succinate --> fumarate ---> malate ---> oxaloacetate
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dehydrogenation, hydration, oxidation.
succinate dehydrogenase is an iron sulfur protein. |
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Regulation of Pyruvate Dehydrogenase Complex
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Acetyl CoA inhibits complex
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____, ____, & ____ inhibit oxidative decarboxylation of pyruvate to acetyl CoA
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ATP, NADH, and Acetyl CoA
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___ and ___ inhibit conversion of isocitrate to alpha ketoglutarate
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ATP and NADH
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____, ____, and ___ inhibit the coversion of alpha-ketoglutarate to succinyl coa
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ATP, NADH, and Succinyl CoA
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Oxaloacetate can be converted to
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AA, Purines and pyrimidines
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Succinyl CoA can be converted to
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Porphyrins
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Citrate can be converted to
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Fatty Acids and Sterols
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Alpha-Ketoglutarate can be convertd to
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AA & purines
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Pyruvate can be carboxylated to
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pyruvate carboxylase to regenerate oxaloacetate
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Arsenic Poisoning
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Arsenic reacts with thiols, such as dihydrolipoamide, to inactivate the pyruvate dehydrogenase complex
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Starch
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glucose polymer
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2 main fractions of starch
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Amylose (1,4 linkages) -- several hundred monomers
Amylopectin (1,4 linkages and 1,6 linkages every 25 monomers)- 5000 monomers |
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Alpha-Amylase
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begins digestion of 1,4 linkages in mouth
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Hydrolysis of glycosidic bonds
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catalyzed by glycosidases
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Inverting Glycosidases
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1 Sn2 reaction; carboxylate acts as a general base to deprotonate water as it attacks oxonium ion.
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Retaining Glycosidases
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2 Sn2 reactions; carboxylate adds to oxonium ion & water attacks from opposite side.
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Glycosidases proceed through an ________ intermediate
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oxonium ion
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Pentose Phosphate Pathway
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Allows metabolism of 5-carbon sugars; produces NADPH; produces ribose-5-phosphate
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Two stages of Pentose Phosphate Pathway
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1. Oxidative
2. Non-Oxidative |
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Net Reaction of Pentose Phosphate Pathway
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3Glucose-6-Phosphate + 6NADP+ + 3H2O --> 2 Fructose-6-Phosphate + GAP + 3 CO2 + 6NADPH/H+
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Step 1 of pentose phosphate pathway
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oxidation of G6P to 6 - phosphogluconolactone; NADPH released
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Step 2 of pentose phosphate pathway
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hydrolysis of lactone; forms an open chain carboxylate
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Step 3 of pentose phosphate pathway
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oxidation of c3 hydroxyl release NADPH and CO2
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Step 4 of pentose phosphate pathway
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isomerizations occure by keto-enol tautomerizations.
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Step 5 of pentose phosphate pathway
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xylulose 5-phosphate reacts with ribose-5-phosphate to give GAP and sedoheptulose 7 phosphate
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Step 6 of Pentose phosphate pathway
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GAP and sedoheputulose 7 phosphate exhange a c3 unit
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Step 7
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products exchange a c2 unit
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Oxidative Phosphorylation
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process by which reducing power from NADH and FADH2 is used to synthesize ATP; occurs in mitochondria; flow of protons out of matrix leads to a proton gradient, as they flow back into the matrix ATP is synthesized
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3 electron-driven proton pumps create the proton motive force:
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NADH - Q Oxidoreductase (complex 1)
Q-cytochrome c oxidoreductase (complex 3) Cytochrome c oxidase (complex 4) |
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VDAC high conductance
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ATP and ions can enter
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VDAC low conductance
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ions can enter
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____ terminus can regulate VDAC conductance
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amino
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Isoforms of VDAC in humans:
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VDAC1, VDAC2, VDAC3
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Coenzyme Q
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ubiquinone
Quinone can be reduced by 1 e- to form semiquinone Semiquinone can be reduced by 1 e- to form ubiquinol |
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Structure of complex 1
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4 protons pumped out of matrix
NADH is oxidized Q is reduced to QH2 |
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Mechanism of Complex 1
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NADH binds to complex 1 (on vertical arm) and transfers 2 electrons to FMN.
The electrons are transferred through three 4fe-4s clusters to Q, which becomes QH2. This reduction causes 2 protons to be pupmed out of the matrix onto QH2. Electrons leave, protons leave QH2 to cytosol. Electrons transferred to mobile Q in membrane, 2 more protons pumped out. |
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Complex 2
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transfer of electrons from FADH2 to ETC
FADH2 transfers 2 e-'s to Fe-S centers and then to Q. No protons transferred during this complex. |
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Complex 3
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Three hemes (the 2 heme b's are not covalently attached to a protein; the heme c is covalently attached to a protein by a thioester linkage with a cystein). 2 Fe-S clusters present. Iron in cytochrome c alternates between +2 and +3 states
QH2 + 2 Cytc ox + 2H+ matrix --> Q + 2cytc red + 4 H+ imspace |
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complex IV
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oxidizes cyt c reduced by complex 3. reduces oxygen to water.
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ATP yield per molecule of glucose
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about 30 molecules of ATP formed per molecule of glucose:
2 from glycolysis 2 from TCA cycle 26 from oxidative phosphorylation |
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lipids are broken down into:
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glycerol and fatty acids
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How is glycerol recovered?
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it is converted to DHAP, and intermediate in glycolysis
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Fatty acids are activated
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by coupling with CoA; occurs in mitochondrial matrix; driven by hydrolysis of ATP
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Carnitine
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used to carry activated (long chain) fatty acids into the mitochondrial matrix: Acyl Carnitine is exchanged for free carnitine
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B-oxidation of Fatty Acids
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FAD-dependent oxidation; Hydration; NAD+ dependent oxidation; thiolysis
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Ubiquitin: ___ terminus of ubiquitin is conjugated to proteins
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C
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Amino Acid degradation begins with removal of amino group - mediated by:
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PLP/PAP
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Fates of Carbon Skeletons of Amino Acids: Pyruvate
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ala, cys, gly, ser, thr, trp
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Fates of Carbon Skeletons of Amino Acids: Acetyl CoA
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Ile, Leu, Trp
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Fates of Carbon Skeletons of Amino Acids: Acetoacetyl CoA
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Leu, Lys, Phe, Trp, Tyr
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Fates of Carbon Skeletons of Amino Acids: AlphaKetoGlutarate
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arg, glu, gln, his, pro
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Fates of Carbon Skeletons of Amino Acids: Succinyl CoA
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Ile, Met, Thr, Val
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Fates of Carbon Skeletons of Amino Acids: Fumarate
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Asp, Phe, Tyr
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Fates of Carbon Skeletons of Amino Acids: Oxaloacetate
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Asp, Asn
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