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Block 2 Flashcards

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
Q

Name for a 6-carbon cyclized aldose?

Name for a 5-carbon cyclized aldose?

A
  • Pyranose

* Furanose

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26
Q

Anomeric carbon

A

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).

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27
Q

Glycosidic bond

A

Where anomeric carbon is bound to another sugar. There is then no mutorotation between alpha and beta forms.

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28
Q

Reducing sugar

A

Sugars with a free aldehyde (C1 of aldoses) can reduce metals. Polysaccharides become non-reducing sugars.

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29
Q

Advanced Glycation Endproducts (AGEs)

Formation

A
  • Glucose forms a a Shiff’s base with Lysine

* Vicinal -OH leads to Amadori rearrangement

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30
Q

Energy charge
Equation?
Typical value?

A
  • ( [ATP] + 1/2[ADP] ) / ( [ATP] + [ADP] + [AMP] )

* 0.80 - 0.95

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31
Q

Glucose-6-phosphate

Branch point for which pathways (3)?

A
  • Glycolysis
  • Gluconeogenesis
  • Pentose phosphate
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32
Q

Plasma glucose
Normal range?
Hypoglycemia?
Critical?

A
  • 80 - 100 mg/dL
  • 60 mg/dL
  • 40 mg/dL
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33
Q

GLUT1 and GLUT3
Expression?
Km? Why?

A
  • 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.
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34
Q

GLUT2
Expression?
Km? Why?

A
  • Liver, ß-islet cells, basolateral side of intestinal cells

* Km = 15-20mM. Flux is driven by plasma glucose level.

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35
Q

GLUT4
Expression?
Km?
Regulation by insulin?

A
  • Skeletal muscles and fat cells
  • Km = 5mM
  • Insulin increases GLUT4 translocation to membrane surface.
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36
Q

GLUT5
Expression?
Main function?

A
  • Apical side of small intestine cells

* Mainly uptakes fructose

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37
Q

SGLT1
Expression?
Main function?

A
  • Apical side of intestine cells

* Sodium / glucose (or galactose) co-porter

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38
Q

Glucose trapping

How does it work?

A

Hexokinase converts glucose to G-6-P, which cannot pass through GLUT channel proteins.

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39
Q

Glucokinase
Expression?
What is its similarity to hexokinase?
What is its difference from hexokinase?

A
  • Liver and ß-islet cells
  • Catalyzes glucose –> G-6-P
  • Is not inhibited by G-6-P
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40
Q

Glycogen
Main glycosidic bond?
Branching glycosidic bond?
Approximate ratio?

A
  • alpha(1-4)
  • alpha(1-6)
  • 10:1
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41
Q

Glycogen phosphorylase

A

Cleaves glycogen at alpha(1-4) glycosidic bonds into G-1-P

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42
Q

Phosphoglucomutase

A

Converts G-1-P into G-6-P

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43
Q

Glucose-6-phosphatase

A

Found only on liver ER (lumenal). G-6-P is transported into ER, converted to glucose, exported to cytosol, then exported into blood stream.

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44
Q

Debranching enzyme

A

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.

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45
Q

UDP-glucose pyrophosphorylase

A

Adds a UDP group to G-1-P. PPi hydrolysis commits this step.

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46
Q

Glycogen synthase

A

Adds UDP-glucose onto an existing glycogen chain, alpha(1-4) linkages only. Glycogen chain must be >4 units long though.

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47
Q

Glycogenin

A

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.

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48
Q

Branching enzyme

A

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).

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49
Q

Regulation of glycogen phosphorylase

A
  • Phosphorylated into more active form by phosphorylase kinase (yielding phosphorylase a)
  • De-phosphorylated into less active form by phosphorylase phosphatase 1 (yielding phosphorylase b)
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50
Q

ATP value of NADH

ATP value of FADH2

A
  • 2.5 ATP

* 1.5 ATP

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51
Q

Energy from glucose is captured by these molecules (4)

A
  • ATP
  • NADH
  • GTP
  • FADH2
52
Q

Conversion of phosphoenolpyruvate (PEP) to pyruvate is highly favorable because

A

Phosphate group is stabilized by resonance after it is cleaved from PEP.

53
Q

Adenylate kinase

A

ATP + AMP ADP + ADP

54
Q

Creatine phosphokinase

A

Creatine + ATP Phosphocreatine + ADP

55
Q

NADH vs. NADPH

A
  • NADH is used in catabolism

* NADPH is used in anabolism

56
Q

Acetyl-CoA

Components of structure (3)?

A
  • ADP
  • Pantothenic acid
  • ß-mercapto-ethylamine
57
Q

HbA1c test
Reflects how many months?
Why?

A
  • 3 months

* Lifetime of an RBC

58
Q

Glucose sensing in ß-cells

A

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
Q

Phosphorylase
• Hormonal regulation
• Glucagon vs. epinephrine

A
  • 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
Q

How insulin increases glycogen synthesis

A

Activates protein phosphatase I (PPI)
This enzyme dephosphorylates:
• Glycogen phosphorylase a –> b
• Glycogen synthase b –> a

61
Q

Hexokinase/Glucokinase
Rxn?
Regulation?

A
  • Phosphorylates glucose to G-6-P, which traps sugar in the cell.
  • G-6-P inhibits hexokinase
62
Q

Phosphoglucose Isomerase

A

reversibly converts G-6-P to F-6-P.

63
Q

PFK-1
Rxn?
Regulation?
Implications of negative regulation?

A
  • 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
Q

Fructose bisphosphatase-2 (FBPase-2)
Rxn?
Regulation?

A
  • F26BP –> F6P

* Activated by glucagon (via PKA)

65
Q

Aldolase

A

Cleaves F16BP into DHAP and G3P

66
Q

Triosephosphate isomerase (TIM)

A

Interconverts DHAP and G3P.

Only G3P proceeds through glycolysis.

67
Q

Glyceradldehyde-3-phosphate dehydrogenase
Rxn?
How is it poisoned by arsenate?

A

• 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
Q

Phosphoglycerate kinase

A

Substrate level phosphorylation of ADP.

Converts 1,3-BPG into 3-phosphglycerate.

69
Q

Actions of:
bisphosphoglycerate mutase
bisphosphoglycerate phosphatase

A
  • RBC enzyme that converts 1,3-BPG into 2,3-DPG.

* RBC enzyme that converts 2,3-DPG into 3-PG.

70
Q

Phosphoglycerate mutase

A

3-PG –> 2-PG

71
Q

Enolase

A

2-PG –> PEP

72
Q

Pyruvate kinase
Rxn?
Regulation?

A

• PEP + ADP –> pyruvate + ATP
Substrate level phosphorylation
• F-1,6-BP is an allosteric activator; ATP and alanine are inhibitors; inhibited by PKA

73
Q

Anaerobic glycolysis function is?

Enzyme responsible?

A
  • To replenish NAD+ for further glycolysis, since mitochondria cannot do this without oxygen.
  • Lactate dehydrogenase
74
Q

Fructokinase

A

Fructose –> fructose-1-phosphate

liver only

75
Q

Fruktose-1-phosphate aldolase

A

Fructose-1-phosphate –> DHAP + glyceraldehyde

liver only

76
Q

Triose kinase

A

Glyceraldehyde –> G3P

liver only

77
Q

Galactokinase

A

Galactose –> Galactose-1-P

78
Q

Galactose-1-phosphate uridyltransferase

A

Galactose-1-P + UDP-glucose –> UDP-galactose + glucose-1-phosphate

79
Q

UDP-hexose 4-epimerase

A

UDP-galactose –> UDP-glucose

80
Q

Most inherited defects of glycolysis affect _______.

All of the glycolysis defects result in _________ due to ________.

A
  • Pyruvate kinase
  • Hemolytic anemia
  • Inadequate ATP in RBCs
81
Q

Glycolytic enzymes that catalyze irreversible reactions (3)

A
  • Hexokinase/glucokinase
  • Phosphofructokinase-1
  • Pyruvate kinase
82
Q

Gluconeogenesis

Unique enzymes not in glycolysis (4)?

A
  • Pyruvate carboxylase
  • PEP carboxylase
  • Fructose 1,6-bisphosphatase
  • Glucose 6-phosphatase
83
Q

Biotin

Typical role

A

Fixing CO2 on metabolic intermediates

84
Q

Pyruvate carboxylase

A

Pyruvate –> oxaloacetate

mitochondrion

85
Q

Mitochondrial malate dehydrogenase

A

Oxaloacetate –> malate

mitochondrion

86
Q

Aspartate aminotransferase

A

Oxaloacetate + glutamine –> aspartate + alpha-ketoglutarate

87
Q

Mitochondrial malate dehydrogenase

A

Malate –> oxaloacetate

cytoplasm

88
Q

PEP carboxylase

A

Oxaloacetate –> PEP

89
Q

Glucose-6-phosphatase (G6Pase)

A

G6P –> glucose

liver only; ER lumen

90
Q

Cori cycle

A

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
Q

PKA as an effector of glucagon in the liver

List its targets (3)

A
  • 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
Q 
Which glycolytic enzymes:
Require ATP input?
Provide ATP output?
Require NADH input?
Provide NADH output? 
Require free phosphate input?
A
  • Hexokinase/Glucokinase; Phosphofructokinase-1
  • Phosphoglycerate kinase; Pyruvate kinase
  • Lactate dehydrogenase
  • Glyceraldehyde-3-phosphate dehydrogenase
  • Glyceraldehyde-3-phosphate dehydrogenase
93
Q

NADPH vs. NADH
Functional differences
Concentration differences

A
  • 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
Q

Glucose-6-phosphate dehydrogenase
Rxn?
Role in PPP?
Regulation?

A
  • G6P–> 6-phosphogluconolactone + NADPH
  • Committed step into pentose phosphate pathway (PPP)
  • Not allosterically regulated (regulated by substrate availability
95
Q

6- phosphogluconolactone hydrolase

A

glucose-6-phosphate dehydrogenase –>

6-phosphogluconate

96
Q

6-phosphogluconate dehydrogenase

A

6-phosphogluconate –> ribulose-5-phosphate + CO2 + NADPH

97
Q

Phosphopentose isomerase

also known as ribose phosphate isomerase

A

Ribulose-5-phosphate ribose-5-phosphate

98
Q

Phosphopentose epimerase

ribulose phosphate 3-epimerase

A

Ribulose-5-phosphate xylulose-5-phosphate

99
Q

Transketolase
Rxns?
How many carbons transferred?

A
  • xyulose-5-phosphate + ribose-5-phosphate G3P + Sedoheptulose 7-phosphate
  • 2 carbons
  • erythrose-4-phosphate + xyulose-5-phosphate F6P + G3P
  • 2 carbons
100
Q

Transaldolase
Rxn?
How many carbons transferred?

A
  • G3P + Sedoheptulose 7-phosphate F6P + Erythrose-4-phosphate
  • 3 carbons
101
Q

Glucose-6-phosphate dehydrogenase deficiency

A

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
Q

Glutathione disulphide reductase

A

GSSG + NADPH –> 2GSH NADP+ +H+

103
Q

PPP

Most active in tissues making these products (2)?

A
  • Lipids

* Steroid hormones

104
Q 
Pyruvate dehydrogenase
Feedback inhibitors (3)?
A
  • NADH
  • Acetyl-CoA
  • ATP
105
Q

Thiamine (B1)
What kind of reaction does it do?
What are the enzymes that use it (4)?
Deficiency?

A

• Transfers aldose units

  • Transketolase
  • PDH
  • a-KG dehydrogenase
  • Branched chain a-KG dehydrogenase

• Beriberi

106
Q

Biotin
How does it work?
Enzyme that uses it?

A

• Biotin + bicarbonate + ATP –> carboxybiotin + ADP
Then, carboxybiotin adds CO2 to substrate
• Pyruvate carboxylase

107
Q

Citrate synthetase’s rxn is mostly regulated by

A

Availability of oxaloacetate

108
Q

What is the key regulated enzyme of the TCA cycle?

What regulates it?

A
  • Isocitrate dehydrogenase

* Inhibited by ATP and NADH; activated by ADP and AMP

109
Q

a-ketoglutarate dehydrogenase
Rxn?
Regulation (4)?

A
  • a-KG –> Succinyl-CoA

* Inhibited by NADH, ATP, GTP, succinyl-CoA

110
Q

Rate of mutation on mitochondria is ____ times faster than the host genome.

111
Q

MELAS
What does it stand for?
What causes it?
What does it do?

A
  • 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
Q

MERRF
What does it stand for?
What causes it?
What does it do?

A
  • Myoclonic epilepsy ragged red fibers
  • A8344G mutation in the Lys-tRNA
  • Biogenesis mutation
113
Q

LHON
What does it stand for?
What causes it?
What does it do?

A
  • Leber’s hereditary optic neruopathy
  • Mutations in complex I (missense)
  • Affects retinal ganglion almost exclusively
114
Q

PGC-1alpha, a mitochondrial TF

What activates it (3)? What activates those?

A
  • AMPK, high AMP
  • CREB, high Ca++
  • SIRT1, high NAD+
115
Q

PGC-1alpha activation by CREB

Full pathway, with feedback.

A

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
Q

Import receptors on OMM of mitochondria

A

TOMS (translocases of outer mitochondrial membrane)

117
Q

SAM complex of mitochondrial inner membrane space

A

Sorting and assembly machinery

118
Q

TIMS of inner mitochondrial membrane

A

Translocases of inner mitochondrial membrane

119
Q

MIA proteins of mitochondrial inner membrane

A

Machinery for protein import and assembly

120
Q

Heat shock proteins
Outside the Mt?
Inside the Mt?
Chaperonins for refolding, assembly, and sorting?

A
  • Hsp70
  • mtHSP70
  • Hsp60
121
Q

Bcl-2 and Bcl-xL
Location?
Function?

A
  • OMM

* Promote apoptosis by preventing cytochrome c leakage.

122
Q

Mitochondria role in apoptosis

A

TNFa –> Caspase 8 –> t-Bid –> Bcl-2 inactivated (anti-apoptotic); Bax and Bak are activated (pro-apoptotic)

123
Q

Complex I
Name?
Function?
How does it transfer electrons?

A
  • NADH-ubiquinone oxidoreductase
  • Extracts 1 proton from NADH (yes?) and pumps 4 protons
  • Coenzyme Q
124
Q

Complex II
Name?
Function?

A
  • Succinate-ubiquinone oxidoreductase

* Succinate –> Fumarate

125
Q

Complex III
Name?
Function?
How does it transfer electrons?

A
  • Ubiquinol-cytochrome c oxidoreductase
  • Pumps two protons
  • Cytochrome c
126
Q

Complex IV
Name?
Function?
How does it transfer electrons?

A
  • Cytochrome c oxidase (ATP synthase)
  • Pumps 4 protons
  • O2

MtC (3 decks)

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