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CHEM 441A > Midterm 3 > Flashcards

Midterm 3 Flashcards

1
Q

What are the 3 general steps for cell signaling?

A
  1. Reception - Ligand (primary messenger) binds to receptor
  2. Transduction - Via secondary messengers
  3. Response - Cellular responses
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2
Q

What are the 5 features of signal transducing systems?

A
  1. Specificity - ligand specific for receptor
  2. Amplification - Enzymes amplify enzymes, signal increased exponentially
  3. Modularity - Chemical modifications (phosphorylation)
  4. Desensitization/Adaptation - Feedback circuit to shutdown signal
  5. Integration - When 2 signals have opposite effect, net effect will occur
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3
Q

Hormones can be categorized into what 3 categories?

A
  1. Endocrine - distant target cell (e.g. insulin)
  2. Autocrine - self target (e.g. growth factor)
  3. Paracrine - nearby target cell (e.g. neurotransmitters)
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4
Q

Amino acid derived hormones are derived from which amino acid? What are 2 examples?

A

Tyrosine

e.g. epinephrine, dopamine

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5
Q

What are peptide hormones? What are 2 examples?

A

Hormones consisting of 2-100 amino acids.

e.g. Insulin, glucagon

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6
Q

Which hormones can and cannot enter the cell via diffusion?

A

`AA derived - CANNOT enter cell so binds to receptor

Peptide - CANNOT enter cell so binds to receptor

Steroid - CAN diffuse through hydrophobic membrane

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7
Q

Steroid hormones are derived from __________.

A

cholesterol

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8
Q

Where do steroid hormones bind and what is the response?

A

Bind to nuclear receptors inside cytoplasm that regulate transcription factors and control gene expression

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9
Q

What are the 5 classes of receptor proteins in eukaryotes?

A
  1. G protein-coupled receptors (GPCR)
  2. Receptor tyrosine kinases
  3. Tumor Necrosis Factor (TNF)
  4. Nuclear receptors
  5. Nicotinic Acetylcholine receptor
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10
Q

What are nicotinic acetylcholine receptors?

A

Nicotinic acetylcholine receptors are ligand-gated ion channels.

  1. Acetylcholine binds to the α subunits of the nicotinic acetylcholine receptor.
  2. Ion channel opens and allows Na+ and K+ ions to flow across the membrane and depolarize the cell.
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11
Q

Cyclic AMP (cAMP) is a ________ messenger that is activated by _________ __________.

A

secondary

adenylate cyclase

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12
Q

ATP + adenylate cyclase → _______ + 2Pi

A

cAMP

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13
Q

cAMP + cAMP phosphodiesterase → ___________

A

AMP (inactivated)

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14
Q

cAMP is a positive modulator that activates ________ _________ __ which activates many other kinases.

A

Protein kinase A

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15
Q

PIP2 + PLC → _____ + ______

A

DAG + IP3

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16
Q

Even though DAG and IP3 are both secondary messengers, how do they differ?

A

DAG - activates Protein kinase C (PKC) which phosphorylates target proteins - turns OFF glycogen synthesis

IP3 - opens Ca2+ channels on ER - turns ON glycogen degredation

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17
Q

How are signals amplified?

A
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18
Q

What is the structure of GPCR’s and what kind of perceptions are they involved in?

A

7 transmembrane α helices (serpentine) that are considered glycoproteins because carbohydrate functional groups are attached to the extracellular domain

N-terminus outside, C-terminus inside

Involved in sensory perceptions (vision, taste, smell)

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19
Q

What ligand binds to the ß2-adrenergic receptor?

A

Epinephrine

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20
Q

Compare agonists and antagonists.

A

Agonist - mimics natural ligand

Antagonist - binds to receptor but no structural changes occur (similar to inhibitors)

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21
Q

Primary receptors are mostly ___________.

A

hormones

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22
Q

Epinephrine has 2 pathways. What are they?

A

ß2-adrenergic receptor

α1-adrenergic receptor

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23
Q

What is the general pathway for GPCR activation?

A
  1. Ligand binds to GPCR leading to a conformational change
  2. GTP replaces GDP in Gα subunit and subunits dissociate into Gα–GTP and Gβγ
  3. Downstream signaling
  4. Termination of signal
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24
Q

GPCR’s have __________ G proteins attached to them

A

heterotrimeric (3 different subunits)

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25
Q

What 3 metabolic responses occur after cAMP activates PKA?

A
  1. Decrease glycogen synthesis
  2. Increased glycogen degredation
  3. Increase glucose synthesis
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26
Q

What happens when Ca2+ is released from ER in response to IP3 binding?

A

Ca2+ binds to calmodulin which activates protein kinases to help generate glucose

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27
Q

What is the pathway when epinephrine binds to ß2-adrenergic receptor?

A
  1. Epinephrine binds to GPCR causing a conformational change
  2. GTP replaces GDP which activates adenylate cyclase
  3. Adenylate cyclase makes cAMP
  4. cAMP activates PKA
  5. PKA increases blood sugar levels
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28
Q

What is the pathway when epinephrine binds to α1-adrenergic receptor?

A
  1. Epinephrine binds to GPCR causing a conformational change
  2. GTP replaces GDP which activates PLC
  3. PLC dissociates PIP2 → DAG + IP3
  4. DAG and IP3 help increase blood sugar levels
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29
Q

What happens when epidermal growth factor binds to an EGFR?

A
  1. Receptors dimerize
  2. Phosphorylate each other at tyrosine residues
  3. GRB2 attaches to phosphotyrosine residues
  4. SOS attaches to GRB2 which activates Ras through GDP-GTP exchange
  5. Ras-GTP activates MAP kinase → cell division
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30
Q

How can a mutated Ras protein cause cancer?

A

Ras never gets turned off and is constantly signaling for cell division

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31
Q

What is the insulin signaling pathway?

A
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32
Q

During insulin signaling, which 3 tyrosine residues need to be phosphorylated in order for a conformational change to occur?

A

1158

1162

1163

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33
Q

What are the 2 pathways that insulin can take?

A
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34
Q

What is the structure of the insulin receptor?

A

The insulin receptor is an RTK consisting of a cross-linked tetrameric α2β2 complex.

The α subunit is extracellular and contains the insulin binding sites (only one molecule of insulin is required to stimulate receptor signaling)

β subunit anchors the α subunit to the plasma membrane through a transmembrane region (TM) and contains the intracellular tyrosine kinase domain (TK), as well as a short C-terminal region (CT).

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35
Q

How does cAMP activate PKA?

A

cAMP binds to the Regulatory subunits (R) which activates the two PKA monomers

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36
Q

During the epinephrine signaling pathway, how does PKA keep the process going?

A
  1. PKA activates BARK
  2. BARK phosphorylates GPCR inviting Beta-Arrestin to bind to it
  3. Beta-Arrestin prevents the heterotrimeric protein from binding which keeps process going
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37
Q

What are TNF receptors?

A

Tumor necrosis factor receptors that control:

apoptosis

Immune measures - fever, allergy

Primary messenger is cytokine

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38
Q

Why would mutation of a tyrosine residue to glutamate in the intracellular portion of a growth factor receptor lead to increased tumor formation?

A

Unlike tyrosine, a glutamate will leave the receptor “constitutively” active and no longer responsive to the phosphatases that shut off such signaling.

A receptor with a glutamate in place of a tyrosine is a “phosphomimetic.” That is, the protein mimics the phosphorylated state of tyrosine because of its’ negative charge.

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39
Q

What is the structure of glucose? How many chiral centers does it have when it is linear vs when it is cyclic?

A

Linear Glucose - 4

Cyclic Glucose - 5

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40
Q

What are epimers?

A

Two monosaccharides that differ in the –OH position around one chiral carbon

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41
Q

Glucose exists mostly in what form?

A

ß-D-Glucopyransoe

ß because -OH is up at C1

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42
Q

Compare D and L isomers of carbohydrates.

A

Look at highest numbered chiral carbon, if:

OH on left - L

OH on right - D

In this case, the highest numbered chiral carbon is 5.

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43
Q

Why doesn’t sucrose test positive during Benedict’s Test?

A

There is no free -OH at Carbon 1

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44
Q

All monosaccharides are ________ agents.

A

reducing

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45
Q

What is the requirement for a monosaccharide to be oxidized?

A

Must have a free -OH group at C1

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46
Q

What is Benedict’s Test?

A

Tests for the presence of monosaccharides and disaccharides. The reduction of Cu2+ to Cu+ changes the color from blue to red.

Blue = No sugar

Red = Sugar present

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47
Q

What is Trehalose composed of? Bond?

A

2 glucose monomers

α (1→1) glycosidic linkage

48
Q

What is maltose composed of?

A

2 glucose monomers

α(1→4) glycosidic linkage

49
Q

What is lactose composed of?

A

Glucose + Galactose (ß 1-4)

50
Q

What is Sucrose composed of?

A

Glucose + Fructose

51
Q

Compare starch and glycogen.

A

Both store glucose.

Starch (plants) - Less branched

Glycogen (animals) - Highly branched

52
Q

Starch (amylose) is broken down by ________ into ________ via hydrolysis.

A

amylase

maltose

53
Q

Compare catabolism and anabolism.

A

Catabolism - breaks down complex molecules to generate energy

Anabolism - uses energy to build molecules

54
Q

What is flux and how is it determined?

A

Rate at which substrates and products (metabolites) are interconverted.Determined by:

1. Enzyme activity

2. Bioavailability

55
Q

How much energy is given off in either of these reactions?

ATP + H2O → ADP + Pi

or

ADP + H2O → AMP + Pi

A

-30.5 KJ/mol

56
Q

How much energy is given off in this reaction?

ATP + H2O → AMP + 2Pi

A

-45.6 KJ/mol

57
Q

What are 3 types of work that use chemical energy?

A
  1. Osmotic - Maintains [solute] across membranes
  2. Chemical - Biosynthesis and degredation of organic molecules
  3. Mechanical - muscle contractions in animals
58
Q

What is the Formula for Energy Charge (EC) and what does it explain?

A

Normal physiologic range: 0.7 - 0.9

  1. 7 indicates ATP levels are low and ADP levels are maxed
  2. 9 indicates ATP levels are maxed and ADP levels are low
59
Q

What is the Graph for Energy Charge (EC) and what does it explain?

A

Normal physiologic range: 0.7 - 0.9

  1. 7 indicates ATP levels are low and ADP levels are maxed
  2. 9 indicates ATP levels are maxed and ADP levels are low
60
Q

NAD+ is the ________ form and NADH is the ________ form.

A

oxidized

reduced

61
Q

FADH+ is considered _________ while FADH2 is fully reduced.

A

semiquinone

62
Q

What is Glycolysis in General?

A

Splitting 1 molecule of glucose (6C) into 2 molecules of pyruvate (3C). Consists of 10 enzymatic reactions: ATP Investment (Reactions 1-5) and ATP Payoff (6-10)

63
Q

Under anaerobic conditions, what is the primary pathway for ATP generation?

A

glycolysis

64
Q

What is the overall reactoins for glycolysis?

A

Generates:

2 pyruvate

2 NADH + 2 H+

2 ATP

2 H2O

65
Q

Glycolysis occurs in the _______ while the pyruvate conversion and TCA Cycle occurs in the __________ __________. Where does ETC reside?

A

cytoplasm

mitochondrial matrix

mitochondiral inner membrane

66
Q

In which steps of glycolysis does ATP hydrolysis occur? Why does this occur in these steps?

A

Step 1 and Step 3

In both of these steps, a phosphate group is added. This phosphate comes from ATP.

67
Q

What step is the major control point in the glycolytic pathway? What is it regulated by?

A

Step 3 in which Fructose-6-P is phosphorylated. It is regulated by ATP, ADP and AMP levels. Citrate is also an inhibitor.

68
Q

In which step of glycolysis is 2 NADH molecules formed?

A

Step 6

NAD+ acts as a coenzyme

69
Q

What happens in step 5 of glycolysis?

A

DHAP isomerizes to G3P therefore we now have 2 G3P molecules.

70
Q

In which steps of glycolysis is ATP produced?

A

Setp 7 (2 ATP) and Step 10 (2 ATP)

These are the 2 substrate level phosphorylation reactions in glycolysis

71
Q

What are the 3 ways in which pyruvate is metabolized? What does this depend on?

A

Availability of O2

Aerobic - ATP production (TCA Cycle and ETC)

Anaerobic - Lactate or Ethanol production (Fermentation)

72
Q

What is the Pasteur Effect?

A

The inhibition of ethanol fermentation by O2 in favor of pyruvate being converted to Acetyl CoA and entering the TCA Cycle.

73
Q

What is the Warburg Effect (cancer and glycolysis)?

A

Hypoxia activates HIF-1 which in turn (1) Increases glycolytic enzymes and (2) Grows blood vessels

74
Q

How is NAD+ regenerated?

A

oxaloacetate CANNOT move through the mitochondrial membrane

  1. NADH + oxaloacetate → NAD+ + malate
  2. Malate moves into the mitochondria
  3. Malate + NAD+ → NADH + oxaloacetate

NADH goes to ETC

75
Q

What is the overall reaction for pyruvate?

A
76
Q

What is the pyruvate dehydrogenase complex composed of?

A

3 Enzymes:

Pyruvate decarboxylase (E1) – 24 subunits

Lipoate transacetylase (E2) – 24 subunits

Lipoate dehydrogenase (E3) – 12 subunits

Total of 60 subunits

77
Q

What are the 5 coenzymes required by the pyruvate dehydrogenase complex?

A

CoA-SH

TPP (Thiamine pyrophosphate)

lipoamide (α-lipoic acid)

NAD+

FAD

78
Q

What is the active functional group on TPP (Thiamine pyrophosphate)

A

Thiozole

79
Q

What is the active functional group on lipoamide (α-lipoic acid)?

A

Disulfide group in its reduced form

80
Q

What is the active functional group on CoA-SH?

A

SH (thiol)

81
Q

What is the structure of Acetyl-CoA?

A
82
Q

What is the active functional group on NAD+?

A
83
Q

What is the active functional groups on FAD?

A
84
Q

What are the steps for pyruvate → acetyl-CoA?

A
  1. pyruvate + TPP → CO2 + Hydroxyethyl-TPP (E1)
  2. Hydroxyethyl-TPP + lipoamide → TPP + Acetyllipoamide (E1)
  3. Acetyllipoamide + CoA → Acetyl-CoA + dihydrolipoamide (E2)
  4. Dihydrolipoamide + FAD → lipoamide + FADH2
  5. FADH2 + NAD+ → FAD + NADH + H+
85
Q

In general, what is generated during one TCA cycle?

A

1 GTP

1 FADH2

3 NADH

2 CO2

86
Q

Compare a synthase enzyme vs. a synthetase enzyme.

A

Synthase - NO ATP hydrolysis involved

Synthetase - involves ATP hydrolysis

87
Q

In which steps of the TCA cycle is NADH generated?

A

3, 4, and 8

88
Q

In which steps of the TCA cycle is GTP generated?

A

5

89
Q

In which steps of the TCA cycle is FADH2 generated?

A

6

90
Q

Which molecule can bind to succinate dehydrogenase and act as a competitive inhibitor for succinate? Which step of the TCA cycle would this stop?

A

malonate

Step 6

91
Q

How is the TCA cycle regulated? What activates and what inhibits?

A

Activates - Substrates (Acetyl-CoA) and Low Energy molecules (NAD)

Inhibits - Products (Citrate) and High Energy molecules (NADH)

92
Q

How is glycolysis regulated? What activates and what inhibits?

A

Activates - Substrates (Glucose) and Low Energy molecules (ADP, NAD)

Inhibits - Products (Glucose-6-phosphate) and High Energy molecules (ATP, NADH)

93
Q

How is step 3 of glycolysis regulated? What activates and what inhibits?

A

Activates - Fructose 2,6 BP, AMP and ADP

Inhibits - Citrate and ATP

94
Q

What is required to synthesize NAD+ ?

A

Niacin (Vitamin B3)

95
Q

What is required to synthesize FAD?

A

Riboflavin (Vitamin B2)

96
Q

What is required to synthesize Thiamine?

A

Vitamin B1

97
Q

What is lipoamide derived from?

A

Lipoic acid

98
Q

What are the components of CoA?

A

Pantothenic acid (Vitamin B5 )

ß-Mercaptoethylamine (thiol group)

3’, 5’ - ADP

99
Q

What is CoA derived from?

A

Pantothenic acid (Vitamin B5 )

100
Q

What are the 3 regulatory steps in glycolysis along with the regulatory enzymes?

A

1, 3, and 10

101
Q

What are the 3 main regulatory enzymes in the TCA cycle?

A
  • Citrate synthase
  • Isocitrate dehydrogenase
  • a-Ketoglutarate dehydrogenase complex
102
Q

Which TCA intermediates serve as precursors to other molecules?

A

Citrate → Fatty acids

Oxaloacetate → glucose/malate

a-ketoglutarate → amino acids

Succinyl-CoA → heme

103
Q

What are anaplerotic reactions? Name 2 examples.

A

Reactions that replenish citrate cycle intermediates

  1. Pyruvate + pyruvate carboxylase → oxaloacetate
  2. Phosphoenolpyruvate + Phosphoenolpyruvate carboxylase → oxaloacetate
104
Q

What reaction forms oxaloacetate from pyruvate?

A
105
Q

What reactions forms oxaloacetate from phosphoenolpyruvate?

A
106
Q

What are Proton uncoupling effects?

A

An uncoupler molecule can transfer H+ bypassing ATP Synthase

So heat will be generated but NO ATP is generated

107
Q

How many substrate level phosphorylations occur in cellular respiration?

A

3 total

2 in glycolysis

1 in TCA Cycle

108
Q

What effect does Oligomycin have on the ETC?

A

It inhibits proton flow through ATP Synthase resulting in a buildup of protons in the intermembrane space eventually leading to cell death.

109
Q

Where is the ETC located?

A

Inner membrane (cristae) of the mitochondrion

110
Q

How does the electron transport chain work?

A
  • Carriers alternate between reduced and oxidized states
  • Electrons are transferred from NADH or FADH2 to the ETC
  • As electrons go down the chain they drop in free energy
  • Ultimately they are passed to O2, forming H2O
112
Q

What does electron transfer in the ETC cause proteins to pump out of the mitochondrial matrix to the intermembrane space?

A

H+ creating a concentration gradient across the membrane

115
Q

What ultimately generates the majority of ATP during cellular respiration?

A

H+ moves down its concentration gradient through ATP synthase which phosphorylates ADP → ATP

116
Q

What are the 5 complexes composing the ETC?

A

Complex I - NADH - ubiquinone oxidoreductase

Complex II - Succinate dehydrogenase

Complex III - Ubiquinone-cytochrome C oxidoreductase

Complex IV - Cytochrome oxidase

Complex V - ATP Synthase

117
Q

How many protons are pumped into the intermembrane space per NADH?

A

Complex I - 4H+

Complex II - none

Complex III - 4H+

Complex IV - 2H+

Total of 10H+ pumped out

118
Q

How many protons are transported through ATP Synthase to make 1 ATP molecule?

A

4H+

119
Q

For every 1 NADH molecule, you can generate ______ ATP molecules.

A

2.5

120
Q

For every 1 FADH2 molecule, you can generate ______ ATP molecules.

A

1.5

CHEM 441A (4 decks)

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