Part 3

Front 1

defining components of metabolic pathway

Back 1

-starting point
-intermediates
-product

Front 2

what do enzymes do for metabolic pathways

Back 2

-provide specificity
-efficiency
-regulation

Front 3

2 types of metabolic pathways

Back 3

Anabolic: synthetic, requires energy.
Catabolic: degrative, produces energy.

Front 4

What do metabolic pathways "couple"?

Back 4

-Endergonic and Exergonic reactions so that the overall pathway is able to proceed, with a negative free energy change.

Front 5

NAD

Back 5

Nicotinamide adenine dinucleotide

acceptor of 2 electrons in oxidation of fuel molecules.
one H goes to NADH, the other to solvent

Front 6

FAD and FMN

Back 6

flavin adenine dinucleotide
flavin mononucleotide
-accepts 2 electrons and 2 H.

Front 7

Major role of NADPH

Back 7

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

Front 8

activated carrier of electrons for reductive biosynthesis:

Back 8

NADPH

Front 9

Activated carriers of electrons for fuel oxidation:

Back 9

NAD+, FAD+ and FMN

Front 10

activated carrier of 2-carbon fragments:

Back 10

Coenzyme A

Front 11

oxidative phosphorylation

Back 11

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.

Front 12

Where does oxidative phosphorylation take place

Back 12

mitochondria

Front 13

proton pump 1

Back 13

NADH-Q oxidoreductase

Front 14

proton pump 2

Back 14

Q-cytochrome c oxidoreductase

Front 15

proton pump 3

Back 15

cytochrome c oxidase

Front 16

what drives ATP synthase

Back 16

the flow of protons back into the mitochondrial matrix

Front 17

what happens to O2 in oxidative phosphorylation?

Back 17

oxygen gas is reduced; NADH and FADH2 are oxidized. ADP is phosphorylated.

Front 18

electron transport chain

Back 18

a set of membrane proteins that are functional in oxidative reduction of oxygen.

Front 19

What happens to the electron transfer potential of NADH or FADH2 in oxidative phosphorylation?

Back 19

it is converted to phosphoryl transfer potential in ATP.

Front 20

E prime not

Back 20

electron transfer potential - reduction (aka, redox) potential of NADH or FADH2

Front 21

is the reduction potential of NADH positive or negative?

Back 21

negative; it has a lower affinity for electrons than does oxygen gas.

Front 22

is the reduction potential of oxygen negative or positive?

Back 22

positive; it will take protons from NADH or FADH2.

Front 23

whats the approximate change in free energy for the reduction of O2? big or little?

Back 23

-52.6 - pretty big!! lots of energy released.

Front 24

what are the different electron-carrying groups in the protein constituents of the e-transport chain?

Back 24

flavins
iron-sulfur clusters
quinones
hemes
copper ions

Front 25

how are electrons transferred through the mitochondrial inner membrane?

Back 25

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.

Front 26

what makes metabolic pathways efficient, and how do you know they're efficient?

Back 26

coupling of exergonic with endergonic reactions.
because the overall change in free energy (delta G) is negative.

Front 27

3 Stages of Catabolism

Back 27

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.

Front 28

Aerobic Respiration

Back 28

complete oxidation of glucose through the couple pathways of Glycolysis and the Citric Acid Cycle

Front 29

What type of reaction is ATP -> ADP/AMP

Back 29

HYDROLYSIS

Front 30

most common phosphate hydrolyzed from ATP in catabolic pathways:

Back 30

the gamma phosphate!

Front 31

names of the phosphates on ATP

Back 31

gamma
beta
alpha

Front 32

What allows hydrolysis of ATP to be favorable?

Back 32

resonance stabilization of the orthophosphate (HPO3 2-)

Front 33

what is ATP made up of?

Back 33

Adenine
Ribose
3 Phosphates

Front 34

Which phosphate on ATP is hydrolyzed in ANABOLIC pathways?

Back 34

gamma AND beta; leaves AMP + PPi

Front 35

Which phosphate on ATP is hydrolyzed in ANABOLIC pathways?

Back 35

gamma AND beta; leaves AMP + PPi

Front 36

what is the central role of ATP in bioenergetic pathways?

Back 36

Cells USE ATP for motion, active transport, biosyntheses, and signal amplification.
Cells MAKE ATP by oxidation of fuel molecules or photosynthesis.

Front 37

Give an example of a couple reaction:

Back 37

The very first reaction of Glycolysis.
Glucose + ATP + H2O -> Glucose-6-phosphate + ADP

Front 38

What type of reaction is involved in catabolic reactions that result in a NET production of atp?

Back 38

OXIDATION

Front 39

OXIDATION

Back 39

loss of electrons from the substrate.

Front 40

what are oxidation reactions coupled to?

Back 40

reduction of another substrate or cofactor.

Front 41

reduction:

Back 41

gain of electrons.

Front 42

What type of reaction is NAD+ -> NADH?

Back 42

a reduction.

Front 43

what is adenosine composed of?

Back 43

adenine plus ribose

Front 44

what are the 3 components of NAD?

Back 44

nicotinamide ring and adenosine

(adenine + ribose = adenosine)

Front 45

2 major electron carriers on the oxidation of fuel molecules:

Back 45

NAD+ and FAD

Front 46

what does NAD recieve when it oxidizes molecules?

Back 46

1 proton and 2 electrons.

the other proton is in the solvent

Front 47

what is the reactive part of FAD?
What does it accept in oxidations?

Back 47

its Isoalloxazine ring.
accepts 2 electrons and 2 protons.

Front 48

Cofactors that all contain phosphates and adenine:

Back 48

NAD, ATP, FAD, and Coenzyme A

Front 49

activated acyl carrier

Back 49

Coenzyme A

Front 50

2 examples of redox reactions

Back 50

Succinate/FAD -> Fumarate/FADH2

Malate/NAD+ -> Oxaloacetate/NADH H+

Front 51

Example of a Ligation reaction

Back 51

Pyruvate + CO2 + ATP + H2O ->
Oxaloacetate + ADP + Pi + H+

Front 52

Example of an Isomerization reaction

Back 52

Citrate -> Isocitrate
via Aconitase

Front 53

Example of a Group-transfer reaction:

Back 53

Glucose + ATP -> Glucose-6-ph + ADP

Front 54

Example of a Ligation reaction

Back 54

Pyruvate + CO2 + ATP + H2O ->
Oxaloacetate + ADP + Pi + H+

Front 55

Example of a Group-transfer reaction:

Back 55

Glucose + ATP -> Glucose-6-ph + ADP

Front 56

Example of a Hydrolytic Reaction

Most common for?

Back 56

Protein + H2O -> two smaller peptides


Protein digestion.

Front 57

2 Examples of addition or removal of functional groups to form or undo double bonds

Back 57

Fructose-1,6-BPG -> Dihydroxyacetone + glyceraldehyde-3-P

Front 58

6 fundamental reactions that are the basis of metabolism:

Back 58

-redox
-ligation
-isomerization
-grouptransfer
-hydrolysis
-double bond addition or formation

Front 59

what do anabolic reactions produce?

Back 59

energy rich, complex molecules from simpler ones.

Front 60

what do catabolic reactions produce?

Back 60

ATP - energy to use

Front 61

3 names for cofactors:

Back 61

Coenzymes, cosubstrates, prosthetic groups

Front 62

Chemical composition of carbohydrates:

Back 62

Cn(H2O)n

Front 63

what is the simplest ketose?

Back 63

dihydroxyacetone phosphate

a triose

Front 64

what is the simplest aldose?

Back 64

glyceraldehyde

Front 65

relationship between D and L isomers

Back 65

enantiomers; have the same chemical properties unless other chiral molecules are present. Mirror images.

Front 66

Relationship between diastereomers of sugars:

Back 66

NOT chemically equivalent; they behave differently

Front 67

5-Carbon diastereomers:

Back 67

ribose and arabinose

Front 68

6-Carbon diastereomers

Back 68

allose altrose glucose and mannose

Front 69

diasteomers

Back 69

chemically distinct optical isomers

Front 70

two ketoses to know right off the bat:

Back 70

dihydroxyacetone and d-fructose

Front 71

3 aldoses to know right off the bat

Back 71

d-glyceraldehyde
d-ribose
d-glucose

Front 72

what is a cyclic isomer of a carbohydrate called

Back 72

anomer

Front 73

what type of reaction forms anomers?

Back 73

intermolecular reaction of an alcohol and carbonyl

Front 74

What are the conformational characteristics to know about Beta-d-glucopyranose?

Back 74

All the axial groups are HYDROGENS
All the equat. groups are OH

most stable

Front 75

oligosaccharide

Back 75

a carbohydrate of a few units

Front 76

monosaccharides

Back 76

carbohydrates of one single unit

Front 77

polysaccharides

Back 77

carbohydrates of many units

Front 78

what type of carbohydrate is glucose?

Back 78

a monosaccharaide obviously

Front 79

sucrose - what type of carb

Back 79

oligosaccharide

Front 80

starch/cellulose; what type of carb

Back 80

polysaccharide

Front 81

how are di(oligo)saccharides and polysaccharides formed?

Back 81

polymerization of monosaccharides

Front 82

Is glycolysis catabolic or anabolic?

Back 82

catabolic

Front 83

how many substrate/products in glycolysis?

Back 83

11

Front 84

how many carbons in fructose

Back 84

6

Front 85

Overall point of STAGE ONE of glycolysis

Back 85

Hexose Phosphorylation

Front 86

Overall point of stage two of glycolysis

Back 86

Hexose to Triose

Front 87

Overall point of stage three of glycolysis

Back 87

ATP and pyruvate production

Front 88

what's the essence of what happens in glycolysis?

Back 88

one molecule of glucose is metabolized into two molecules of pyruvate wiht the concomitant net production of 2 ATP.

Front 89

kinase

Back 89

enzymes that catalyze the transfer of a phosphoryl group from ATP to an acceptor

Front 90

enzyme 1 of gly

Back 90

hexokinase

Front 91

enzyme 2 of gly

Back 91

g6-p isomerase

Front 92

enzyme 3 of gly

Back 92

phosphofructokinase

Front 93

enzyme 4 of gly

Back 93

aldolase

Front 94

what type of reaction is reaction 4 of glycolysis?

Back 94

A reverse aldol condensation;

Front 95

enzyme for reaction 5 of gly

Back 95

triose phosphate isomerase

Front 96

enzyme of reaction 6 of gly

Back 96

g3p dehydrogenase

Front 97

reaction 7 enzyme for gly

Back 97

phosphoglycerate kinase

Front 98

reaction 8 enzyme for gly

Back 98

phosphoglycerate mutase

Front 99

reaction 9 enzyme for gly

Back 99

enolase

Front 100

reaction 10 enzyme for gly

Back 100

pyruvate kinase

Front 101

phosphofructokinase PFK

Back 101

the pacesetter of glycolysis;
allosteric enzyme of reaction 3

Front 102

how does isomerization of G6P proceed?

Back 102

phosphoglucose isomerase opens the glucose ring, isomerizes the aldehyde at C1 to be a ketone at C2, and re-closes the ring.

Front 103

what type of reaction does aldolase catalyze?

Back 103

a reverse aldol condensation.

Front 104

what is special about 1,3-BPG?

Back 104

it is an ACYL phosphate; has a high phosphoryl transfer potential, so can create ATP.

Front 105

What REALLY happens in formin 1,3-BPG?

Back 105

NAD+ oxidizes it to a carboxylic acid, then the orthophosphate and cooh join to form the acyl-phosphate product.

Front 106

Special features of G3P dehydrogenase that allow phosphorylation of the aldehyde:

Back 106

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.

Front 107

What is the role of the thioester intermediate in reaction 6 of gly?

Back 107

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.

Front 108

2 reactions that make up reaction 6 of gly:

Back 108

Favorable oxidation
Unfavorable phosphorylation

KEY: high-energy thioester intermediate.

Cys, His, and NAD+

Front 109

What reaction is named for the reverse reaction in glycolysis?

Back 109

Reaction seven
enzyme: phosphoglycerate kinase

It really takes OFF a phosphate.

Front 110

what is the first ATP generating reaction in gly

Back 110

reaction 7; dephosphorylation of 1,3-BPG

Front 111

What is the actual substrate of phosphoglycerate mutase?

Back 111

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.

Front 112

How does one make 2,3-BPG?

Back 112

by isomerizing 1,3 BPG with BPG-mutase.

Front 113

BPG Mutase what does it do

Back 113

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.

Front 114

what does enolase do?

Back 114

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.

Front 115

What are the three fates of pyruvate?

Back 115

-Ethanol
-Lactate
-Acetyl CoA

Front 116

What two enzymes are used in alcoholic fermentation?

Back 116

Pyruvate Decarboxylase
Alcohol Dehydrogenase

Front 117

what does pyruvate decarboxylase do?

Back 117

decarboxylates pyruvate.

Front 118

What are the two steps of alcoholic fermentation?

Back 118

1. Decarboxylation to give Acetaldehyde
2. reduction by NADH to give Ethanol.

Front 119

What is alcoholic fermentation active in?

Back 119

Yeast under anaerobic conditions

Front 120

alcoholic fermentation converts pyruvate to:

Back 120

CO2 plus ethanol.

Front 121

alcoholic fermentation regenerates:

Back 121

NAD+

Front 122

What does lactate dehydrogenase do?

Back 122

reduces the carbonyl of pyruvate to an alcohol, but the CO2 is left on.

Front 123

Why is alcoholic fermentation or lactic acid fermentation important?

Back 123

It regenerates NAD+ so that glycolysis can continue even under anaerobic conditions.

Front 124

What is lactate dehydrogenase active in?

Back 124

Lactic Acid fermentation in muscles during anaerobic excercise.

Front 125

What types of reactions are in Glycolysis?

Back 125

4 phosphate transfers by KINASES
3 isomerizations by ISOMERASE/MUTASES
1 redox by DEHYDROGENASE
1 dehydration by ENOLASE
1 aldol cleavage by ALDOLASE

Front 126

Which reactions of glycolysis have a negative, favorable free energy change?

Back 126

Only the ones with kinases.
Some are negative, but very minorly and may be positive.

Front 127

What is a phosphorolysis reaction?

Back 127

when a phosphate (Pi) hydrolyzes the thioester bond in phosphoglycerate dehydrogenase. analogous to water hydrolysis.

Front 128

where does glycolysis take place

Back 128

in the cytosol

Front 129

where does CAC take place

Back 129

in mitochondria in eukaryotes

Front 130

what are iron sulfur proteins?

Back 130

nonheme iron protiens; iron-sulfur clusters that act as electron carriers in the ETC.

Front 131

what makes Fe-S complexes distinct from quinones and flavins?

Back 131

hydrogen bonding does not accompany electron transport with.

Front 132

What happens at NADH-Q oxidoreductase?

Back 132

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.

Front 133

what is special about succinate-Q reductase complex?

Back 133

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.

Front 134

what is a cytochrome?

Back 134

an electron-transferring protein that contians a heme prosthetic group.

Front 135

what happens in the Q cycle?

Back 135

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.