Glossary of Part 3
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- defining components of metabolic pathway
- -starting point
- what do enzymes do for metabolic pathways
- -provide specificity
- 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.
- 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
-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:
- 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
- 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?
- 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
- most common phosphate hydrolyzed from ATP in catabolic pathways:
- the gamma phosphate!
- names of the phosphates on ATP
- What allows hydrolysis of ATP to be favorable?
- resonance stabilization of the orthophosphate (HPO3 2-)
- what is ATP made up of?
- 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?
- loss of electrons from the substrate.
- what are oxidation reactions coupled to?
- reduction of another substrate or cofactor.
- 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
- 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
- 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:
-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:
- what is the simplest ketose?
- dihydroxyacetone phosphate
- what is the simplest aldose?
- 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
- chemically distinct optical isomers
- two ketoses to know right off the bat:
- dihydroxyacetone and d-fructose
- 3 aldoses to know right off the bat
- what is a cyclic isomer of a carbohydrate called
- 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
- a carbohydrate of a few units
- carbohydrates of one single unit
- carbohydrates of many units
- what type of carbohydrate is glucose?
- a monosaccharaide obviously
- sucrose - what type of carb
- starch/cellulose; what type of carb
- how are di(oligo)saccharides and polysaccharides formed?
- polymerization of monosaccharides
- Is glycolysis catabolic or anabolic?
- how many substrate/products in glycolysis?
- how many carbons in fructose
- 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.
- enzymes that catalyze the transfer of a phosphoryl group from ATP to an acceptor
- enzyme 1 of gly
- enzyme 2 of gly
- g6-p isomerase
- enzyme 3 of gly
- enzyme 4 of gly
- 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
- 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
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?
- What two enzymes are used in alcoholic fermentation?
- Pyruvate Decarboxylase
- 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:
- 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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