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Block 2 Flashcards

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1
Q

K(eq)

Equation

A

K(eq) = products / reactants

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2
Q

∆G°

Equation

A

∆G° = -R • T • ln( Keq )

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3
Q

Value of R in kcal / (mol • K)

A

R= 1.98 x 10^(-3) kcal / (mol • K)

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4
Q

Thermodynamic control vs. kinetic control

A
  • Thermodynamic control is changing the free energy of either the reactants or the products.
  • Kinetic control is changing the activation energy of the transition state (affecting the kinetics, but not the energy of the reaction).
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5
Q

Major classes of enzymes (6)

A
  • Oxidoreductase
  • Transferases
  • Hydrolases
  • Lyases
  • Isomerases
  • Ligases
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6
Q

Enzymes tightly bind the ______

A

transition state

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7
Q

Hydrophobic enzyme microenvironments affect pKa how?

A

Increases pKa

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8
Q

Peptidases

Require these two steps

A
  • Polarization of peptide carboxyl group to form an oxyanion
  • Proximity of nucleophile to attack the carbonyl carbon
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9
Q

Carboxypeptidases

How is the oxyanion formed?

A

By a Zn2+ on the enzyme

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10
Q

This amino acid can act as a general acid or as a general base

A

Histidine

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11
Q

Serine proteases utilize this triad for covalent catalysis.

Are they adjacent in the peptide?

A
  • Ser - His - Asp

* Not adjacent

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12
Q

How does a serine protease work?

A
  • Histidine’s nitrogen acts as a base to abstract a hydrogen from serine
  • Serine’s oxygen acts as a nucleophile to the substrate’s carbonyl carbon
  • Histidine’s hydrogen acts as a conjugate acid to the (cleaved) substrates nitrogen
  • Histidine’s nitrogen again acts a a base to abstract a hydrogen from water
  • The hydroxide acts as a nucleophile to the carbonyl carbon
  • Histidine again acts as an acid, donating a proton to serine’s oxygen (freeing the substrate)
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13
Q

Specific vs. general acid-base reaction

A

Specific uses water, general does not.

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14
Q

Lineweaver-Burk plots
Y intercept?
X intercept?
Slope?

A

A plot of 1/Vo vs. 1/[S]
• (set 1/[S] = 0) = 1/Vmax
• (set 1/vo = 0) = -1/Km
• The slope is Km/Vmax

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15
Q

Competitive inhibition
Mechanism?
Effect on Lineweaver-Burk plot?

A
  • Inhibitor binds to enzyme

* Increases slope

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16
Q

Noncompetitive inhibition
Mechanism?
Effect on Lineweaver-Burk plot?

A
  • Inhibitor binds to enzyme and enzyme-substrate complex

* Reduces Vmax

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17
Q

Uncompetitive inhibition
Mechanism?
Effect on Lineweaver-Burk plot?

A
  • Inhibitor binds to enzyme-substrate complex
  • Reduces Vmax
  • Apparent Km is decreased
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18
Q

Cooperativity in allosteric binding changes the ____

A

Km

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19
Q

Monosacharides

Two kinds, based on location of carbonyl carbon

A
  • Aldose

* Ketose

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20
Q

Epimer

A

Sugars with multiple chiral carbons, differing at only one

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21
Q

Diastereomers

A

Sugars differing at one or more chiral carbons

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22
Q

Enantiomers

A

Mirror image at all chiral atoms

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23
Q

Absolute configuration

A

Dextro (D) and Levo (L). Refers to the carbon furthest from the carbonyl carbon.

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24
Q

Cyclization of monosacharides
Intermediate for aldoses?
Intermediate for ketoses?

A
  • Hemiacetal

* Hemiketal

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25
Name for a 6-carbon cyclized aldose? | Name for a 5-carbon cyclized aldose?
* Pyranose | * Furanose
26
Anomeric carbon
Carbon 1. Not chiral until it cyclizes. Though, do to mutorotation it will exist in both forms. Termed alpha (-OH down) and beta (-OH up).
27
Glycosidic bond
Where anomeric carbon is bound to another sugar. There is then no mutorotation between alpha and beta forms.
28
Reducing sugar
Sugars with a free aldehyde (C1 of aldoses) can reduce metals. Polysaccharides become non-reducing sugars.
29
Advanced Glycation Endproducts (AGEs) | Formation
* Glucose forms a a Shiff's base with Lysine | * Vicinal -OH leads to Amadori rearrangement
30
Energy charge Equation? Typical value?
* ( [ATP] + 1/2[ADP] ) / ( [ATP] + [ADP] + [AMP] ) | * 0.80 - 0.95
31
Glucose-6-phosphate | Branch point for which pathways (3)?
* Glycolysis * Gluconeogenesis * Pentose phosphate
32
Plasma glucose Normal range? Hypoglycemia? Critical?
* 80 - 100 mg/dL * 60 mg/dL * 40 mg/dL
33
GLUT1 and GLUT3 Expression? Km? Why?
* Most cells of the body. Dependent cells include neurons (mostly GLUT3) and RBCs (GLUT1 only) * Km = 1mM, so always saturated. These cells must take in glucose at a rate commensurate with their typical metabolic rate.
34
GLUT2 Expression? Km? Why?
* Liver, ß-islet cells, basolateral side of intestinal cells | * Km = 15-20mM. Flux is driven by plasma glucose level.
35
GLUT4 Expression? Km? Regulation by insulin?
* Skeletal muscles and fat cells * Km = 5mM * Insulin increases GLUT4 translocation to membrane surface.
36
GLUT5 Expression? Main function?
* Apical side of small intestine cells | * Mainly uptakes fructose
37
SGLT1 Expression? Main function?
* Apical side of intestine cells | * Sodium / glucose (or galactose) co-porter
38
Glucose trapping | How does it work?
Hexokinase converts glucose to G-6-P, which cannot pass through GLUT channel proteins.
39
Glucokinase Expression? What is its similarity to hexokinase? What is its difference from hexokinase?
* Liver and ß-islet cells * Catalyzes glucose --> G-6-P * Is not inhibited by G-6-P
40
Glycogen Main glycosidic bond? Branching glycosidic bond? Approximate ratio?
* alpha(1-4) * alpha(1-6) * 10:1
41
Glycogen phosphorylase
Cleaves glycogen at alpha(1-4) glycosidic bonds into G-1-P
42
Phosphoglucomutase
Converts G-1-P into G-6-P
43
Glucose-6-phosphatase
Found only on liver ER (lumenal). G-6-P is transported into ER, converted to glucose, exported to cytosol, then exported into blood stream.
44
Debranching enzyme
Hydrolyzes glycogen at alpha(1-6) branch points, releases free glucose. It does this by first transferring 3 glucose residues to the other branch, and cleaving the last remaining glucose residue.
45
UDP-glucose pyrophosphorylase
Adds a UDP group to G-1-P. PPi hydrolysis commits this step.
46
Glycogen synthase
Adds UDP-glucose onto an existing glycogen chain, alpha(1-4) linkages only. Glycogen chain must be >4 units long though.
47
Glycogenin
The prime mover of glycogen synthesis. Protein auto-glycosylates itself, using UDP-glucose to attach glucose to a tyrosine residue, up to 8 units long.
48
Branching enzyme
Aka glucosyl alpha-4,6-transferase. When alpha(1-4) glucose chains reach at least 11 residues, branching enzyme can come in and move a 7 glucose unit chain to a 6 position on a nearby chain (the 6 position must be at least 4 units from nearest existing branch point).
49
Regulation of glycogen phosphorylase
* Phosphorylated into more active form by phosphorylase kinase (yielding phosphorylase a) * De-phosphorylated into less active form by phosphorylase phosphatase 1 (yielding phosphorylase b)
50
ATP value of NADH | ATP value of FADH2
* 2.5 ATP | * 1.5 ATP
51
Energy from glucose is captured by these molecules (4)
* ATP * NADH * GTP * FADH2
52
Conversion of phosphoenolpyruvate (PEP) to pyruvate is highly favorable because
Phosphate group is stabilized by resonance after it is cleaved from PEP.
53
Adenylate kinase
ATP + AMP ADP + ADP
54
Creatine phosphokinase
Creatine + ATP Phosphocreatine + ADP
55
NADH vs. NADPH
* NADH is used in catabolism | * NADPH is used in anabolism
56
Acetyl-CoA | Components of structure (3)?
* ADP * Pantothenic acid * ß-mercapto-ethylamine
57
HbA1c test Reflects how many months? Why?
* 3 months | * Lifetime of an RBC
58
Glucose sensing in ß-cells
Glucose enters cell through GLUT2, is metabolized (on supply, not on demand, unlike all other cells). ATP then inhibits a potassium pump on the cell surface, which affects calcium ??? increasing insulin production.
59
Phosphorylase • Hormonal regulation • Glucagon vs. epinephrine
* Hormone --> GPCR --> adenylate synthase --> cAMP --> PKA --> (inactivates glycogen synthase into b form, and) active phosphorylase kinase --> phosphorylase a (active form). * Glucagon only works on the liver; epinephrine works on both liver and skeletal muscle.
60
How insulin increases glycogen synthesis
Activates protein phosphatase I (PPI) This enzyme dephosphorylates: • Glycogen phosphorylase a --> b • Glycogen synthase b --> a
61
Hexokinase/Glucokinase Rxn? Regulation?
* Phosphorylates glucose to G-6-P, which traps sugar in the cell. * G-6-P inhibits hexokinase
62
Phosphoglucose Isomerase
reversibly converts G-6-P to F-6-P.
63
PFK-1 Rxn? Regulation? Implications of negative regulation?
* catalyzes the conversion of fructose-6-phosphate to fructose-1,6-bisphosphate (FBP) * inhibited by ATP (with competition from AMP and ADP); inhibited by citrate (H+ from TCA); F-2,6-BP is an allosteric activator. * Inhibiting PFK-1 causes a buildup of G-6-P, which becomes G-1-P, UDP-glucose, then glycogen.
64
Fructose bisphosphatase-2 (FBPase-2) Rxn? Regulation?
* F26BP --> F6P | * Activated by glucagon (via PKA)
65
Aldolase
Cleaves F16BP into DHAP and G3P
66
Triosephosphate isomerase (TIM)
Interconverts DHAP and G3P. | Only G3P proceeds through glycolysis.
67
Glyceradldehyde-3-phosphate dehydrogenase Rxn? How is it poisoned by arsenate?
• Converts G3P into 1,3-bisphosphoglycerate (1,3-BPG). Generates an NADH • AsO4[3-] hydrolyzes before NAD+ has a chance to take a hydrogen to form NADH
68
Phosphoglycerate kinase
Substrate level phosphorylation of ADP. | Converts 1,3-BPG into 3-phosphglycerate.
69
Actions of: bisphosphoglycerate mutase bisphosphoglycerate phosphatase
* RBC enzyme that converts 1,3-BPG into 2,3-DPG. | * RBC enzyme that converts 2,3-DPG into 3-PG.
70
Phosphoglycerate mutase
3-PG --> 2-PG
71
Enolase
2-PG --> PEP
72
Pyruvate kinase Rxn? Regulation?
• PEP + ADP --> pyruvate + ATP Substrate level phosphorylation • F-1,6-BP is an allosteric activator; ATP and alanine are inhibitors; inhibited by PKA
73
Anaerobic glycolysis function is? | Enzyme responsible?
* To replenish NAD+ for further glycolysis, since mitochondria cannot do this without oxygen. * Lactate dehydrogenase
74
Fructokinase
Fructose --> fructose-1-phosphate | liver only
75
Fruktose-1-phosphate aldolase
Fructose-1-phosphate --> DHAP + glyceraldehyde | liver only
76
Triose kinase
Glyceraldehyde --> G3P | liver only
77
Galactokinase
Galactose --> Galactose-1-P
78
Galactose-1-phosphate uridyltransferase
Galactose-1-P + UDP-glucose --> UDP-galactose + glucose-1-phosphate
79
UDP-hexose 4-epimerase
UDP-galactose --> UDP-glucose
80
Most inherited defects of glycolysis affect _______. | All of the glycolysis defects result in _________ due to ________.
* Pyruvate kinase * Hemolytic anemia * Inadequate ATP in RBCs
81
Glycolytic enzymes that catalyze irreversible reactions (3)
* Hexokinase/glucokinase * Phosphofructokinase-1 * Pyruvate kinase
82
Gluconeogenesis | Unique enzymes not in glycolysis (4)?
* Pyruvate carboxylase * PEP carboxylase * Fructose 1,6-bisphosphatase * Glucose 6-phosphatase
83
Biotin | Typical role
Fixing CO2 on metabolic intermediates
84
Pyruvate carboxylase
Pyruvate --> oxaloacetate | mitochondrion
85
Mitochondrial malate dehydrogenase
Oxaloacetate --> malate | mitochondrion
86
Aspartate aminotransferase
Oxaloacetate + glutamine --> aspartate + alpha-ketoglutarate
87
Mitochondrial malate dehydrogenase
Malate --> oxaloacetate | cytoplasm
88
PEP carboxylase
Oxaloacetate --> PEP
89
Glucose-6-phosphatase (G6Pase)
G6P --> glucose | liver only; ER lumen
90
Cori cycle
Anaerobic production of lactate by muscles. Lactate travels to liver via blood stream. Liver converts lactate to glucose via gluconeogenesis. Glucose is released into blood stream. Muscles take up blood glucose.
91
PKA as an effector of glucagon in the liver | List its targets (3)
* PKA phosphorylates phosphorylase kinase, which phosphorylates glycogen phosphorylase b, turning it into active glycogen phosphorylase a, which breaks down glycogen into glucose. * PKA phosphorylates (to inactivate) PFK-2, which normally would catalyze F1P-->F16BP, an allosteric stimulator of PFK-1, used in glycolysis. * PKA phosphorylates (to inactivate) pyruvate kinase, which normally catalyzes PEP-->pyruvate, used in glycolysis.
92
``` Which glycolytic enzymes: Require ATP input? Provide ATP output? Require NADH input? Provide NADH output? Require free phosphate input? ```
* Hexokinase/Glucokinase; Phosphofructokinase-1 * Phosphoglycerate kinase; Pyruvate kinase * Lactate dehydrogenase * Glyceraldehyde-3-phosphate dehydrogenase * Glyceraldehyde-3-phosphate dehydrogenase
93
NADPH vs. NADH Functional differences Concentration differences
* NADPH is for synthesis and maintaining a reducing environment; NADH is for energy production * NADPH:NADP+ is 70:1, while NADH:NAD is 1/700.
94
Glucose-6-phosphate dehydrogenase Rxn? Role in PPP? Regulation?
* G6P--> 6-phosphogluconolactone + NADPH * Committed step into pentose phosphate pathway (PPP) * Not allosterically regulated (regulated by substrate availability
95
6- phosphogluconolactone hydrolase
glucose-6-phosphate dehydrogenase --> | 6-phosphogluconate
96
6-phosphogluconate dehydrogenase
6-phosphogluconate --> ribulose-5-phosphate + CO2 + NADPH
97
Phosphopentose isomerase | also known as ribose phosphate isomerase
Ribulose-5-phosphate ribose-5-phosphate
98
Phosphopentose epimerase | ribulose phosphate 3-epimerase
Ribulose-5-phosphate xylulose-5-phosphate
99
Transketolase Rxns? How many carbons transferred?
* xyulose-5-phosphate + ribose-5-phosphate G3P + Sedoheptulose 7-phosphate * 2 carbons * erythrose-4-phosphate + xyulose-5-phosphate F6P + G3P * 2 carbons
100
Transaldolase Rxn? How many carbons transferred?
* G3P + Sedoheptulose 7-phosphate F6P + Erythrose-4-phosphate * 3 carbons
101
Glucose-6-phosphate dehydrogenase deficiency
400+ mutations. X-linked. Most common enzyme deficiency. Results in hemolytic anemia (RBCs die young, likely from oxidative stress) If NADP+ binding domain is mutated, results in hereditary nonspherocytic hemolytic anemia. Patients having mild forms may show no clinical manifestations except under conditions of oxidative stress precipitated by administration of oxidant drugs (AAA= Antibiotics, Antimalarials, and Antipyretics), ingestion of fava beans, or infection.
102
Glutathione disulphide reductase
GSSG + NADPH --> 2GSH NADP+ +H+
103
PPP | Most active in tissues making these products (2)?
* Lipids | * Steroid hormones
104
``` Pyruvate dehydrogenase Feedback inhibitors (3)? ```
* NADH * Acetyl-CoA * ATP
105
Thiamine (B1) What kind of reaction does it do? What are the enzymes that use it (4)? Deficiency?
• Transfers aldose units * Transketolase * PDH * a-KG dehydrogenase * Branched chain a-KG dehydrogenase • Beriberi
106
Biotin How does it work? Enzyme that uses it?
• Biotin + bicarbonate + ATP --> carboxybiotin + ADP Then, carboxybiotin adds CO2 to substrate • Pyruvate carboxylase
107
Citrate synthetase's rxn is mostly regulated by
Availability of oxaloacetate
108
What is the key regulated enzyme of the TCA cycle? | What regulates it?
* Isocitrate dehydrogenase | * Inhibited by ATP and NADH; activated by ADP and AMP
109
a-ketoglutarate dehydrogenase Rxn? Regulation (4)?
* a-KG --> Succinyl-CoA | * Inhibited by NADH, ATP, GTP, succinyl-CoA
110
Rate of mutation on mitochondria is ____ times faster than the host genome.
~10
111
MELAS What does it stand for? What causes it? What does it do?
* Mitochondrial myopathy and encephalitis with lactic acidosis and stroke-like episodes * Mutation in A3243G of Leu-tRNA of mitochondrial genome * Biogenesis mutation. Causes encephalopathy
112
MERRF What does it stand for? What causes it? What does it do?
* Myoclonic epilepsy ragged red fibers * A8344G mutation in the Lys-tRNA * Biogenesis mutation
113
LHON What does it stand for? What causes it? What does it do?
* Leber's hereditary optic neruopathy * Mutations in complex I (missense) * Affects retinal ganglion almost exclusively
114
PGC-1alpha, a mitochondrial TF | What activates it (3)? What activates those?
* AMPK, high AMP * CREB, high Ca++ * SIRT1, high NAD+
115
PGC-1alpha activation by CREB | Full pathway, with feedback.
Cold --> NADr --> cAMP --> PKA --> CREB [P] --> PGC-1alpha --> bind coactivator NRF1 --> transcribes oxidative phosphorylation proteins --> increased ATP --> decreased AMPK --> AMPK no longer activates PGC-1alpha
116
Import receptors on OMM of mitochondria
TOMS (translocases of outer mitochondrial membrane)
117
SAM complex of mitochondrial inner membrane space
Sorting and assembly machinery
118
TIMS of inner mitochondrial membrane
Translocases of inner mitochondrial membrane
119
MIA proteins of mitochondrial inner membrane
Machinery for protein import and assembly
120
Heat shock proteins Outside the Mt? Inside the Mt? Chaperonins for refolding, assembly, and sorting?
* Hsp70 * mtHSP70 * Hsp60
121
Bcl-2 and Bcl-xL Location? Function?
* OMM | * Promote apoptosis by preventing cytochrome c leakage.
122
Mitochondria role in apoptosis
TNFa --> Caspase 8 --> t-Bid --> Bcl-2 inactivated (anti-apoptotic); Bax and Bak are activated (pro-apoptotic)
123
Complex I Name? Function? How does it transfer electrons?
* NADH-ubiquinone oxidoreductase * Extracts 1 proton from NADH (yes?) and pumps 4 protons * Coenzyme Q
124
Complex II Name? Function?
* Succinate-ubiquinone oxidoreductase | * Succinate --> Fumarate
125
Complex III Name? Function? How does it transfer electrons?
* Ubiquinol-cytochrome c oxidoreductase * Pumps two protons * Cytochrome c
126
Complex IV Name? Function? How does it transfer electrons?
* Cytochrome c oxidase (ATP synthase) * Pumps 4 protons * O2

MtC (3 decks)

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