Part 3

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defining components of metabolic pathway: -starting point
-intermediates
-product
what do enzymes do for metabolic pathways: -provide specificity
-efficiency
-regulation
2 types of metabolic pathways: Anabolic: synthetic, requires energy.
Catabolic: degrative, produces energy.
What do metabolic pathways "couple"?: -Endergonic and Exergonic reactions so that the overall pathway is able to proceed, with a negative free energy change.
NAD: Nicotinamide adenine dinucleotide

acceptor of 2 electrons in oxidation of fuel molecules.
one H goes to NADH, the other to solvent
FAD and FMN: flavin adenine dinucleotide
flavin mononucleotide
-accepts 2 electrons and 2 H.
Major role of NADPH: reducing agent in biosynthesis (which is reduction of oxidized molecules) It donates 2 Hydrides (4 e-) to reduce carbonyls to methyl groups.
Phosphate group sets it apart from normal NAD
activated carrier of electrons for reductive biosynthesis:: NADPH
Activated carriers of electrons for fuel oxidation:: NAD+, FAD+ and FMN
activated carrier of 2-carbon fragments:: Coenzyme A
oxidative phosphorylation: the process in which ATP is formed as a result of the transfer of electrons from NADH or FADH2 to O2 by a series of electron carriers.
Where does oxidative phosphorylation take place: mitochondria
proton pump 1: NADH-Q oxidoreductase
proton pump 2: Q-cytochrome c oxidoreductase
proton pump 3: cytochrome c oxidase
what drives ATP synthase: the flow of protons back into the mitochondrial matrix
what happens to O2 in oxidative phosphorylation?: oxygen gas is reduced; NADH and FADH2 are oxidized. ADP is phosphorylated.
electron transport chain: a set of membrane proteins that are functional in oxidative reduction of oxygen.
What happens to the electron transfer potential of NADH or FADH2 in oxidative phosphorylation?: it is converted to phosphoryl transfer potential in ATP.
E prime not: electron transfer potential - reduction (aka, redox) potential of NADH or FADH2
is the reduction potential of NADH positive or negative?: negative; it has a lower affinity for electrons than does oxygen gas.
is the reduction potential of oxygen negative or positive?: positive; it will take protons from NADH or FADH2.
whats the approximate change in free energy for the reduction of O2? big or little?: -52.6 - pretty big!! lots of energy released.
what are the different electron-carrying groups in the protein constituents of the e-transport chain?: flavins
iron-sulfur clusters
quinones
hemes
copper ions
how are electrons transferred through the mitochondrial inner membrane?: PROTEIN MEDIATION
well, proteins are actually great at conducting electricity; because the proteins bearing electron transfer groups are buried dee within the membrane, they conduct e- at about 10^4/sec.
what makes metabolic pathways efficient, and how do you know they're efficient?: coupling of exergonic with endergonic reactions.
because the overall change in free energy (delta G) is negative.
3 Stages of Catabolism: Stage 1: breakdown of large food molecules into smaller units. No energy.
Stage 2: Small molecules degraded to simple units central to metabolism. Substrate level phosphorylation.
Stage 3: ATP is produced from complete oxidation of acetyl unit of acetyl CoA.
Aerobic Respiration: complete oxidation of glucose through the couple pathways of Glycolysis and the Citric Acid Cycle
What type of reaction is ATP -> ADP/AMP: HYDROLYSIS
most common phosphate hydrolyzed from ATP in catabolic pathways:: the gamma phosphate!
names of the phosphates on ATP: gamma
beta
alpha
What allows hydrolysis of ATP to be favorable?: resonance stabilization of the orthophosphate (HPO3 2-)
what is ATP made up of?: Adenine
Ribose
3 Phosphates
Which phosphate on ATP is hydrolyzed in ANABOLIC pathways?: gamma AND beta; leaves AMP + PPi
what is the central role of ATP in bioenergetic pathways?: Cells USE ATP for motion, active transport, biosyntheses, and signal amplification.
Cells MAKE ATP by oxidation of fuel molecules or photosynthesis.
Give an example of a couple reaction:: The very first reaction of Glycolysis.
Glucose + ATP + H2O -> Glucose-6-phosphate + ADP
What type of reaction is involved in catabolic reactions that result in a NET production of atp?: OXIDATION
OXIDATION: loss of electrons from the substrate.
what are oxidation reactions coupled to?: reduction of another substrate or cofactor.
reduction:: gain of electrons.
What type of reaction is NAD+ -> NADH?: a reduction.
what is adenosine composed of?: adenine plus ribose
what are the 3 components of NAD?: nicotinamide ring and adenosine

(adenine + ribose = adenosine)
2 major electron carriers on the oxidation of fuel molecules:: NAD+ and FAD
what does NAD recieve when it oxidizes molecules?: 1 proton and 2 electrons.

the other proton is in the solvent
what is the reactive part of FAD? What does it accept in oxidations?: its Isoalloxazine ring.
accepts 2 electrons and 2 protons.
Cofactors that all contain phosphates and adenine:: NAD, ATP, FAD, and Coenzyme A
activated acyl carrier: Coenzyme A
2 examples of redox reactions: Succinate/FAD -> Fumarate/FADH2

Malate/NAD+ -> Oxaloacetate/NADH H+
Example of a Ligation reaction: Pyruvate + CO2 + ATP + H2O ->
Oxaloacetate + ADP + Pi + H+
Example of an Isomerization reaction: Citrate -> Isocitrate
via Aconitase
Example of a Group-transfer reaction:: Glucose + ATP -> Glucose-6-ph + ADP
Example of a Hydrolytic Reaction Most common for?: Protein + H2O -> two smaller peptides

Protein digestion.
2 Examples of addition or removal of functional groups to form or undo double bonds: Fructose-1,6-BPG -> Dihydroxyacetone + glyceraldehyde-3-P
6 fundamental reactions that are the basis of metabolism:: -redox
-ligation
-isomerization
-grouptransfer
-hydrolysis
-double bond addition or formation
what do anabolic reactions produce?: energy rich, complex molecules from simpler ones.
what do catabolic reactions produce?: ATP - energy to use
3 names for cofactors:: Coenzymes, cosubstrates, prosthetic groups
Chemical composition of carbohydrates:: Cn(H2O)n
what is the simplest ketose?: dihydroxyacetone phosphate

a triose
what is the simplest aldose?: glyceraldehyde
relationship between D and L isomers: enantiomers; have the same chemical properties unless other chiral molecules are present. Mirror images.
Relationship between diastereomers of sugars:: NOT chemically equivalent; they behave differently
5-Carbon diastereomers:: ribose and arabinose
6-Carbon diastereomers: allose altrose glucose and mannose
diasteomers: chemically distinct optical isomers
two ketoses to know right off the bat:: dihydroxyacetone and d-fructose
3 aldoses to know right off the bat: d-glyceraldehyde
d-ribose
d-glucose
what is a cyclic isomer of a carbohydrate called: anomer
what type of reaction forms anomers?: intermolecular reaction of an alcohol and carbonyl
What are the conformational characteristics to know about Beta-d-glucopyranose?: All the axial groups are HYDROGENS
All the equat. groups are OH

most stable
oligosaccharide: a carbohydrate of a few units
monosaccharides: carbohydrates of one single unit
polysaccharides: carbohydrates of many units
what type of carbohydrate is glucose?: a monosaccharaide obviously
sucrose - what type of carb: oligosaccharide
starch/cellulose; what type of carb: polysaccharide
how are di(oligo)saccharides and polysaccharides formed?: polymerization of monosaccharides
Is glycolysis catabolic or anabolic?: catabolic
how many substrate/products in glycolysis?: 11
how many carbons in fructose: 6
Overall point of STAGE ONE of glycolysis: Hexose Phosphorylation
Overall point of stage two of glycolysis: Hexose to Triose
Overall point of stage three of glycolysis: ATP and pyruvate production
what's the essence of what happens in glycolysis?: one molecule of glucose is metabolized into two molecules of pyruvate wiht the concomitant net production of 2 ATP.
kinase: enzymes that catalyze the transfer of a phosphoryl group from ATP to an acceptor
enzyme 1 of gly: hexokinase
enzyme 2 of gly: g6-p isomerase
enzyme 3 of gly: phosphofructokinase
enzyme 4 of gly: aldolase
what type of reaction is reaction 4 of glycolysis?: A reverse aldol condensation;
enzyme for reaction 5 of gly: triose phosphate isomerase
enzyme of reaction 6 of gly: g3p dehydrogenase
reaction 7 enzyme for gly: phosphoglycerate kinase
reaction 8 enzyme for gly: phosphoglycerate mutase
reaction 9 enzyme for gly: enolase
reaction 10 enzyme for gly: pyruvate kinase
phosphofructokinase PFK: the pacesetter of glycolysis;
allosteric enzyme of reaction 3
how does isomerization of G6P proceed?: phosphoglucose isomerase opens the glucose ring, isomerizes the aldehyde at C1 to be a ketone at C2, and re-closes the ring.
what type of reaction does aldolase catalyze?: a reverse aldol condensation.
what is special about 1,3-BPG?: it is an ACYL phosphate; has a high phosphoryl transfer potential, so can create ATP.
What REALLY happens in formin 1,3-BPG?: NAD+ oxidizes it to a carboxylic acid, then the orthophosphate and cooh join to form the acyl-phosphate product.
Special features of G3P dehydrogenase that allow phosphorylation of the aldehyde:: Cys 149 forms a thioester bond;
a Hydride is donated from G3P to a tightly bound NAD+ adjacent to the Cys.
His on the other side of Cys deprotonates and drives the reaction to reform the carbonyl.
Couples favorable formation of COOH and unfavorable Pi addition.
What is the role of the thioester intermediate in reaction 6 of gly?: Its free energy is high; a high-energy intermediate; so that the activation energy of the phosphate addition is not so huge that the reaction won't proceed.
2 reactions that make up reaction 6 of gly:: Favorable oxidation
Unfavorable phosphorylation

KEY: high-energy thioester intermediate.

Cys, His, and NAD+
What reaction is named for the reverse reaction in glycolysis?: Reaction seven
enzyme: phosphoglycerate kinase

It really takes OFF a phosphate.
what is the first ATP generating reaction in gly: reaction 7; dephosphorylation of 1,3-BPG
What is the actual substrate of phosphoglycerate mutase?: 2,3-BPG. Present in catalytic amounts it allows dephosphorylation of 2-3 BPG to give 2-phosphoglycerate. Then the 3-phosphoglycerate that you put in just gets phosphorylated to regenerate 2,3-BPG.
How does one make 2,3-BPG?: by isomerizing 1,3 BPG with BPG-mutase.
BPG Mutase what does it do: makes 2,3-BPG from 1,3-BPG.
2,3-BPG is used to generate 2-phosphoglycerate from 3-phosphoglycerate. the enzyme used is phosphoglycerate mutase.
what does enolase do?: dehydrates 2-phospholycerate to give a very unstable phosphoenolate anion. The Phosphate group traps the unstable molecule until it can phosphorylate ADP to give ATP. that transfer is VERY FAVORABLE.
What are the three fates of pyruvate?: -Ethanol
-Lactate
-Acetyl CoA
What two enzymes are used in alcoholic fermentation?: Pyruvate Decarboxylase
Alcohol Dehydrogenase
what does pyruvate decarboxylase do?: decarboxylates pyruvate.
What are the two steps of alcoholic fermentation?: 1. Decarboxylation to give Acetaldehyde
2. reduction by NADH to give Ethanol.
What is alcoholic fermentation active in?: Yeast under anaerobic conditions
alcoholic fermentation converts pyruvate to:: CO2 plus ethanol.
alcoholic fermentation regenerates:: NAD+
What does lactate dehydrogenase do?: reduces the carbonyl of pyruvate to an alcohol, but the CO2 is left on.
Why is alcoholic fermentation or lactic acid fermentation important?: It regenerates NAD+ so that glycolysis can continue even under anaerobic conditions.
What is lactate dehydrogenase active in?: Lactic Acid fermentation in muscles during anaerobic excercise.
What types of reactions are in Glycolysis?: 4 phosphate transfers by KINASES
3 isomerizations by ISOMERASE/MUTASES
1 redox by DEHYDROGENASE
1 dehydration by ENOLASE
1 aldol cleavage by ALDOLASE
Which reactions of glycolysis have a negative, favorable free energy change?: Only the ones with kinases.
Some are negative, but very minorly and may be positive.
What is a phosphorolysis reaction?: when a phosphate (Pi) hydrolyzes the thioester bond in phosphoglycerate dehydrogenase. analogous to water hydrolysis.
where does glycolysis take place: in the cytosol
where does CAC take place: in mitochondria in eukaryotes
what are iron sulfur proteins?: nonheme iron protiens; iron-sulfur clusters that act as electron carriers in the ETC.
what makes Fe-S complexes distinct from quinones and flavins?: hydrogen bonding does not accompany electron transport with.
What happens at NADH-Q oxidoreductase?: 1. NADH gives its electrons to FMN one at a time with a semiquinone radical intermediate.
2. FMNH2 gives its e- to Fe/S clusters.
3. Fe/S clusters give e- to CoQ to give Coenzyme QH2. 4 H+ pump out of matrix to cytosol.
4. Electrons from bound CoQ are transferred to a 4FE/4S center.
5. E- are transferred to mobile Q in the membrane.
what is special about succinate-Q reductase complex?: It is an integral membrane protein.
FADH2 is made when succinate is oxidized to fumarate. FADH2 does not leave; its two electrons trnasfer to Fe/S centers and then to Q in ETC.
what is a cytochrome?: an electron-transferring protein that contians a heme prosthetic group.
what happens in the Q cycle?: 2 molecules of QH2 are oxidized by binding to Qo, giving off 4 H+ to cytsol
2 H+ are picked up by the QH2 formed at Q1. 2 molecules of Cytochrome C are reduced to be e- rich and continue in chain.

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