Biochem 508: Exam 1

Front 1

What are the "energy-conserving" products from each of the major catabolic pathways (6)?

Back 1

- Glycolysis - ATP, NADH
- TCA (Krebs) Cycle - GTP, NADH, FADH2
- β-oxidation of Fatty Acids - NADH FADH2
- Oxidation of α-keto acids (from A.A.) - NADH, FADH2
- Oxidative Phosphorylation - ATP
- Photophosphorylation - ATP, NADPH

Front 2

In biosynthesis, what is the normal "energy donor" (cofactor)?

Back 2

NADPH

Front 3

Where do anabolic / biosynthetic processes usually occur in the cell? As compared to catabolic processes?

Back 3

Anabolic - Cytosol
Catabolic - Mitochondria

Front 4

Why must anabolic (cytosol) and catabolic (mitochondria) processes take place in localized areas of the cell?

Back 4

To maintain distinct pools / ratios:
- Cytosol: high [NADPH]/[NADP+]
- Mitochondria: high [NAD+]/[NADH]

Front 5

What are common features of anabolic pathways?

Back 5

- Reductive (NADPH)
- Divergent
- Regulated (at branch points, reciprocally with catabolism)
- Localized (usually in cytosol)
- Tissue-specific (a lot in the liver)
- "Irreversible" (ATP shifts equilibrium towards product)
- Some separate/distinct pathways compared to catabolism

Front 6

What does coordinately regulated or reciprocal regulation refer to?

Back 6

Anabolic and catabolic pathways are regulated at the pathways which are unique to each; the same regulator has opposite effects on each path
(i.e., epinephrine stimulates β oxidation and inhibits fatty acid synthesis)

Front 7

Why are anabolic pathways described as "irreversible"?

Back 7

ATP hydrolysis (converted to ADP + Pi) which shifts the equilibrium towards the product

Front 8

In the Pentose Phosphate Pathway, what starting molecule is converted to what end molecule? What is the product used for in biosynthesis?

Back 8

Glucose 6-Phosphate --> Ribose 5-Phosphate (+2NADPH)
--> Nucleotides, coenzymes (ATP, NADH, FADH2, CoA), DNA, RNA

Front 9

What pathway present in most organisms serves to interconvert hexoses and pentoses and is a source of reducing equivalents (NADPH) and pentoses for biosynthetic processes?

Back 9

Pentose Phosphate Pathway (aka phosphogluconate or hexose monophosphate pathway)

Front 10

What are the intermediates between glucose 6-phosphate and ribose 5-phosphate in the oxidative reactions of the pentose phosphate pathway?

Back 10

Glucose 6-Phosphate
-->
6-Phosphoglucono-δ-lactone
-->
6-Phosphogluconate
-->
D-Ribulose 5-Phosphate
-->
D-Ribose 5-Phosphate

Front 11

Which enzymes and cofactors convert glucose 6-phosphate and ribose 5-phosphate in the oxidative part of the pentose phosphate pathway?

Back 11

1. Glucose 6-Phosphate Dehydrogenase (Mg2+ and NADP+ --> NADPH + H+)
2. Lactonase (H2O and Mg2+)
3. 6-Phosphogluconate dehydrogenase (Mg2+ NADP+ --> NADPH + H+ and CO2)
4. Phosphopentose Isomerase

Front 12

What specifically happens in the reactions catalyzed by glucose 6-P dehydrogenase and 6-phosphogluconate dehydrogenase (pentose phosphate pathway)?

Back 12

NADP+ is converted to NADPH and H+
(Mg2+ is a cofactor)

* 6-phosphogluconate dehydrogenase also releases CO2 to change from a 6C molecule to a 5C molecule

Front 13

In the Pentose Phosphate Pathway, what starting molecule is converted to what end molecule? What is the product used for in biosynthesis?

Back 13

Glucose 6-Phosphate --> Ribose 5-Phosphate
--> Nucleotides, coenzymes (ATP, NADH, FADH2, CoA), DNA, RNA

Front 14

What pathway present in most organisms serves to interconvert hexoses and pentoses and is a source of reducing equivalents (NADPH) and pentoses for biosynthetic processes?

Back 14

Pentose Phosphate Pathway (aka phosphogluconate or hexose monophosphate pathway)

Front 15

What are the intermediates between glucose 6-phosphate and ribose 5-phosphate in the oxidative reactions of the pentose phosphate pathway?

Back 15

Glucose 6-Phosphate
-->
6-Phosphoglucono-δ-lactone
-->
6-Phosphogluconate
-->
D-Ribulose 5-Phosphate
-->
D-Ribose 5-Phosphate

Front 16

Which enzymes and cofactors convert glucose 6-phosphate and ribose 5-phosphate in the oxidative part of the pentose phosphate pathway?

Back 16

1. Glucose 6-Phosphate Dehydrogenase (Mg2+ and NADP+ --> NADPH + H+)
2. Lactonase (H2O and Mg2+)
3. 6-Phosphogluconate dehydrogenase (Mg2+ NADP+ --> NADPH + H+ and CO2)
4. Phosphopentose Isomerase

Front 17

What specifically happens in the reactions catalyzed by glucose 6-P dehydrogenase and 6-phosphogluconate dehydrogenase (pentose phosphate pathway)?

Back 17

NADP+ is converted to NADPH and H+
(Mg2+ is a cofactor)

* 6-phosphogluconate dehydrogenase also releases CO2 to change from a 6C molecule to a 5C molecule

Front 18

What is the purpose of the non-oxidative portion of the pentose phosphate pathway?

Back 18

To recycle ribose 5-P back into glucose 6-P to make more NADPH

Front 19

What determines whether glucose 6-phosphate will enter glycolysis or the pentose phosphate pathway?

Back 19

If the ratio of [NADP+]/[NADPH] ratio is high, more NADPH is needed, so will go to pentose phosphate pathway; if [NADPH] is high, then first step of pathway is inhibited and glycolysis takes over

Front 20

What are the intermediates of the nonoxidative portion of the pentose phosphate pathway?

Back 20

Ribose 5-P + Xylulose 5-P
-->
Sedoheptulose 7-P + Glyceraldehyde 3-P
-->
Fructose 6-P (to glucose 6-P) + Erythrose 4-P
-->
Erythrose 4-P + Xylulose 5-P
-->
Fructose 6-P (to glucose 6-P) + Glyceraldehyde 3-P (to fructose 6-P to glucose 6-P)

Front 21

Which enzyme is used in nonoxidative (pentose phosphate pathway) when xylulose 5-P is present?

Back 21

Transketolase

Front 22

Which enzyme is used in nonoxidative (pentose phosphate pathway) in between transketolases (with glyceraldehyde 3-P and sedoheptulose 7-P)?

Back 22

Transaldolase

Front 23

What happens during carbon-assimilation reactions?

Back 23

Reactions in which CO2 is converted into simple (reduced) organic compounds

Front 24

What happens during carbon-fixation reactions?

Back 24

The reaction, catalyzed by rubisco during photosynthesis or by other carboxylases, in which atmospheric CO2 is initially incorporated (fixed) into an organic compound (triose phosphate 3-phosphoglycerate)

Front 25

Where does 3-phosphoglycerate (a triose phosphate) come from? And what is it used for?

Back 25

- From carbon fixation of CO2
- Precursor of more complex biomolecules, like sugars, polysaccharides, and metabolites

Front 26

What happens in the Calvin Cycle?

Back 26

In a cyclic pathway in plants, carbon dioxide is fixed and produces triose phosphates

Front 27

What happens in the first stage of CO2 assimilation (Calvin Cycle), generally and specifically?

Back 27

Carbon-Fixation Reaction:
- Condensation of CO2 (3) with a 5C acceptor, Ribulose 1,5-bisphosphate (3)
- Forms two molecules of 3-phosphoglycerate (6)

Front 28

What happens in the second stage of CO2 assimilation (Calvin Cycle), generally and specifically?

Back 28

Reduction
- 3-Phosphoglycerate (6) is reduced to triose phosphates, glyceraldehyde 3-pphosphate (6)

Front 29

What happens in the third stage of CO2 assimilation (Calvin Cycle), generally and specifically?

Back 29

Regeneration of Acceptor
- Five of six molecules of triose phosphate regenerate three molecules of ribulose 1,5-bisphosphate (starting material)
- Sixth molecule of triose phosphate is the net product of photosynthesis and can be used as fuel, building materials, transport, or storage

Front 30

What is the enzyme rubisco responsible for? What is its long name?

Back 30

- Catalyzes the covalent attachment of CO2 to the 5C sugar ribulose 1,5-bisphosphate and cleavage of the unstable 6C intermediate to form two molecules of 3-phosphoglycerate
- Ribulose 1,5-bisphosphate carboxylase/oxygenase

Front 31

What is the mechanism of the reaction catalyzed by Rubisco?

Back 31

- Ribulose 1,5-BisP forms an enediolate after attack by Lys side chain
- CO2 is polarized by proximity to Mg2+, undergoes nucleophilic attack by enediolate (forms 6C)
- Water added (hydroxylation)
- Cleavage of hydrated intermediate forms 3-phosphoglycerate (forms carbanion)
- Carbanion protonated by Lys to generate another molecule of 3-phosphoglycerate

Front 32

What is the overall reaction catalyzed by Rubisco?

Back 32

Ribulose 1,5-bisphosphate + CO2 --> 2 molecules of 3-phosphoglycerate

Front 33

Which step of the Calvin Cycle has steps which are similar to glycolysis? How so? What is different?

Back 33

Step 2: conversion of 3-phosphoglycerate to glyceraldehyde 3-phosphate
- two steps are basically the reversal of glycolysis (intermediate 1,3-bisphosphoglycerate)
- cofactor is NADPH instead of NADH

Front 34

What is the function of the enzyme transketolase?

Back 34

It is found in the Calvin Cycle and the Pentose Phosphate Pathway
- Transfers a 2-C group, carried temporarily by TPP, from a ketose donor to an aldose acceptor

Front 35

Which enzyme requires the cofactor TPP?

Back 35

Transketolase

Front 36

How does light regulate the Calvin Cycle?

Back 36

- Light activates photosystem I and e- flow to ferredoxin
- Ferredoxin passes e- to the disulfide-containing protein thioredoxin
- Reduce thioredoxin donates e- to the light-activated enzyme of the Calvin Cycle, breaking its disulfide bond, activating the enzyme
- At night the Cys residues are reoxidized to their disulfide linkage and enzymes are inactivated

Front 37

What happens during photorespiration? Why is it bad?

Back 37

When a plant consumes O2 and produces CO2 (driven by light)
- costly side reaction of photosynthesis
- a result of the lack of specificity of the enzyme rubisco

Front 38

Which type of plants directly enter the Calvin Cycle (with CO2 reacting with Ribulose 1,5-BisPhosphate to form 3-phosphoglycerate)

Back 38

C3 Plants

Front 39

What type of plants temporarily fix CO2 into a four Carbon compound before beginning the Calvin Cycle?

Back 39

C4 Plants

Front 40

What is the purpose of the Hatch-Slack pathway in C4 plants?

Back 40

To avoid wasteful photorespiration (conversion of O2 to CO2 with Rubisco)

Front 41

What happens in the Hatch-Slack (C4) Pathway?

Back 41

- CO2 is fixed with PEP into a 4C (oxaloacetate) compound in mesophyll cells
- Converted to Malate
- Passes into bundle-sheath cells via plasmodesmata
- Malate reduced to CO2 and pyruvate
- CO2 enters Calvin Cycle and Pyruvate goes back into the mesophyll cell to become PEP
- This mechanism is important for making the plant more efficient

Front 42

How is CO2 brought into C4 plants?

Back 42

PEP carboxylase combines CO2 with PEP to make Oxaloacetate (in the mesophyll cells)

Front 43

How do CAM plants regulate photosynthesis?

Back 43

At night - stomata open - CO2 fixed into malate
During day - stomata closed - CO2 released from malate

Front 44

Which enzyme releases CO2 from malate in the bundle-sheath cell?

Back 44

Malic enzyme

Front 45

The biosynthesis of lipids requires what molecule that is not involved in breakdown?

Back 45

Malonyl-CoA

Front 46

How is malonyl-CoA formed?

Back 46

Acetyl-CoA + CO2 + ATP --> Malonyl-Coa + ADP + Pi

Enzyme: acetyl-CoA carboxylase (biotin)

Front 47

Generally speaking, how are fatty acids synthesized?

Back 47

With a four-step sequence catalyzed by a system collectively referred to as fatty acid synthase - extends the chain by two carbons

Front 48

What keeps the fatty acid synthase (FAS) together with its multiple domains?

Back 48

Acyl Carrier Protein (ACP)

Front 49

What prosthetic group is on ACP? What is important about it?

Back 49

4'-phosphopanthetheine
(attaches to ACP at a Serine; ends with -SH which allows it to bind to malonyl groups)

Front 50

What are the four basic steps of Fatty Acid Synthesis?

Back 50

1. Condensation
2. Reduction of Carbonyl Group
3. Dehydration
4. Reduction of the Double Bond

Front 51

What happens during the first step of Fatty Acid Synthesis?

Back 51

Condensation:
- Acetyl group is transferred to the malonyl group on the -SH of ACP
- CO2 is released

Front 52

What happens during the second step of Fatty Acid Synthesis?

Back 52

Reduction of the Carbonyl Group

Front 53

What happens during the third step of Fatty Acid Synthesis?

Back 53

Dehydration

Front 54

What happens during the fourth step of Fatty Acid Synthesis?

Back 54

Reduction of the Double Bond

Front 55

What are the four basic steps of Fatty Acid Synthesis?

Back 55

1. Condensation
2. Reduction of Carbonyl Group
3. Dehydration
4. Reduction of the Double Bond

Front 56

What happens during the first step of Fatty Acid Synthesis?

Back 56

Condensation:
- Acetyl group is transferred to the malonyl group on the -SH of ACP
- CO2 is released

Front 57

What happens during the second step of Fatty Acid Synthesis?

Back 57

Reduction of the Carbonyl Group
- NADPH --> NADP+
- Carbonyl reduced to alcohol

Front 58

What happens during the third step of Fatty Acid Synthesis?

Back 58

Dehydration
- H2O is released
- Double bond forms

Front 59

What happens during the fourth step of Fatty Acid Synthesis?

Back 59

Reduction of the Double Bond
- NADPH --> NADP+
- Double bond replaced by single bond

Front 60

After the first round of fatty acid synthesis what molecule has been made? What happens next?

Back 60

Butyryl-ACP has been made - must be moved to where the acetyl-CoA was initially and a new molecule of malonyl-Coa attaches to the -SH group of ACP to continue

Front 61

What are the sources of NADPH for lipid synthesis in various tissues?

Back 61

- Liver, mammary gland: Pentose Phosphate Pathway (glucose 6P --> pentose-P + CO2)
- Adipose tissue: Malic enzyme (reduce malate to pyruvate generates NADPH)
- Plant chloroplasts: photosynthetic e- transfer

Front 62

How is citrate involved in fatty acid synthesis?

Back 62

Acetyl-Coa is generated in the mitochondrial matrix, but is required in the cytosol and cannot be directly shuttled to the cytosol, therefore uses an indirect citrate transporter

Front 63

Outline the steps of acetyl-Coa in the matrix getting to the cytosol.

Back 63

- Acetyl-CoA + Oxaloacetate w/ Citrate Synthase --> Citrate
- Citrate uses Citrate transporter of inner membrane to pass through out of the mitos to the cytosol
- Citrate in the cytosol is converted to Acetyl-CoA and Oxaloacetate via Citrate Lyase (requires ATP hydrolysis)

Front 64

Where is Acetyl-CoA produced? Where is it required for fatty acid synthesis?

Back 64

Mitos
Cytosol

Front 65

How does citrate regulate fatty acid synthesis?

Back 65

- Activates fatty acid synthesis
- When Acetyl-CoA and ATP increase, citrate is transported out of mitos and is converted to cytosolic Acetyl-Coa (precursor for F.A. synthesis)
- Inhibits phosphofructokinase-1 of glycolysis

Front 66

How does palmitoyl-CoA regulate fatty acid synthesis? Why does that make sense?

Back 66

Palmitate (16:0) is the principal product of fatty acid synthesis and inhibits the conversion of Acetyl-CoA to Malonyl-CoA (to inhibit FAS)

Front 67

How does glucagon regulate fatty acid synthesis? Why does that make sense?

Back 67

Glucagon inhibits conversion of Acetyl-CoA to Malonyl-CoA (don't want to store energy, need to raise blood glucose)

Front 68

How does insulin regulate fatty acid synthesis? Why does that make sense?

Back 68

Insulin triggers activation of conversion of Citrate to Acetyl-CoA (want to store energy as fatty acids, want to reduce blood glucose levels)

Front 69

How does Malonyl-CoA affect fatty acyl-carnitine transport into mitochondria?

Back 69

Malonyl-CoA inhibits the FA carrier, Carnitine, from taking FA into the mitox (where they can go through β-oxidation)

Front 70

How can a double bond (point of unsaturation) be introduced into fatty acids?

Back 70

Fatty Acyl-CoA desaturase, a mixed-function oxidase uses e- transfer, ultimately oxidizing the saturated fat to a monounsaturated fat and NADPH to NADP+

Front 71

What is meant by the term "essential" fatty acids?

Back 71

Group of polyunsaturated fatty acids produced by plants, but not by humans, required in the human diet

Front 72

What are some differences between fatty acid synthesis and beta-oxidation?

Back 72

(synthesis vs beta-oxidation)
Location: Cytoplasm vs. Mitochondria
Enzymes: Multifunctional vs. separate
Cofactor: NADPH vs. NAD/FAD
Energy: requires ATP vs. yields ATP
Regulation: Acetyl-CoA Carboxylase vs. Acetyl-CoA availability

Front 73

L-Glycerol 3-Phosphate is a precursor for triacylglycerols; what are the two methods for formation?

Back 73

1. Dihydroxyacetone phosphate (from glycolysis) reduced by "glycerol 3-P dehydrogenase" w/ NADH + H+ --> NAD+

2. "Glycerol kinase" adds a Pi to Glycerol (1 ATP required)

Front 74

What are the two precursors for triacylglycerols and glycerophospholipids?

Back 74

Fatty Acyl-CoA
L-glycerol 3-phosphate

Front 75

What is the structure of phosphatidylglycerol?

Back 75

A phospholipid (glycerol backbone) with glycerol as the head group (-OH on glycerol made a phosphoester linkage to phosphate)

Front 76

What is the structure of phosphatidylethanolamine?

Back 76

Same structure as phosphatidylserine with the carboxylic acid (CO2) removed

Front 77

What is the structure of phosphatidylcholine?

Back 77

A phospholipid (glycerol backbone) with the following alcohol:
HO-CH2-CH2-N+(CH3)3
which attacked the phosphate head group

Front 78

How can CDP-diglyceride be converted to phosphatidylcholine?

Back 78

- CDP-diglyceride first converted to phosphatidylserine
- Converted to phosphatidylethanolamine (w/ head group switch)
- Converted to phosphatidylcholine (w/ 3 Ado-Met / SAM ---> 3 AdoHcy)

Front 79

What are the four stages of creating lanosterol (compound from which all steroids are derived)?

Back 79

1. Condensation of 3 acetate units to form 6C mevalonate
2. Conversion of mevalonate to two activated isoprenes
3. Condensation of 6 activated isoprenes to form squalene
4. Conversion of squalene to 4-ring steroid nucleus (Lanosterol)

Front 80

Where does mevalonate come from? What does it synthesize?

Back 80

From 3 x Acetate (CH3-COO-)
Converts to isoprenes

Front 81

In what stage of cholesterol biosynthesis does HMG-CoA play a role? What is it formed from?

Back 81

Stage 1: synthesis of mevalonate from acetate
- Formed from three molecules of Acetyl-CoA

Front 82

How does HMG-CoA get converted in the first stage of cholesterol synthesis to the desired product of Mevalonate?

Back 82

HMG-CoA reductase w/ 2-NADPH + 2H+
(releases CoA-SH)

Front 83

What drug inhibitor can affect cholesterol synthesis? What enzyme does it affect specifically?

Back 83

Statin - inhibits HMG-CoA reductase which converts HMG-CoA to Mevalonate during the first stage of cholesterol synthesis

Front 84

What is meant by an "activated isoprene" (made during stage 2 of cholesterol synthesis)? What two are formed?

Back 84

Isoprene unit (5C) with PPi attached to end
- Isopentenyl Pyrophosphate
- Dimethylallyl Pyrophosphate

Front 85

What reactions occur during stage 3 of cholesterol synthesis?

Back 85

Condensation of Six Activated Isoprene Units to Form Squalene:
- Isopentenyl-PP + Dimethylallyl-PP
(Head-to-Tail condensation)
--> 10C Geranyl-PP + Isopentenyl-PP
(Head-to-Tail condensation)
--> 15C Farnesyl-PP + 15C Farnesyl-PP
(Head-to-Head condensation)
--> 30C Squalene

Front 86

What are the 5C, 10C, 15C, and 30C isoprene derivatives in the pathway to cholesterol?

Back 86

5C: Isopentenyl-Pyrophosphate
Dimethylallyl-PP
10C: Geranyl-PP
15C: Farnesyl-PP
30C: Squalene

Front 87

What are examples of isoprenoids other than sterols that are derived from isopentenyl-PP?

Back 87

- Quinone e- carriers: ubiquinone, plastoquinone
- Dolichols
- Phytol chain of chlorophyll
- Rubber
- Vitamins A, E, K
- Carotenoids
- Plant hormones abscisic acid and gibberellic acid

Front 88

What is a cholesteryl ester formed from?

Back 88

Cholesterol + Fatty Acyl-CoA combined to form an ester at the -OH on cholesterol
(enzyme: acyl-CoA-cholesterol acyl transferase, ACAT)

Front 89

Why is the structure of cyclooxygenase important for medicine development ("super aspirins")?

Back 89

Cyclooxygenase impacts eicosanoid synthesis in two parts of the pathway; there are two functions of it; by inhibiting only one part you can get rid of fever, inflammation, pain, without the side effect of gastric ulcers!
(unfortunately, they have their own side effects like risk of heart attack and stroke)

Front 90

What is a bile acid (and its salt) and what is the function?

Back 90

Relatively hydrophilic cholesterol derivatives that are synthesized in the liver and aid in lipid digestion

Front 91

What is the purpose of ACAT (acyl-CoA-cholesterol acyl transferase)?

Back 91

To put a fatty-acyl-CoA on the -OH of cholesterol to form a cholesteryl ester

Front 92

How are lipids carried in the blood? Why is this necessary?

Back 92

Lipids must be carried as plasma lipoproteins, macromolecular complexes of specific carrier proteins, because they are essentially insoluble in water

Front 93

What is a plasma lipoprotein called when it is free of its lipid?

Back 93

Apolipoprotein (apo designates lacking)

Front 94

What is the composition difference between HDL and LDL?

Back 94

HDL have significantly more protein; LDL have significantly more cholesterol

Front 95

What are the four types of plasma lipoproteins?

Back 95

Chylomicrons
VLDL
LDL (bad)
HDL (good)

Front 96

What is the composition and structure of an LDL?

Back 96

23% protein
37% cholesterol (high)
20% phospholipid
10% triacylglycerol (low)
ApoB-100 (major protein of LDL; receptors recognize this protein and mediate uptake of cholesterol)

Front 97

What happens during reverse cholesterol transport?

Back 97

HDL takes cholesterol from peripheral tissues and carries it back to the liver; the liver converts it into bile acids and secretes it

Front 98

How does cholesterol enter cells?

Back 98

Receptor-Mediated Endocytosis

Front 99

How does receptor-mediated endocytosis work?

Back 99

- LDL with apoB-100 protein is recognized by LDL receptors on cell surfaces
- LDL is endocytosed into an endosome
- Endosome fuses with a lysosome which enzymatically degrades the lysosome
- **apoB-100 protein is degraded to amino acids
- **Cholesterol of cell is released into cytosol
- **LDL receptors are not degraded and return to the cell surface to function in further uptake

Front 100

What is the molecular defect in familial hypercholesterolemia? What signs are there of it?

Back 100

- Blood levels of cholesterol are extremely high (severe atherosclerosis develops in childhood)
- Caused by defective LDL receptor and lack receptor-mediated uptake of cholesterol carried by LDL (therefore cholesterol is not cleared from the blood)

Front 101

What is an ABC transporter? What substrates are transported by such transporters?

Back 101

- ATP-Binding Cassette - uses ATP hydrolysis to drive transport across membrane (reverse cholesterol transport)
- Transports free cholesterol from in the cell to outside of the cell

Front 102

What is the defect in Tangier disease? What does this cause?

Back 102

Tangier disease - does not have ABC transporters - failure of reverse cholesterol transport
- HDL virtually absent which prevents them from exporting cholesterol like they should so it accumulates in tissues

Front 103

What type of enzyme catalyzes oxidations in which molecular oxygen is the e- acceptor but O2 atoms do not appear in the oxidized product?

Back 103

Oxidase

Front 104

What type of enzymes catalyze oxidative reactions in which oxygen atoms are directly incorporated into the substrate molecule, forming a new hydroxyl or carboxyl group? What are the two types?

Back 104

Oxygenase
- Dioxygenase (both O2 atoms incorporated into organic substrate)
- Monooxygenase (only one oxygen atom incorporated into substrate, the other is reduced to H2O)

Front 105

Which type of oxygenase requires two substrates? What for?

Back 105

Monooxygenase - main substrate accepts one of the two oxygen atoms, and a cosubstrate furnishes hydrogen atoms to reduce the other oxygen atom to H2O

Front 106

What are the other names for monooxygenases?

Back 106

Hydroxylases (because main substrate is usually hydroxylated)
Also mixed-function oxidases or mixed-function oxygenases, to indicate that they oxidize two different substrates simultaneously

Front 107

What enzyme converts cholesterol to Pregnenolone?

Back 107

Mitochondrial side-chain cleavage enzyme (SCC) with cytochrome P-450 (+ O2)

Front 108

What is protein is used in the most numerous and most complex monooxygenation reactions?

Back 108

Cytochrome P-450 (heme protein)

Front 109

What is a substance capable of causing cancer called?

Back 109

Carcinogen

Front 110

What is a substance foreign to the organism called?

Back 110

Xenobiotic

Front 111

Why are P-450 proteins named as such?

Back 111

It absorbs light strongly at 450 nm

Front 112

What is the role of NADPH in cytochrome P-450 reactions? What is the role of cytochrome P-450 reductase?

Back 112

- NADPH provides the reducing equivalents to convert one of the oxygen atoms to H2O
- Cytochrome P-450 reductase is an Fe-S protein which passes the reducing equivalents to cytochrome P-450

Front 113

What are examples of xenobiotic substances?

Back 113

Foreign substances:
- Drugs
- Industrial solvents/waste (choloform, benzene, chlorinated biphenyls, etc.)
- Cigarette components (benzopyrene, nitrosamines)
- Heavy metals

Front 114

How does P-450-catalyzed hydroxylation help to dispose of hydrophobic xenobiotics?

Back 114

It adds an -OH, (which a sugar can be attached to) converting the molecule from non-polar to polar; now soluble in water; passes into blood and goes to kidney where it can be excreted from body

Front 115

Why is it important to know whether drugs induce a certain P-450?

Back 115

There may be drug interactions that may affect the rate at which the drugs are metabolized; could cause lethal levels

Front 116

What organisms can fix nitrogen?

Back 116

Only bacteria have the enzymes;
- free-living: cyanobacteria and azotobacter
- symbionts: in root nodules of legumes

Front 117

What is the first step of the nitrogen cycle?

Back 117

Fixation (reduction) of atmospheric nitrogen (N2) by nitrogen-fixing bacteria to yield ammonia (NH3 or NH4+)

Front 118

What occurs during the process of nitrification?

Back 118

Ammonia is oxidized to nitrite (NO2-) and then on to nitrate (NO3-)

Front 119

How does nitrate (NO3-) cycle back to atmospheric nitrogen (N2)?

Back 119

Denitrification

Front 120

What is an example of symbiosis in plants?

Back 120

Nitrogen-fixing bacteria live in the root nodules of legumes

Front 121

What is the overall reaction of the nitrogenase complex?

Back 121

N2 + 10H+ + 8e- + 16 ATP --> 2NH4+ + 16ADP + 16 Pi + H2

Front 122

What are the components of the nitrogenase complex?

Back 122

Dinitrogenase Reductase: dimer, oxidizes/reduces by one e-, 2 ATP binding sites

Dinitrogenase: tetramer, redox center with Mo, Fe, S

Front 123

What is the significance of the high activation barrier for nitrogen fixation?

Back 123

Because it must take place at biological temperatures and at a low pressure, the barrier is overcome by the binding and hydrolysis of 16 ATP; also in symbiotic relationships, the plant can provide energy from carbohydrates

Front 124

What happens when the nitrogenase complex tries to go in the presence of oxygen? Why?

Back 124

The enzymes are inactivated by oxygen; they are extremely labile

Front 125

How can the toxicity of oxygen be overcome in a symbiosis?

Back 125

The plant bathes the bacteria in leghemoglobin, which is an oxygen-binding heme protein that binds all available oxygen so that it cannot interfere w/ fixation

Front 126

What amino acids provide the critical entry point for ammonia (NH4+)?

Back 126

Glutamate and Glutamine

Front 127

What are the two steps in the pathway for NH3 incorporation?

Back 127

1. Glutamine Synthetase: Glutamate + NH4+ + ATP --> Glutamine + ADP + Pi + H+
2. Glutamate Synthase: α-Ketoglutarate + Glutamine + NADPH + H+ --> 2 Glutamate + NADP+
Net: α-Ketoglutarate + NH4+ + NADPH + ATP --> Glutamate + NADP+ ADP + Pi

Front 128

What enzyme is a primary regulatory point in nitrogen metabolism? Why does this make sense?

Back 128

Glutamine Synthetase - entry point for reduced nitrogen into organic compounds

Front 129

How is Glutamine Synthetase regulated?

Back 129

1. Cumulative allosteric inhibition - six end products of glutamine metabolism inhibit the conversion of glutamate to glutamine
2. Covalent Modification - ATP donates AMP to enzyme (inactive), when AMP removed (active)

Front 130

Which amino acids that we need to know come from 3-Phosphoglycerate (from glycolysis)?

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--> Serine --> Glycine

Front 131

Which amino acids that we need to know come from α-Ketoglutarate (from Kreb's cycle)?

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--> Glutamate --> Glutamine

Front 132

Which amino acids that we need to know come from Erythrose 4-P + Phosphoenolpyruvate (PEP)?

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Tryptophan, Phenylalanine, Tyrosine (aromatic amino acids)

Front 133

What is concerted inhibition?

Back 133

When a pathway branches to two products, both products must be present to inhibit the starting molecule; makes sure you don't stop making something when one is high and the other is not

Front 134

What is a major precursor for porphyrins?

Back 134

Glycine

Front 135

What are some important examples of porphyrins?

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Heme proteins such as hemoglobin and cytochromes

Front 136

What amino acid precursors make glutathione?

Back 136

Glutamate
Cysteine
Glycine

Front 137

What amino acid precursor makes catecholamines (dopamine, epinephrine, norepinephrine)?

Back 137

Tyrosine

Front 138

What is histamine derived from?

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Histidine (amino acid) with the CO2 removed. Requires PLP.

Front 139

What is serotonin derived from?

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Trypotophan ---> 5-Hydroxy-tryptophan --> Serotonin (PLP required to remove CO2 from amino acid)

Front 140

How is PRPP (activated sugar) synthesized?

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Ribose-5-P + ATP --> PRPP + AMP

Front 141

How are purine and pyrimidine synthesis different?

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With purines, ring structure is built up one or a few atoms at a time, attached to ribose throughout the process
With pyrimidines, the nucleotide ring is synthesized first as orotate, attached to the ribose sugar and then converted to the common pyrimidine nucleotide

Front 142

What is the significance of IMP (Inosinate MonoPhosphate)?

Back 142

It is a precursor for AMP and GMP

Front 143

What is the mode of action of azaserine?

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It is a glutamine analog which strongly inhibits glutamine amidotransferases (suicide inactivator)

Front 144

What is the purpose of the enzyme ribonucleotide reductase?

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It converts ribonucleotides to deoxyribonucleotides (building blocks of DNA) by direct reduction at the 2'-carbon atom of the D-ribose to form the 2'-deoxy derivative

Front 145

What are the two methods of nucleotide biosynthesis; essentially what does that mean?

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- De Novo Pathway - begin with metabolic precursors: amino acids, ribose 5P, CO2, NH3
- Salvage Pathway - recycle the free bases and nucleotides released from nucleic acid breakdown

Front 146

Which amino acid is a critical precursor for purine synthesis? Which for pyrimidine synthesis?

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Purine - Glycine
Pyrimidine - Aspartate

Front 147

Which amino acids are important for providing amino groups for nucleotide synthesis?

Back 147

Glutamine provides 2xN for purines and 1xN for pyrimidine
Aspartate also gives a 1xN for each
Glycine provides 1xN for purines

Front 148

Where do the atoms originate from for a purine molecule?

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C - from CO2
N - from aspartate
2C - THF
2N - glutamine amide
N-C=C - glycine

Front 149

Where do the atoms originate from for a pyrimidine molecule?

Back 149

N - glutamine amide
C - HCO3
C-C-C-N - aspartate

Front 150

What is the significance of orotate being converted to orotidylate?

Back 150

This is the step in pyrimidine synthesis when the elements of the pyrimidine ring get attached to the ribose sugar; about to be converted to UMP or CTP; uses PRPP --> PPi