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137 Cards in this Set

  • Front
  • Back
obtain chemical energy through oxidation of foodstuffs generated by phototrophs
Use energy of sunlight to convert energy-poor molecules into energy-rich molecules from which energy can be derived.
Convert energy into biologically useful fuels (carbohydrates, fats) --> (Carbon dioxide, water, useful energy)

Reactions that require energy
useful energy + small molecules --> complex molecules.

Kinases are coupled with:
Usually Mg2+ (sometimes Mn2+)
Structural Basis of the high phosphoryl transfer potential of ATP
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.
NAD+ and FAD
NAD+ (reactive part?)
nicotinamide ring, a pyridine derivative synthesized by the vitamin niacin
FAD (reactive part?)
isoalloxazine ring, a derivative of riboflavin
NADPH (what is the tag that allows enzymes to distinguish between electrons for reduction and oxidation?)
the extra-phosphoryl group
Coenzyme A
Important carrier of acyl groups; terminal sulfhydral group is the reactive site. Acetyl group linked to CoA by a thioester bond.
Bronsted - Lowry Acid
a substance that donates a proton (hydrogen ion, H+)
Bronsted - Lowry Base
a substance that accepts a proton (hydrogen ion, H+)
Lewis Acid
A substance that accepts an electron Pair
Lewis Base
A substance that donates an electron pair.
Iron sulfur clusters can act as...
Lewis Acids (Four Iron Atoms - three of which are coordinated to a sulfur and a cysteine - one can coordinate with oxygen).
Electrophilic Addition Reactions can be used in the synthesis of...
Sn1 Reactions
Proceed through a carbocation intermediate; synthesis of terpenes
Sn2 reactions
inversion of stereochemistry; The biosynthesis of epinephrine from norepinephrine occurs by an Sn2 reaction with SAM
Pyruvate + PAP -->
Conjugate Addition
Fumarate (plus water) to Malate
Reactivity of Acyl Groups (from least to most)
acyl phosphate
a molecule that can be converted from achiral to chiral in one step
ATP is a coenzyme for
Coenzyme A is a coenzyme for
Acyl Transfers
NAD+ is a coenzyme for
FAD is a coenzyme for
Tetrahydrofolate is a coenzyme for
transfer of C1 units (derived from folic acid)
Lipoic Acid is a coenzyme for
acyl transfer
Thiamine Diphosphate is a coenzyme for
Biotin is a coenzyme for
SAM is a coenzyme for
Methyl Transfer
Many _____ reactions depend on PLP
decarboxylation / amination/ deamination / Epimerization
Net gain of how many ATP in glycolysis
Net gain of how many NADH in glycolysis
In glycolysis, glucose is broken down into
Glucose --> Glucose 6 phosphate
catalyzed by hexokinase.
What is the importance of hexokinase:
keeps glucose from leaving the cell once it enters.
What cofactor is required for hexokinase?
Mg 2+
Glucose + ___ --> Glucose - 6 - phosphate + ____
Phosphorylation of Glucose
- goes through a pentacoordinated intermediate
- inversion of configuration at the phosphorous
What residue on hexokinase acts as the base to deprotonate glucose
Induced Fit
Hexokinase; Substrate induced cleft is a feature of kinases
G-6P --> F-6P
isomerization reaction; catalyzed by phosphoglucose isomerase; tautomerization mechanism

Goes from ring structure, to open chain, converted to fructose, closed chain
Phosphorylation of F-6P
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
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.
1,6 BP --> DHAP & GAP
Catalyzed by Aldolase. its a retro-aldol conversion.
DHAP is much more abundant than GAP, though Le Chatlier's principle drives formation of GAP
8 parallel beta strands form core; 8 alpha helices form outer ring. perfect enzyme (kinetics)
What residue of TIM is the general acid-base catalyst?
Glutamate 165
What residue of TIM protonates the developing tetrahedral oxyanion
GAP --> 1,3 BPG
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
1,3 BPG --> 3-glycerate
Catalyzed by phosphoglycerate kinase. 2 molecules of ATP produced (one for each 3 carbon molecule).
ADP Phosphorylation from 1,3 BPG to 3-glycerate occurs via
nucleophilic substitution
3PG --> 2 PG
Phsophoglycerate mutase catalyzes this reaction.

In animals and yeast, this reaction involves a histidine residue.
2 PG --> phosphoenolpyruvate
catalyzed by enolase; loss of water.

The base that extracts thhe acidic alpha hydrogen is lysine 345.
PEP --> pyruvate
pyruvate kinase catalyzes this reaction; ATP is formed
Redox Balancing
Must regenerate NAD-
Pyruvate -> ethanol
Pyruvate --> acetaldehyde catalyzed by Pyruvate decarboxylase (release of CO2)

Acetaldehyde --> ethanol catalyzed by Alcohol dehydrogenase (release of NAD-)
Pyruvate Decarboxylase requires what cofactor?
Alcohol Dehydrogenase uses an active site ____ atom to polarize ____ of acetylaldehyde
zinc; carbonyl
Pyruvate --> lactate
catalyzed by lactate dehydrogenase.
TCA Cycle Dependent on
the availability of oxygen as the ultimate acceptor of electrons and the electron transport chain to shuttle electrons to oxygen
Acetyl CoA
shuttles 2 carbon fragments to the TCA cycle.
___ (#) decarboxylations occur during the TCA cycle
TCA cycles occur in
the mitochondrial matrix
Pyruvate is ______ to form Acetyl CoA
Pyruvate Carrier
Pyruvate is exchanged for hydroxide
Pyruvate Dehydrogenase Complex
made up of E1, E2, & E3

Three Steps: Decarboxylation, Oxidation, and Transfer to Acetyl CoA
CoFactors for pyruvate dehydrogenase complex
TPP, Lipoic Acid, NAD+, FAD, CoA
TPP has a pKa of
Decarboxylation of pyruvate depends on what cofactor:
Acetyl group of the pyruvate is oxidized and transferred to
lipoic acid; E1
Acetyl Group Transfered to CoA
E2; leaves a dihydrolipoamide
dihydrolipoamide oxidized to ____. Depends on ____ as a cofactor. catalyzed by ___.
lipoamide. FAD. E3.
TCA cycle: oxaloacetate to citrate
oxaloacetate + acetyl CoA --> citryl CoA (aldol condensation)

citryl CoA --> citrate (hydrolysis)

catalyzed by citrate synthase.
coordinated kinetics
oxaloacetate binds first; acetyl coA binds second - prevents hydrolysis of acetyl CoA.
Citrate --> Isocitrate
Dehydration followed by a hydration. Catalyzed by Aconitase, an Fe-S protein.
Isocitrate --> alpha-ketoglutarate
oxidation reaction, catalyzed by isocitrate dehydrogenase.

isocitrate --> oxalosuccinate --> alpha-ketoglutarate

NAD+ is reduced to NADH; CO2 is released.
alpha-ketoglutarate --> succinyl coA
oxidative decarboxylation, results in release of CO2 and NADH
succinyl CoA --> Succinate
GTP is synthesized from GDP and Pi. CoA is released
Succinate --> fumarate ---> malate ---> oxaloacetate
dehydrogenation, hydration, oxidation.

succinate dehydrogenase is an iron sulfur protein.
Regulation of Pyruvate Dehydrogenase Complex
Acetyl CoA inhibits complex
____, ____, & ____ inhibit oxidative decarboxylation of pyruvate to acetyl CoA
ATP, NADH, and Acetyl CoA
___ and ___ inhibit conversion of isocitrate to alpha ketoglutarate
____, ____, and ___ inhibit the coversion of alpha-ketoglutarate to succinyl coa
ATP, NADH, and Succinyl CoA
Oxaloacetate can be converted to
AA, Purines and pyrimidines
Succinyl CoA can be converted to
Citrate can be converted to
Fatty Acids and Sterols
Alpha-Ketoglutarate can be convertd to
AA & purines
Pyruvate can be carboxylated to
pyruvate carboxylase to regenerate oxaloacetate
Arsenic Poisoning
Arsenic reacts with thiols, such as dihydrolipoamide, to inactivate the pyruvate dehydrogenase complex
glucose polymer
2 main fractions of starch
Amylose (1,4 linkages) -- several hundred monomers

Amylopectin (1,4 linkages and 1,6 linkages every 25 monomers)- 5000 monomers
begins digestion of 1,4 linkages in mouth
Hydrolysis of glycosidic bonds
catalyzed by glycosidases
Inverting Glycosidases
1 Sn2 reaction; carboxylate acts as a general base to deprotonate water as it attacks oxonium ion.
Retaining Glycosidases
2 Sn2 reactions; carboxylate adds to oxonium ion & water attacks from opposite side.
Glycosidases proceed through an ________ intermediate
oxonium ion
Pentose Phosphate Pathway
Allows metabolism of 5-carbon sugars; produces NADPH; produces ribose-5-phosphate
Two stages of Pentose Phosphate Pathway
1. Oxidative
2. Non-Oxidative
Net Reaction of Pentose Phosphate Pathway
3Glucose-6-Phosphate + 6NADP+ + 3H2O --> 2 Fructose-6-Phosphate + GAP + 3 CO2 + 6NADPH/H+
Step 1 of pentose phosphate pathway
oxidation of G6P to 6 - phosphogluconolactone; NADPH released
Step 2 of pentose phosphate pathway
hydrolysis of lactone; forms an open chain carboxylate
Step 3 of pentose phosphate pathway
oxidation of c3 hydroxyl release NADPH and CO2
Step 4 of pentose phosphate pathway
isomerizations occure by keto-enol tautomerizations.
Step 5 of pentose phosphate pathway
xylulose 5-phosphate reacts with ribose-5-phosphate to give GAP and sedoheptulose 7 phosphate
Step 6 of Pentose phosphate pathway
GAP and sedoheputulose 7 phosphate exhange a c3 unit
Step 7
products exchange a c2 unit
Oxidative Phosphorylation
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
3 electron-driven proton pumps create the proton motive force:
NADH - Q Oxidoreductase (complex 1)
Q-cytochrome c oxidoreductase (complex 3)
Cytochrome c oxidase (complex 4)
VDAC high conductance
ATP and ions can enter
VDAC low conductance
ions can enter
____ terminus can regulate VDAC conductance
Isoforms of VDAC in humans:
Coenzyme Q
Quinone can be reduced by 1 e- to form semiquinone
Semiquinone can be reduced by 1 e- to form ubiquinol
Structure of complex 1
4 protons pumped out of matrix
NADH is oxidized
Q is reduced to QH2
Mechanism of Complex 1
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.
Complex 2
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.
Complex 3
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
complex IV
oxidizes cyt c reduced by complex 3. reduces oxygen to water.
ATP yield per molecule of glucose
about 30 molecules of ATP formed per molecule of glucose:
2 from glycolysis
2 from TCA cycle
26 from oxidative phosphorylation
lipids are broken down into:
glycerol and fatty acids
How is glycerol recovered?
it is converted to DHAP, and intermediate in glycolysis
Fatty acids are activated
by coupling with CoA; occurs in mitochondrial matrix; driven by hydrolysis of ATP
used to carry activated (long chain) fatty acids into the mitochondrial matrix: Acyl Carnitine is exchanged for free carnitine
B-oxidation of Fatty Acids
FAD-dependent oxidation; Hydration; NAD+ dependent oxidation; thiolysis
Ubiquitin: ___ terminus of ubiquitin is conjugated to proteins
Amino Acid degradation begins with removal of amino group - mediated by:
Fates of Carbon Skeletons of Amino Acids: Pyruvate
ala, cys, gly, ser, thr, trp
Fates of Carbon Skeletons of Amino Acids: Acetyl CoA
Ile, Leu, Trp
Fates of Carbon Skeletons of Amino Acids: Acetoacetyl CoA
Leu, Lys, Phe, Trp, Tyr
Fates of Carbon Skeletons of Amino Acids: AlphaKetoGlutarate
arg, glu, gln, his, pro
Fates of Carbon Skeletons of Amino Acids: Succinyl CoA
Ile, Met, Thr, Val
Fates of Carbon Skeletons of Amino Acids: Fumarate
Asp, Phe, Tyr
Fates of Carbon Skeletons of Amino Acids: Oxaloacetate
Asp, Asn