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Biochemistry > BMB 466 Final Exam > Flashcards

BMB 466 Final Exam Flashcards

Chapter 21-23

1
Q

What is nitrogen fixation?

A

The process by which atmospheric N2(g) is converted into nitrogen-containing compounds useful in biochemical processes

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2
Q

What is required for nitrogen fixation?

A
  1. Nitrogenase Protein
  2. Reductant (Ferrodoxin)
  3. ATP
  4. Anaerobic conditions
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3
Q

What are diazotrophs?

A

Prokaryotes that fix atmospheric nitrogen into bioavailable forms

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4
Q

What are rhizobia?

A

Bacteria that fix nitrogen in leguminous plants (beans)

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5
Q

What are the two parts of the nitrogenase complex?

A

Fe-Protein (γ2)
MoFe-Protein (α2β2)

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6
Q

What is the Fe-Protein?

A

Homodimer with a single 4Fe-4S cluster and 2 ATP binding sites

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7
Q

What is the MoFe-Protein?

A

Heterotrimer with MoFe cofactor and P-cluster

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8
Q

What makes up the MoFe-Protein?

A

[4Fe-3S] and [1Mo-3Fe-3S] groups bridged by 3 sulfide ions

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9
Q

How much ATP is used in the nitrogenase complex?

A

4 ATP per pair of electrons (12 ATP to go from N2 to NH3)

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10
Q

What provides electrons to the Fe-Protein?

A

Ferrodoxin

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11
Q

What is the mechanism of the nitrogenase complex?

A
  1. Ferrodoxin provides electrons to Fe-Protein
  2. Fe-Protein binds to MoFe-Protein
  3. ATP-induced conformational change allows for electron transfer
  4. Dissociation of Fe-Protein from MoFe-Protein
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12
Q

What is the rate-limiting step of the nitrogenase complex?

A

Dissociation of Fe-Protein from MoFe-Protein

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13
Q

How many electrons are actually transferred in nitrogen fixation? How many do we consider are transferred? Why?

A

6 electrons are actually transferred, however, the reaction is considered an 8 electrons transfer due to competing reactions causing inefficiency

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14
Q

What reaction is competing with the nitrogenase complex from reducing nitrogen?

A

2 H+ —> H2(g)

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15
Q

What is the difference between ammonia and ammonium?

A

Ammonia: NH3
Ammonium: NH4+

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16
Q

What is nitrogen assimilation?

A

The coordination of NH3 into biomolecules for biological use

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17
Q

What are the substrates and products of CPS I?

A

NH3 + HCO3- —> Carbamoyl-P

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18
Q

What is the difference between CPS I and CPS II?

A

CPS I uses ammonia as a nitrogen donor and is involved in urea biosynthesis
CPS II uses glutamine as a nitrogen donor and is involved in pyrimidine biosynthesis

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19
Q

Where are the two CPS enzymes localized?

A

CPS I: Mitochondria
CPS II: Cytosol

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20
Q

What reaction is catalyzed by glutamine synthetase?

A

Amination of the gamma-carboxyl of glutamate to glutamine

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21
Q

What are the substrates of glutamine synthetase?

A

Glutamate, ATP, and NH4+

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22
Q

What is the mechanism of glutamine synthetase?

A

ATP hydrolysis to phosphorylate glutamate and then incorporation (not transfer) of NH4+ replacing the phosphate to make glutamine

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23
Q

What is the structure of alpha-ketoglutarate?

A

(-)OOC-CH2-CH2-CO-COO(-)

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24
Q

Is an aminotransferase enzyme envolved in nitrogen assimilation?

A

No; assimilation is incorporation of nitrogen into biomolecules. An aminotransferase is transfering an amine already on a biomolecule.

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25
Q

What two ways can alpha-ketoglutarate be used to produce glutamate?

A
  1. Amminated by an amino acid to glutamate via an aminotransferase (not assimilation)
  2. Nitrogen assimilation via glutamate synthase
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26
Q

What reaction is catalyzed by glutamate synthase?

A

Reductive amination of alpha-ketoglutarate to glutamate

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27
Q

What donates electrons to glutamate synthase?

A

NADPH

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28
Q

Why is glutamate not an essential ammino acid if humans do not have glutamate synthase like bacteria and plants?

A

Humans can produce glutamate via aminotransferase reactions, but it is not assimilation.

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29
Q

What is the overall reaction of glutamate synthase?

A

alpha-ketogluterate + glutamine + NADPH + H+ —> 2 glutamate + NADP+

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30
Q

What intermediate is formed in the reaction catalyzed by glutamate synthase?

A

alpha-Iminoglutarate

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31
Q

What is the steps of the glutamate synthase reaction?

A
  1. Deamination of glutamine to glutamate and NH3
  2. NH3 incorporates into a-ketoglutarate forming a-iminoglutarate
  3. Electrons are donated by NADPH to FADH2, then to FMNH2, then to a-Iminoglutarate
  4. Oxidation of FMNH2 causes the reduction of a-Iminoglutarate to glutamate
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32
Q

What is a lysosome?

A

Organelle used to degrade cellular substances

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33
Q

What is autophagy?

A

process by which damaged or unneeded organelles are digested by the lysosome to be recycled by the cell

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34
Q

What are cathepsins?

A

Lysosomal proteases with an acidic pH optima

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35
Q

What protects cells from lysosomal leakage of proteases?

A

Cathepsins have very acidic pH optima and many are inactive at cytosolic pH

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36
Q

What is the internal pH of lysosomes?

A

pH = ~5

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37
Q

Is lysosome protein degradation specific?

A

Depends on energy conditions:
Well-Fed State = non-specific
Starvation State = specific for tissues that atrophy in response to fasting (i.e liver and muscle)

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38
Q

What causes protein degradation?

A

Depletion of carb and fat stores, muscle disuse or injury, uterine regression

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39
Q

What is ubiquitin?

A

Small protein that marks intracellular proteins for degradation by a proteasome

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40
Q

How is ubiquitin attached to its target protein?

A

C-terminal of ubiquitin attached to side-chain amino group of Lys on target protein

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41
Q

What marks a protein for degradation in eukaryotes?

A

Polyubiquination (50+ ubiquitin molecules)

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42
Q

What is the process of ubiquination?

A
  1. Ubiquitin attached to E1
  2. Ubiquitin transfered to E2
  3. Ubiquitin transfered to target protein Lys
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43
Q

What is the name and function of the E1 step of ubiquitination?

A

Ubiquitin-activating Enzyme (E1) uses two ATP equivalences (ATP->AMP) to conjugate the terminal carboxyl group to the the enzyme

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44
Q

What is the name and function of the E2 step of ubiquitination?

A

Ubiquitin-conjugating Enzyme (E2s) transfers ubiquitin to specific Cys sulfhydral on an E2 enzyme

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45
Q

What is the name and function of the E3 step of ubiquitination?

A

Ubiquitin-protein Ligase (E3) transfers activated ubiquitin to the sidechain amino group of Lys to form an isopeptide bond with the condemned protein

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46
Q

What is the function of a proteosome?

A

Degrade ubiquinated proteins

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47
Q

What is the makeup of a proteosome complex? What are the densities (S) of the components?

A

The 26S Proteosome is made up of a 20S proteosome and two 19S caps

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48
Q

What are the functions of the two compents of the proteosome?

A

Caps: recognize ubiquitin and use ATP to unfold protein and feed into proteosome
(20S) Proteosome: generate amino acid fragments from polypeptide chain

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49
Q

How many active sites are in the 20S proteosome? Where are they located?

A

3 active sites inside of the hollow core formed by 27 subunits

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50
Q

What is the target of each of the three active sites in the 20S proteosome?

A

β1: Acidic residues
β2: Basic residues
β3: Hydrophobic residues

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51
Q

Describe the receptors tyrosine kinase signaling pathway:

A
  1. Ligand binding allows for Sos to bind to RTK
  2. Sos acts on GDP-bound Ras and exchanges it for GTP, activing Ras
  3. Ras phosphorylates Raf causing a cascade (Ras->Raf->MEK->MAPK)
  4. Transcription factors in the nucleus are activated via phosphorylation
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52
Q

How does insulin illicit a cellular response?

A

Activates Ras signaling cascade to mobilize glucose transporters

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53
Q

Describe the adenylate cyclase signaling pathway:

A
  1. Ligand binding GPCR activates G-protein by exchanging GDP for GTP
  2. G-protein stimulates or inhibits adenylate cyclase (depending on the type of G-protein)
  3. Activated adenylate cyclase uses ATP to produce cAMP
  4. cAMP activates PKA which leads to cellular response
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54
Q

Describe the phosphoinositide signaling pathway:

A
  1. Ligand binding to GPCR activates Gq by exchanging GDP for GTP
  2. GTP-bound Gq stimulates PLC to cleave PIP2 to DAG and IP3
  3. IP3 binds to Ca2+ receptor in ER membrane, causing Ca2+ release into cytosol
  4. Ca2+ activates calmodulin stimulating CaM Kinase and PKC
  5. DAG stimulates PKC
  6. CaM Kinase and PKC activate a cellular response
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55
Q

What receptor does insulin bind to?

A

Receptor tyrosine kinase

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56
Q

What receptor does glucagon bind to?

A

G-Protein Coupled Receptor

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57
Q

What receptor does epinephrine bind to?

A

G-Protein Coupled Receptor

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58
Q

What protein(s) does epinephrine stimulate? What does this depend on?

A

Epinephrine can stimulate PKA, PKC, or both depending on the type of adrenergic receptor

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59
Q

What organ releases insulin?

A

Pancreas

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60
Q

What pathway(s) does insulin stimulate?

A

MAPK (Ras) and PDK1

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61
Q

What are normal blood glucose levels?

A

~5mM

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62
Q

What is the Km of the GLUT4 transporter? Is this low or high?

A

Km = ~2mM
Relatively low to be able to rapidly take up glucose from the blood

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63
Q

What is Km?

A

The substrate concentration needed for half Vmax

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64
Q

What pathway(s) does glucagon stimulate?

A

cAMP formation and PKA activation for glycogen degradation and glucose release from liver

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65
Q

Glucose is released out of liver to the rest of the body through what transporter?

A

GLUT2

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66
Q

PKA signaling from glucagon has what effect on enzymes involved in glycogen synthesis?

A

Phosphorylates glycogen synthase (turns off) and glycogen phosphorylase (turns on) to stimulate glycogen degradation

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67
Q

What does epinephrine binding to liver alpha-adrenoreceptor stimulate?

A
  1. Ca(2+)
  2. Glycogen Breakdown
  3. Glucose formation
  4. Transport out of liver via GLUT2
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68
Q

What does epinephrine binding to liver beta-adrenoreceptor stimulate?

A
  1. cAMP
  2. Glycogen Breakdown
  3. Glucose formation
  4. Transport out of liver via GLUT2
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69
Q

What does epinephrine binding to muscle beta-adrenoreceptor stimulate?

A
  1. cAMP
  2. Glucogen Breakdown
  3. Glycolysis
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70
Q

What is the purpose of organ specialization?

A

Metabolic offloading

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71
Q

How much of the bodys oxygen use is done by the brain?

A

~20% despite making up 2% of body mass

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72
Q

Why does the brain have high metabolic activity?

A

High ETC activity to power Na+/K+ active transport for membrane potential management

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73
Q

What glucose transporter is used by the brain?

A

GLUT3

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74
Q

What are the effects of low blood glucose to the brain?

A

Coma or death

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75
Q

Why is muscle able to “steal” glucose from the brain?

A

GLUT4 (muscle) has a higher affinity to glucose than GLUT3 (brain)

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76
Q

What glucose transporter(s) are used by the muscle?

A

GLUT1 and GLUT4

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77
Q

What is the main fuel source for (skeletal) muscle cells?

A

Glycogen

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78
Q

What is the difference in energy source between skeletal and cardiac muscle?

A

Skeletal: glycogen
Cardiac: fatty-acids

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79
Q

How much of the bodys oxygen use is done by the muscle?

A

~30% at rest

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80
Q

How long is ATP available for without oxygen?

A

~1.5 min

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81
Q

What is the function of phosphocreatine?

A

Store phosphate to rapidly regenerate ATP

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82
Q

What is the reaction of ATP production from phosphocreatine?

A

Phosphocreatine + ADP -> Creatine + ATP
(the reverse reaction regenerates phosphocreatine in resting muscle)

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83
Q

What is the function of the liver as a metabolic clearinghouse?

A

Formation and breakdown of TAGs to release ketone bodies into the blood

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84
Q

What glucose transporter is used by the liver?

A

GLUT2

85
Q

How is liver insulin sensitivity different than other tissues?

A

Liver is insulin sensative but not through the mobilization of glucose transporters; we would not expect an increase in liver glucose uptake after insulin release

86
Q

What allows for glucose transport in and out of the liver?

A

Glucokinase (in liver) has a lower affinity for glucose than Hexokinase in other tissues

87
Q

What conditions is lactate formed in the muscle?

A

Anaerobic conditions

88
Q

Anaerobic conditions cause a buildup of _____ that lactate production allows for regeneration of.

A

NADH

89
Q

What are the two fates of lactate after it has been produced in muscle?

A
  1. Stays in muscle until oxygen delivery is reestablished and it is converted to pyruvate for use in the TCA cycle
  2. Cori cycle: lactate is transported to the liver where it is converted to glucose in gluconeogenesis to be released back into blood for uptake in muscle
90
Q

What is the function of the cori cycle?

A

Offload lactate metabolism to the liver

91
Q

The cori cycles sends lactate from the muscles to the liver, what does the liver do with the lactate?

A

Gluconeogenesis to form glucose (to be released back into the blood for the muscle)

92
Q

Where is ATP produced and used during the cori cycle?

A

Muscle: produces ATP
Liver: uses ATP

93
Q

What is the function of the glucose-alanine cycle?

A

Transport NH4+ from the muscle to the liver when muscle

94
Q

What occurs in the muscle during the glucose-alanine cycle?

A

Pyruvate (from glycolysis) combines with an amino acid via a transamination reaction forming an alpha-keto acid, which is oxidized for energy, and alanine, which is transported to the liver.

95
Q

What happens to alanine when it is received by the liver in the glucose-alanine cycle?

A
  1. Alanine is transaminated (onto alpha-ketogluterate) forming glutamate and pyruvate
  2. Glutamate dehydrogenase uses glutamate to form NH3
  3. NH3 goes into the urea cycle
  4. Pyruvate is used in gluconeogenesis to form glucose
  5. Glucose is released into the bloodstream by the liver
96
Q

What is the overall purpose of the kidney

A

Filters blood to maintain blood pH (bicarbonate) and remove noncellular components

97
Q

What metabolic processes occur in the kidney?

A

Urea cycle and gluconeogenesis

98
Q

What is the fate of glutamine in the kidney?

A
  1. Transaminated to produce NH3 and alpha-ketoglutarate
  2. NH3 is used in the urea cycle
  3. alpha-ketoglutarate is used in gluconeogenesis to form glucose
99
Q

What is the function of adipose?

A

Store fatty acids

100
Q

What is the function of lipoprotein lipases?

A

Hydrolyzes TAGs that are associated with lipoproteins or chylomicrons from the blood

101
Q

In what way is adipose insulin sensitive?

A

Hormone-sensative lipases can hydrolyze stored TAGs to form free-acids for oxidation in liver or muscle

102
Q

What hormones does adipose release to regulate endocrine function?

A

Leptin and adiponectin

103
Q

What is the function of leptin?

A

Regulate appetite

104
Q

What is the function of adiponectin?

A

Division/maintance of fat cells

105
Q

What gene codes for lectin? The leptin receptor?

A

Ob = leptin gene
Db = leptin receptor gene

106
Q

What organ releases epinephrine?

A

Adrenal gland

107
Q

What hormone is released in a fed state?

A

Insulin

108
Q

What hormone is released in a fasted or stressed state?

A

Glucagon and Epinephrine

109
Q

Which biomolecule is prioritized for energy: glucose or fatty acids? Why?

A

Glucose; glycolysis is faster and can be done in anaerobic conditions

110
Q

What metabolic processes are stimulated by glucagon in the muscle and liver?

A

Muscle: glycolysis (for itself)
Liver: gluconeogenesis (for other tissue)

111
Q

What is the response of muscle to insulin?

A

Increased glucose uptake
Increased glycogen synthesis

112
Q

What is the response of muscle to glucagon?

A

No effect

113
Q

What is the response of muscle to epinephrine?

A

Increased glycogenolysis

114
Q

What is the response of adipose tissue to insulin?

A

Increased glucose uptake
Increased lipogenesis
Decreased lipolysis

115
Q

What is the response of adipose tissue to glucagon?

A

Increased lipolysis

116
Q

What is the response of adipose tissue to epinephrine?

A

Increased lipolysis

117
Q

What is the response of the liver to insulin?

A

Increased glycogen synthesis
Increased lipogenesis
Decreased gluconeogenesis

118
Q

What is the response of the liver to glucagon?

A

Decreased glycogen synthesis
Increased glycogenolysis

119
Q

What is the response of the liver to epinephrine?

A

Decreased glycogen synthesis
Increased glycogenolysis
Increased gluconeogenesis

120
Q

What is one of the main enzymes that is sensitive to AMP, ADP, and ATP levels in the cell?

A

Phosphofructokinase

121
Q

What reaction does the nucleoside monophosphate kinase catalyze?

A

AMP + ATP <–> 2 ADP

122
Q

What is the target of AMP-dependent protein kinase in the heart ?

A

PFK-2/FBPase-2

123
Q

What is the effect of F2,6P?

A

F2,6P activates PFK, stimulating glycolysis and inhibiting gluconeogenesis

124
Q

What is the effect of PFK-2/FBPase-2 enzyme phosphorylation in the liver? Heart?

A

Phosphorylation in the liver activates FBPase-2 activity (inhibiting glycolysis), phosphorylation in the heart activates PFK-2 activity (promoting glycolysis)

125
Q

What is the result of PFK-2 activity?

A

Phosphorylates F6P to F2,6P, promoting glycolysis

126
Q

What is the result of FBPase-2 activity?

A

Dephosphorylates F2,6P to F6P, inhibiting glycolysis

127
Q

What is the target of AMP-dependent protein kinase in the liver?

A

Acetyl-CoA carboylase, HMG-CoA reductase, and glycogen synthase

128
Q

What is the effect of AMP-dependent protein kinase in the liver?

A

Inhibits lipid and glycogen synthesis

129
Q

How does the AMP-dependent protein kinase effect Acetyl-CoA carboxylase?

A
  1. Phosphorylation inactivates ACC
  2. ACC cannot convert Acetyl-CoA to Malonyl-CoA (which is an inhibitor of CPT1)
  3. CPT1 can transport Acetyl-CoA into the mitochondria
  4. Beta-oxidation can occur for energy extraction
130
Q

What is the effect of AMP-dependent protein kinase on skeletal muscle?

A

Increase mobilization of GLUT4 transporter to increase glucose uptake; Inhibition of ACC to promote FA oxidation

131
Q

When does blood glucose spike? Otherwise, what does it look like?

A

Blood glucose spikes after a meal but is otherwise held relatively constant due to insulin and glucagon

132
Q

What occurs during an overnight fast?

A

Mobilization of glycogen stores via increased glucagon and decreased insulin

133
Q

What are the changes and functions of insulin and glucagon in an overnight fast?

A

Increased glucagon: FA mobilization and glycogen breakdown
Decrease insulin: decrease muscle glucose uptake to make available for the brain

134
Q

During a 40 hour fast where is glucose coming from?

A

96% of glucose is from liver gluconeogenesis of glycerol and amino acids

135
Q

What occurs during a longer fast (over 40 hours)?

A

Acetyl-CoA used to form ketone bodies in the liver and muscle breakdown slows to protect critical skeletal and cardiac muscle

136
Q

What % of brain fuel is ketone bodies after a 3 day fast? a 40 day fast?

A

3 Day: 30% ketone bodies
40 Day: 70% ketone bodies

137
Q

What condition could result from an extended fast?

A

Acidosis; low blood pH from high number of ketone bodies

138
Q

How long can normal body fat last. in terms of energy?

A

1-2 months

139
Q

What is diabetes?

A

Condition of elevated blood-glucose levels

140
Q

Why do cells illicit a starvation response in diabetic patients if their blood-glucose levels are elevated?

A

Insulin deficiency prevents glucose from being taken up by cells so even though glucose is present in the bloodstream it can not move into cells for oxidation

141
Q

Cells under starvation conditions due to diabetes do what?

A

TAG hydrolysis, FA oxidation, protein breakdown, gluconeogenesis, ketone body synthesis

142
Q

What is the difference between type-1 and type-2 diabetes?

A

Type 1: lose ability to produce insulin
Type 2: deficiency in insulin receptors or signaling due to hyperinsulinemia

143
Q

What is the process that type II diabetes is formed?

A
  1. Hyperglycermia
  2. Hyperinsulinemia
  3. Insulin-receptors are down regulated
  4. More insulin is needed to achieve the same results
144
Q

What is cancer?

A

Rapid cell growth and devision

145
Q

What enzyme is often mutated in cancer cells?

A

Ras; due to its effect on mitotic signaling

146
Q

What is the major energy pathway for cancer cells?

A

Aerobic glycolysis; high glucose uptake even in the presence of oxygen

147
Q

What is the reason cancer cells go through aerobic glycolysis?

A

What a high flux of glycolysis to take advantage of the pentose phosphate pathway to create NADPH and Ru5P for biosynthesis

148
Q

How many reactions are involved in purine synthesis?

A

11 reactions

149
Q

In purine synthesis, how many of the 11 steps are ATP-dependent? How many ATP equivalences are used?

A

6 steps are ATP-dependent and uses 7 eq
5 ATP –> 5 ADP
1 ATP –> 1 AMP

150
Q

Where does the ribose-5-phosphate used in nucleotide metabolism come from?

A

The pentose phosphate pathway

151
Q

What is the first step of purine synthesis? What enzyme catalyzes this reaction?

A

A pyrophosphate (PP) is added to R5P via ribose phosphate pyrophosphokinase to form PRPP

152
Q

What is the structure of ribose-5-phosphate?

A

5 carbon sugar in furanose form (ring is 4 carbons and an oxygen) with a phosphate on the carbon not involved with the ring. Hydroxyl groups are on carbon 1, 2, and 3 all pointing down

153
Q

PRPP formation from R5P is considered a branching point because PRPP can be used to do multiple things. What are they?

A

Amino acid synthesis
Nucleic acid synthesis

154
Q

After the formation of PRPP, what is the second step of purine synthesis?

A

Transfer of glutamine nitrogen to PRPP, releasing the pyrophosphate, forming PRA

155
Q

What is the rate limiting step of purine synthesis?

A

PRPP –> PRA
Amidophosphoribosyl transferase (step 2)

156
Q

What is the backbone structure of a purine base?

A

6 ring structure with a nitrogen at position 1 and 3. Carbons at 5 and 6 are connected to nitrogens which are bridged by a carbon forming a 5 member ring.

157
Q

Where does the N1 of the purine base come from?

A

Backbone of aspartic acid

158
Q

Where does N3 and N9 of the purine base come from?

A

Sidechain of glutamine

159
Q

Where does C4, C5, and N7 of the purine base come from?

A

Glycine backbone

160
Q

Where does the C6 of the purine base come from?

A

CO2 (HCO3-)

161
Q

Where does C2 and C8 of the purine base come from?

A

THF

162
Q

What is the cofactor THF used for?

A

Addition of carbon(s)

163
Q

What is a common prenatal vitamin given to help with DNA synthesis?

A

Folate (Vitamin B9)

164
Q

How is folate (vitamin B9) used by the body in nucleotide synthesis?

A

Reduced twice by NADPH to form THF which is used for carbon addition

165
Q

What is the structure of IMP (based on purine base)?

A

Carboxyl group on 6
Double bond between 2 and 3
Double bond between 4 and 5
Double bond between 7 and 8
9 connected to R5P

166
Q

What is the structure of AMP (based on purine base)?

A

Amine on 6
Double bond between 6 and 1
Double bond between 2 and 3
Double bond between 4 and 5
Double bond between 7 and 8
9 connected to R5P

167
Q

What is the structure of GMP (based on purine base)?

A

Carbonyl on 6
Amine on 2
Double bond between 2 and 3
Double bond between 4 and 5
Double bond between 7 and 8
9 connected to R5P

168
Q

How is AMP formed from IMP?

A

Carbonyl is replaced with nitrogen from aspartate

169
Q

What is the energy source for AMP formation?

A

GTP

170
Q

What is the mechanism (enzymes, intermediates, cofactors) in the formation of AMP from IMP?

A
  1. Adenylosuccinate synthetase catalyzes IMP to adenylosuccinate using aspartate and GTP
  2. Adenylosuccinate lyase catalyzes adenylosuccinate to AMP
171
Q

What is the mechanism (enzymes, intermediates, cofactors) in the formation of GMP from IMP?

A

1.IMP dehydrogenase catalyzes IMP to XMP using NAD+ and water
2. GMP synthetase catalyzes XMP to GMP using glutamine, ATP, and water

172
Q

What reaction does the guanylate kinase catalyze?

A

GMP + ATP <–> GDP + ADP

173
Q

What reaction does the nucleoside diphosphate kinase catalyze?

A

GDP + ATP <–> GTP + ADP

174
Q

What reaction(s) does adenine phosphoribosyltransferase (APRT) catalyze?

A

Adenine + PRPP <–> AMP + PP

175
Q

What reaction(s) does hypoxanthine-guanine phosphoribosyltransferase (HGPRT) catalyze?

A

Hydroxanthine + PRPP <–> IMP + PP
Guanine + PRPP <–> GMP + PP

176
Q

What is the function of nucleotidases?

A

Break nucleotides into nucleosides and phosphate

177
Q

What is the function of purine nucleoside phosphorylase (PNP)?

A

Break nucleoside into R1P and the nitrogenase base

178
Q

How are nitrogenous bases dealt with as waste?

A

Converted to Xanthine and then to uric acid

179
Q

What is the pathway of purine degradation?

A
  1. Nucleotide is converted to nucleoside by nucleotidase
  2. Nucleoside is converted to R1P and xanthine by PNP
  3. Xanthine is converted to uric acid by xanthine oxidase
    ** Adenine is deaminated after step 1, and Guanine is deaminated after step 2 to form xanthine
180
Q

What is gout?

A

The accumulation of uric acid in the joints

181
Q

Why does gout occur?

A

Purine degradation creates uric acid which is very insoluble, so it precipitates out of blood and into joints

182
Q

What medication is used to treat gout? How does it work?

A

Allopurinol; inhibits xanthine oxidase stopping the formation of uric acid from xanthine

183
Q

What disease is caused by a HGPRT deficiency?

A

Lesch-Nyhan Syndrome

184
Q

What symptoms occur in a patient with Lesch-Nyhan Syndrome? What causes these symptoms biochemically?

A

Neurological disorders and a compulsion for self-mutilization caused by uric acid accumulation (since HGPRT cannot salvage nucleosides so all must be degraded)

185
Q

What is the function of the purine nucleotide cycle?

A

Anaplerotic reaction for skeletal muscle to generate fumerate for use in the TCA cycle

186
Q

What enzymes are involved in the purine nucleotide cycle?

A

AMP deaminase
Adenylosuccinate synthetase
Adenylosuccinate

187
Q

What occurs in the purine nucleotide cycle to produce fumarate?

A
  1. AMP is deaminated to IMP
  2. IMP and aspartate combine to form adenylosuccinate
  3. Adenylosuccinate is broken into fumarate and AMP
188
Q

What is the net reaction of the purine nucleotide cycle?

A

H2O + Aspartate + GTP –> NH4+ + GDP + Pi + Fumerate

189
Q

What is the major overall difference between purine and pyrimidine synthesis?

A

Purines are built on top of the sugar-phosphate: Pyrimidines are built into orotate ring and then added to R5P

190
Q

What are the precursors of pyrimidines?

A

Carbamoyal-phosphate and aspartate

191
Q

Where does the C6 and C1 of the pyrimidine backbone come from?

A

Backbone of aspartate

192
Q

Where does the C4 and C5 of the pyrimidine backbone come from?

A

Sidechain of aspartate

193
Q

Where does N3 of the pyrimidine backbone come from?

A

Sidechain of glutamine

194
Q

Where does the C2 of the pyrimidine backbone come from?

A

CO2 (HCO3-)

195
Q

What is the different localizations of CPS I and II?

A

CPS I is in the mitochondria (for urea cycle)
CPS II is in the cytosol (for pyrimidine synthesis)

196
Q

What is the difference in nitrogen imput for CPS I and II?

A

CPS I: free ammonia
CPS II: sidechain of glutamine

197
Q

What is the structure of orate based on pyrimidine base?

A

Carbonyl on 4
Double bond between 5 and 6
Carboxylic acid on 6
Carbonyl on 2

198
Q

What is the function of orotate phosphoribosyl transferase?

A

Combines orotate and PRPP to form OMP

199
Q

What is the function of OMP decarboxylase?

A

Remove carboxylic acid from OMP to form UMP

200
Q

Why is all OMP converted to UMP increase of the other pyrimidines?

A

Regulate U and T bases to insure correct base pairing

201
Q

What intermediates are formed in the conversion of UMP to CTP?

A

UMP -> UDP -> UTP -> CTP

202
Q

What enzyme converts UTP to CTP? What is required for this reaction?

A

CTP Synthetase using glutamine as a nitrogen donor

203
Q

What are pyrimidines degraded to?

A

Malonyl-CoA for FA synthesis

204
Q

What results from folate deficiency?

A

Low levels of vitamin B9 (foltate) lead to fetal development problems

205
Q

What is orotic aciduria?

A

Orotic acid accumulation due to deficiency in orotate phosphoribosyl transferase

206
Q

What is used to treat orotic aciduria?

A

Administration of uridine or cytidine

207
Q

Why are pyrimidines used as an anticancer treatment?

A

Thymine is only used in DNA, so inhibiting its pathway is can stop cell growth

208
Q

How are deoxyribonucleotides formed?

A

Ribonucleotide reducatase removes 2’ OH from a diphosphate nucleotide to form dNDP

209
Q

How is thymine formed?

A

Thymidylate synthase methylates dUMP at 5 position to form dTMP

Biochemistry (17 decks)

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