Midterm 3 Flashcards
(117 cards)
1
Q
What are the 3 general steps for cell signaling?
A
- Reception - Ligand (primary messenger) binds to receptor
- Transduction - Via secondary messengers
- Response - Cellular responses
2
Q
What are the 5 features of signal transducing systems?
A
- Specificity - ligand specific for receptor
- Amplification - Enzymes amplify enzymes, signal increased exponentially
- Modularity - Chemical modifications (phosphorylation)
- Desensitization/Adaptation - Feedback circuit to shutdown signal
- Integration - When 2 signals have opposite effect, net effect will occur
3
Q
Hormones can be categorized into what 3 categories?
A
- Endocrine - distant target cell (e.g. insulin)
- Autocrine - self target (e.g. growth factor)
- Paracrine - nearby target cell (e.g. neurotransmitters)
4
Q
Amino acid derived hormones are derived from which amino acid? What are 2 examples?
A
Tyrosine
e.g. epinephrine, dopamine
5
Q
What are peptide hormones? What are 2 examples?
A
Hormones consisting of 2-100 amino acids.
e.g. Insulin, glucagon
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
7
Q
Steroid hormones are derived from __________.
A
cholesterol
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
9
Q
What are the 5 classes of receptor proteins in eukaryotes?
A
- G protein-coupled receptors (GPCR)
- Receptor tyrosine kinases
- Tumor Necrosis Factor (TNF)
- Nuclear receptors
- Nicotinic Acetylcholine receptor
10
Q
What are nicotinic acetylcholine receptors?
A
Nicotinic acetylcholine receptors are ligand-gated ion channels.
- Acetylcholine binds to the α subunits of the nicotinic acetylcholine receptor.
- Ion channel opens and allows Na+ and K+ ions to flow across the membrane and depolarize the cell.
11
Q
Cyclic AMP (cAMP) is a ________ messenger that is activated by _________ __________.
A
secondary
adenylate cyclase
12
Q
ATP + adenylate cyclase → _______ + 2Pi
A
cAMP
13
Q
cAMP + cAMP phosphodiesterase → ___________
A
AMP (inactivated)
14
Q
cAMP is a positive modulator that activates ________ _________ __ which activates many other kinases.
A
Protein kinase A
15
Q
PIP2 + PLC → _____ + ______
A
DAG + IP3
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
17
Q
How are signals amplified?
A
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)
19
Q
What ligand binds to the ß2-adrenergic receptor?
A
Epinephrine
20
Q
Compare agonists and antagonists.
A
Agonist - mimics natural ligand
Antagonist - binds to receptor but no structural changes occur (similar to inhibitors)
21
Q
Primary receptors are mostly ___________.
A
hormones
22
Q
Epinephrine has 2 pathways. What are they?
A
ß2-adrenergic receptor
α1-adrenergic receptor
23
Q
What is the general pathway for GPCR activation?
A
- Ligand binds to GPCR leading to a conformational change
- GTP replaces GDP in Gα subunit and subunits dissociate into Gα–GTP and Gβγ
- Downstream signaling
- Termination of signal
24
Q
GPCR’s have __________ G proteins attached to them
A
heterotrimeric (3 different subunits)
25
What 3 metabolic responses occur after cAMP activates PKA?
1. Decrease glycogen synthesis
2. Increased glycogen degredation
3. Increase glucose synthesis
26
What happens when Ca2+ is released from ER in response to IP3 binding?
Ca2+ binds to **calmodulin** which activates protein kinases to help generate glucose
27
What is the pathway when epinephrine binds to ß2-adrenergic receptor?
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
28
What is the pathway when epinephrine binds to α1-adrenergic receptor?
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
29
What happens when epidermal growth factor binds to an EGFR?
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**
30
How can a mutated Ras protein cause cancer?
Ras never gets turned off and is constantly signaling for cell division
31
What is the insulin signaling pathway?
32
During insulin signaling, which 3 tyrosine residues need to be phosphorylated in order for a conformational change to occur?
1158
1162
1163
33
What are the 2 pathways that insulin can take?
34
What is the structure of the insulin receptor?
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).
35
How does cAMP activate PKA?
cAMP binds to the **Regulatory subunits (R)** which activates the two PKA monomers
36
During the epinephrine signaling pathway, how does PKA keep the process going?
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
37
What are TNF receptors?
**Tumor necrosis factor** receptors that control:
**apoptosis**
**Immune** measures - fever, allergy
Primary messenger is **cytokine**
38
Why would mutation of a tyrosine residue to glutamate in the intracellular portion of a growth factor receptor lead to increased tumor formation?
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.
39
What is the structure of glucose? How many chiral centers does it have when it is linear vs when it is cyclic?
Linear Glucose - 4
Cyclic Glucose - 5
40
What are epimers?
Two monosaccharides that differ in the –OH position around one chiral carbon
41
Glucose exists mostly in what form?
ß-D-Glucopyransoe
ß because -OH is up at C1
42
Compare D and L isomers of carbohydrates.
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.
43
Why doesn't sucrose test positive during Benedict's Test?
There is no free -OH at Carbon 1
44
All monosaccharides are ________ agents.
reducing
45
What is the requirement for a monosaccharide to be oxidized?
Must have a **free -OH group at C1**
46
What is Benedict's Test?
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**
47
What is Trehalose composed of? Bond?
**2 glucose monomers**
α (1→1) glycosidic linkage
48
What is maltose composed of?
**2 glucose monomers**
α(1→4) glycosidic linkage
49
What is lactose composed of?
**Glucose + Galactose** (ß 1-4)
50
What is Sucrose composed of?
**Glucose + Fructose**
51
Compare starch and glycogen.
Both store glucose.
Starch (plants) - Less branched
Glycogen (animals) - Highly branched
52
Starch (amylose) is broken down by ________ into ________ via hydrolysis.
amylase
maltose
53
Compare catabolism and anabolism.
**Catabolism** - _breaks down_ complex molecules to _generate energy_
**Anabolism** - _uses energy to build molecules_
54
What is flux and how is it determined?
Rate at which substrates and products (metabolites) are interconverted.Determined by:
## Footnote
**1. Enzyme activity**
**2. Bioavailability**
55
How much energy is given off in either of these reactions?
ATP + H2O → ADP + Pi
or
ADP + H2O → AMP + Pi
-30.5 KJ/mol
56
How much energy is given off in this reaction?
ATP + H2O → AMP + 2Pi
-45.6 KJ/mol
57
What are 3 types of work that use chemical energy?
1. **Osmotic** - Maintains [solute] across membranes
2. **Chemical** - Biosynthesis and degredation of organic molecules
3. **Mechanical** - muscle contractions in animals
58
What is the Formula for Energy Charge (EC) and what does it explain?
Normal physiologic range: **0.7 - 0.9**
0. 7 indicates ATP levels are low and ADP levels are maxed
0. 9 indicates ATP levels are maxed and ADP levels are low
59
What is the Graph for Energy Charge (EC) and what does it explain?
Normal physiologic range: **0.7 - 0.9**
0. 7 indicates ATP levels are low and ADP levels are maxed
0. 9 indicates ATP levels are maxed and ADP levels are low
60
NAD+ is the ________ form and NADH is the ________ form.
oxidized
reduced
61
FADH+ is considered _________ while FADH2 is fully reduced.
semiquinone
62
What is Glycolysis in General?
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
Under anaerobic conditions, what is the primary pathway for ATP generation?
glycolysis
64
What is the overall reactoins for glycolysis?
Generates:
2 pyruvate
2 NADH + 2 H+
2 ATP
2 H2O
65
Glycolysis occurs in the _______ while the pyruvate conversion and TCA Cycle occurs in the __________ \_\_\_\_\_\_\_\_\_\_. Where does ETC reside?
cytoplasm
mitochondrial matrix
mitochondiral inner membrane
66
In which steps of glycolysis does ATP hydrolysis occur? Why does this occur in these steps?
**Step 1** and **Step 3**
In both of these steps, a phosphate group is added. This phosphate comes from ATP.
67
What step is the major control point in the glycolytic pathway? What is it regulated by?
**Step 3** in which Fructose-6-P is phosphorylated. It is regulated by ATP, ADP and AMP levels. _Citrate is also an inhibitor_.
68
In which step of glycolysis is 2 NADH molecules formed?
Step 6
NAD+ acts as a coenzyme
69
What happens in step 5 of glycolysis?
DHAP isomerizes to G3P therefore we now have **2 G3P molecules**.
70
In which steps of glycolysis is ATP produced?
**Setp 7** (2 ATP) and **Step 10** (2 ATP)
These are the 2 _substrate level phosphorylation_ reactions in glycolysis
71
What are the 3 ways in which pyruvate is metabolized? What does this depend on?
Availability of **O2**
**Aerobic** - ATP production (TCA Cycle and ETC)
**Anaerobic** - Lactate or Ethanol production (Fermentation)
72
What is the Pasteur Effect?
The inhibition of ethanol fermentation by O2 in favor of pyruvate being converted to Acetyl CoA and entering the TCA Cycle.
73
What is the Warburg Effect (cancer and glycolysis)?
Hypoxia activates **HIF-1** which in turn (1) Increases glycolytic enzymes and (2) Grows blood vessels
74
How is NAD+ regenerated?
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
What is the overall reaction for pyruvate?
76
What is the pyruvate dehydrogenase complex composed of?
3 Enzymes:
**Pyruvate decarboxylase** (E1) – 24 subunits
**Lipoate transacetylase** (E2) – 24 subunits
**Lipoate dehydrogenase** (E3) – 12 subunits
Total of _60 subunits_
77
What are the 5 coenzymes required by the pyruvate dehydrogenase complex?
**CoA-SH**
**TPP** (Thiamine pyrophosphate)
**lipoamide** (α-lipoic acid)
**NAD+**
**FAD**
78
What is the active functional group on TPP (Thiamine pyrophosphate)
Thiozole
79
What is the active functional group on lipoamide (α-lipoic acid)?
**Disulfide** group in its **reduced** form
80
What is the active functional group on CoA-SH?
**SH** (thiol)
81
What is the structure of Acetyl-CoA?
82
What is the active functional group on NAD+?
83
What is the active functional groups on FAD?
84
What are the steps for pyruvate → acetyl-CoA?
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
In general, what is generated during one TCA cycle?
1 GTP
1 FADH2
3 NADH
2 CO2
86
Compare a synthase enzyme vs. a synthetase enzyme.
**Synthase** - NO ATP hydrolysis involved
**Synthetase** - involves ATP hydrolysis
87
In which steps of the TCA cycle is NADH generated?
3, 4, and 8
88
In which steps of the TCA cycle is GTP generated?
5
89
In which steps of the TCA cycle is FADH2 generated?
6
90
Which molecule can bind to succinate dehydrogenase and act as a competitive inhibitor for succinate? Which step of the TCA cycle would this stop?
malonate
Step 6
91
How is the TCA cycle regulated? What activates and what inhibits?
**Activates** - Substrates (Acetyl-CoA) and Low Energy molecules (NAD)
**Inhibits** - Products (Citrate) and High Energy molecules (NADH)
92
How is glycolysis regulated? What activates and what inhibits?
**Activates** - Substrates (Glucose) and Low Energy molecules (ADP, NAD)
**Inhibits** - Products (Glucose-6-phosphate) and High Energy molecules (ATP, NADH)
93
How is step 3 of glycolysis regulated? What activates and what inhibits?
**Activates** - Fructose 2,6 BP, AMP and ADP
**Inhibits** - Citrate and ATP
94
What is required to synthesize NAD+ ?
Niacin (Vitamin B3)
95
What is required to synthesize FAD?
Riboflavin (Vitamin B2)
96
What is required to synthesize Thiamine?
Vitamin B1
97
What is lipoamide derived from?
Lipoic acid
98
What are the components of CoA?
**Pantothenic acid (Vitamin B5 )**
ß-Mercaptoethylamine (**thiol** group)
3', 5' - ADP
99
What is CoA derived from?
Pantothenic acid (Vitamin B5 )
100
What are the 3 regulatory steps in glycolysis along with the regulatory enzymes?
1, 3, and 10
101
What are the 3 main regulatory enzymes in the TCA cycle?
- Citrate synthase
- Isocitrate dehydrogenase
- a-Ketoglutarate dehydrogenase complex
102
Which TCA intermediates serve as precursors to other molecules?
Citrate → Fatty acids
Oxaloacetate → glucose/malate
a-ketoglutarate → amino acids
Succinyl-CoA → heme
103
What are anaplerotic reactions? Name 2 examples.
Reactions that _replenish citrate cycle intermediates_
1. Pyruvate + pyruvate carboxylase → oxaloacetate
2. Phosphoenolpyruvate + Phosphoenolpyruvate carboxylase → oxaloacetate
104
What reaction forms oxaloacetate from pyruvate?
105
What reactions forms oxaloacetate from phosphoenolpyruvate?
106
What are Proton uncoupling effects?
An uncoupler molecule can transfer H+ bypassing ATP Synthase
So _heat_ will be generated but NO ATP is generated
107
How many substrate level phosphorylations occur in cellular respiration?
3 total
2 in glycolysis
1 in TCA Cycle
108
What effect does Oligomycin have on the ETC?
It _inhibits proton flow through ATP Synthase_ resulting in a buildup of protons in the intermembrane space eventually leading to **cell death**.
109
Where is the ETC located?
Inner membrane (**cristae**) of the mitochondrion
110
How does the electron transport chain work?
- 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
What does electron transfer in the ETC cause proteins to pump out of the mitochondrial matrix to the intermembrane space?
**H+** creating a concentration gradient across the membrane
115
What ultimately generates the majority of ATP during cellular respiration?
H+ moves down its concentration gradient through **ATP synthase** which phosphorylates ADP → ATP
116
What are the 5 complexes composing the ETC?
**Complex I** - NADH - ubiquinone oxidoreductase
**Complex II** - Succinate dehydrogenase
**Complex III** - Ubiquinone-cytochrome C oxidoreductase
**Complex IV** - Cytochrome oxidase
**Complex V** - ATP Synthase
117
How many protons are pumped into the intermembrane space per NADH?
Complex I - 4H+
Complex II - none
Complex III - 4H+
Complex IV - 2H+
**Total of 10H+ **pumped out
118
How many protons are transported through ATP Synthase to make 1 ATP molecule?
4H+
119
For every 1 NADH molecule, you can generate ______ ATP molecules.
2.5
120
For every 1 FADH2 molecule, you can generate ______ ATP molecules.
1.5
