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Biochem 2 > Quiz 1 > Flashcards

Quiz 1 Flashcards

1
Q

What gene when mutated causes cystic fibrosis

A

CFTR gene

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2
Q

What does the CFTR gene code for

A

chlorine transporter

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3
Q

Within the cell, what does the chlorine transporter do

A

transports Cl- from inside the cell to the outside

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4
Q

What does the ENaC gene code for

A

a sodium channel

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5
Q

What does the sodium channel do

A

allow the transport for Na from outside to the inside

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6
Q

What happens if the ENaC gene is mutated but the CFTR is working

A

There is excess hydration of the lung tissue

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7
Q

What happens when the CFTR gene is mutated but the ENaC gene is not

A

there is a large influx of sodium resulting in volume depletion

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8
Q

What is passive transport

A

transport that does not use ATP energy

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9
Q

What types of passive transport are there

A

facillitated diffusion
simple diffusion
ionophore mediated
ion channel

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10
Q

What is facilitated diffusion

A

a substrate moves down its electrochemical gradient via a channel

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11
Q

What is simple diffusion

A

nonpolor compounds are drawn down their concentration gradient across the membrane

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12
Q

Does simple diffusion use a channel

A

no

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13
Q

What is ionophore mediated

A

ion is transported down its electrochemical gradient by binding to a protein that transports it across

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14
Q

What is ion channel

A

ions move down electrochemical gradient through the channel

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15
Q

What can occur to the channel in regards to struture

A

can be ligand gated or ion gated

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16
Q

Before equilibrium what is the net flux of ions

A

large flux from high to low gradients, low flux from low to high gradients

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17
Q

At equilibrium, what is the net flux of ions

A

no net flux

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18
Q

Before equilibrium is reached, what is the Vm for ions

A

greater than zero

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19
Q

Why is the Vm greater than zero

A

large flow of negative ions toward positive and large flow of positive to negative, small flow of positive to positive and negative to negative

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20
Q

At equilibrium what is Vm

A

zero

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21
Q

How does a channel/ transporter effect activation energy

A

lowers the delta G for transport

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22
Q

How does the activation, free energy differ between simple diffusion to diffusion with a transporter

A

simple diffusion has a greater free energy whereas the diffusion with a transporter has a lower energy

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23
Q

Why is simple diffusion a higher free energy

A

amount of energy to strip hydration of molecule, energy to move through hydrophobic membrane and then the energy need to rehydrate

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24
Q

Why is diffusion with a transporter lower in free energy

A

easier to strip molecule, easily moves through the channel that matches its charges and easy rehydration

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25
Q

What type of protein is the glucose transporter

A

integral protein

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26
Q

How mmany hydrophobic sections does the glucose transporter have

A

12

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27
Q

What do the 12 hydrophobic sections code for

A

12 transmembrane segments

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28
Q

How many conformations does the glucose transporter have

A

2

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29
Q

What are the two confomations for the glucose transporter

A

T1

T2

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30
Q

In the transmembrane alpha helices, where do the charged and polar amino acids reside

A

in the interior of the alpha helice

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31
Q

Where do the hydrophobic amino acids reside in the transmembrane helices

A

on the exterior

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32
Q

What is the T1 conformation

A

the channel when it is open to the exterior and allows glucose to bind to the channel

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33
Q

What is the T2 conformation

A

when the channel opens to the inside once glucose binds and allows its release

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34
Q

WHat does transportation have

A

enzyme-like properties

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35
Q

What is Kt equivalent to

A

Km

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36
Q

What is Kt

A

1/2 max velocity of glucose entry

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37
Q

In the burk. plot, what is the crossing of the y axis stand for

A

1/vmax

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38
Q

On the burk plot, what does the interception on x axis code for

A

-1/Kt

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39
Q

What is the y axis on the burk plot

A

1/V0

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40
Q

What is the x axis on the burk plot

A

1/ [S]out

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41
Q

what is an epimer

A

differs at 1 carbon on carbons

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42
Q

How do D and L glucose differ

A

on the 6th carbon one is up or down

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43
Q

How does the change on the 6th carbon affect GLUT1

A

changes the rate.

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44
Q

What does the chloride bicarbonate exchanger allow for

A

antiport exchange of Cl- for HCO3-

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45
Q

In respiring tissues what direction does Cl- and HCO3- flow

A

Cl- transported in

HCO3- transported out

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46
Q

In lungs, which direction does Cl- flow and HCO3- flow

A

Cl- flows out

HCO3- flows in

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47
Q

In respiring tissues what direction does CO2 flow

A

CO2 uptake

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48
Q

In lungs what direction does CO2 flow

A

CO2 released

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49
Q

What direction does the bicarbonate formula flow in respiring tissues

A

CO2+ H2O –> HCO3- +H (allows Cl- in)

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50
Q

WHat direction does the bicarbonate formula flow in lungs

A

HCO3-+ H–> H2O+ CO2

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51
Q

What enzyme allows the bicarbonate reaction to move forward or backward

A

carbonic anhydrase

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52
Q

What does active transport require

A

energy

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53
Q

Why does active transport require energy

A

moving substrates against gradient

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54
Q

What types of active transport are there

A

primary and secondary

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55
Q

What is primary transport

A

movement of one substrate against its electrochemical gradient

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56
Q

What is secondary transport

A

moves two items against substrates electrochemical gradient, driven by ion moving down its gradient

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57
Q

What is uniport transport

A

moving 1 substrate

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58
Q

What is cotransport

A

moving two substrates

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59
Q

What is symport

A

when two substrates move through 1 channel in same direction

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60
Q

What is antiport

A

when two substrates move through 1 channel in opposite directions

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61
Q

What are energetic costs

A

change in substrate to the product

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62
Q

How is the energetic costs calculated

A

deltaG= (8.315J/K*mol)(298K) ln (P/S)= J/mol

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63
Q

What is the function of ATPases

A

to create a gradient

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64
Q

WHat is the mechanism of the Na+K+ATPase

A

pump out 3 Na+ and pump 2 K+ in

creates a -50 to -70mV gradient

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65
Q

How much of resting energy is used for the Na+K+ATPase pump

A

25%

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66
Q

What type of protein is the ATPase

A

integral protein

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67
Q

What components make up the P-type ATPase

A

T,S membrane domains

A, P, N domains

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68
Q

What is the first step of P-type ATPase

A

calcium and ATP bind allowing N domain to move

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69
Q

After calcium and ATP bind and N domain moves what occurs

A

ADP phosphorylates an ASP in P domain

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70
Q

After ASP is phosphorylated what occurs

A

conformational change occurs causing calcium to be released to the lumen

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71
Q

What occurs after calcium is released

A

The A domain moves causing ADP to be released

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72
Q

After ADP is released what occurs

A

P domains becomes dephosphorylated

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73
Q

What happens after the P domain becomes dephosphorylated

A

the A domain resets

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74
Q

What happens after the A domain resets

A

P,T, and S domains reset to E1 conformation

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75
Q

What are two inhibitors of Na+K+ATPase

A

oubain

palytoxin

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76
Q

How does ouabain inhibit

A

locs ATPase open and prevents a conformational change

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77
Q

How does palytoxin inhibit

A

locks ATPase into an open channel

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78
Q

What are aquaporins

A

channels that permit water to cross membrane

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79
Q

What type of flow does aquaporins have

A

a constant flow

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80
Q

How many genes for aquaporins have in plants

A

38 genes

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81
Q

Why must H3O+ be kept out of aquaporins

A

H+ would destroy electrochemical potentials

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82
Q

What is an ionophore for K+

A

valinomyocin

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83
Q

Molecules within the aquaporin that help water flow through are what

A

Asn
His
Arg

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84
Q

What types of signals do cells receive constant input from

A

pH, osmotic strength, availability of food, oxygen, light, presence of noxious chemicals, predators, competitors of food

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85
Q

What do the signals that the cells receive elicit

A

appropriate responses

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86
Q

What are appropriate responses

A

moving towards or away from a cell

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87
Q

What is a signal

A

information that is detected by specific receptors and converted to a cellular response

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88
Q

What type of process is the response of a cell

A

chemical process

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89
Q

What is signal transduction

A

conversion of info into a chemical change

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90
Q

What is specificity

A

precise molecular complementary between the signal and receptor molecules

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91
Q

What mediates specificity

A

weak, non covalent forces

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92
Q

In multicellular organisms what else contributes to specificity

A

only certain cell types have certain receptors

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93
Q

What helps achieve sensitivity

A

high affinity
cooperativity
amplification

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94
Q

What helps aid high affinity

A

receptors have a high affinity for signal molecules, affinity is between ligand and the receptor

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95
Q

How is the affinity for the ligand and receptor expressed

A

Kd

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96
Q

What is Kd

A

dissociation constant

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97
Q

What helps aid cooperation

A

ligand receptor interaction, large changes occur in receptor activation with only small changes in ligand concentration

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98
Q

What is amplification

A

where a signal is amplified by an enzyme cascade

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99
Q

What is an enzyme cascade

A

the ligand binds to a receptor, activates an enzyme that is associated with the receptor, that enzyme activates multiple molecules of a second enzyme which also activates many molecules of another enzyme

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100
Q

How fast can an enzyme cascade produce a magnitude

A

milliseconds

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101
Q

Why must signals be terminated

A

so downstream effects are in proportion to strength of the original stimulus

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102
Q

What is modularity

A

interacting signaling proteins allow a cell to mix and match a set of signaling molecules to create complexes with different functions

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103
Q

What are scaffold proteins

A

proteins that have an affinity for several enzymes that interact in cascades and bring those proteins together

104
Q

What do scaffold proteins ensure

A

interactions between proteins and enzymes occur at the right time and location

105
Q

What is densitization

A

when a signal is constantly present the receptor system is desensitized

106
Q

What occurs when the stimulus falls below threshold

A

the system becomes sensitized again

107
Q

What is integration

A

the ability of a system to receive multiple signals and produce a unified response

108
Q

What does integration allow

A

conversing to occur at several levels

109
Q

What does integraiton help maintain

A

homeostasis

110
Q

What are the 6 basic receptor types

A 
g protein coupled
receptor tyrosine kinase
receptor guanyly cyclase
gated ion channels
adhesion receptors
nuclear receptors
111
Q

What does GPCR stand for

A

Gprotein coupled receptors

112
Q

What 3 components make up the G protein pathway

A

G-protein complex, transmembrane receptor, effector enzyme

113
Q

What is the structure of the transmembrane receptor

A

binding site for ligand, 7 transmembrane helical segments

114
Q

What occurs to the G protein to make it active vs inactive

A

The GDP gets swapped out for GTP to become active

115
Q

Where is the effector enzyme located

A

within the membrane

116
Q

What does the enzyme produce

A

the second messenger

117
Q

What does the second messenger do

A

affects downstream targets

118
Q

The human genome encodes how many GPCRs

A

350

119
Q

What are orphan receptors

A

receptors that do not have their natural ligands identified

120
Q

What do adrenergic receptors bind

A

epinephrine

121
Q

What is epinephrine

A

fight or flight hormone, binds to the receptor in the membrane

122
Q

What are the 4 types of adrenergic receptors

A

alpha1
alpha2
beta 1
beta 2

123
Q

What defines the differences in the adrenergic receptors

A

their affinities and responses, location within different tissues

124
Q

What is an agonist

A

structured analogs that bind to the receptor and result in a similar effect to the natural ligand

125
Q

What is an antagonist

A

analogs that bind without triggering the normal effect and block agonists and natural ligands

126
Q

Where are beta adrenergic receptors found

A

muscle, liver, adipose tissue

127
Q

What do beta adrenergic receptors do

A

mediate changes in fuel metabolism and increase the breakdown of glycogen and fats

128
Q

What is the structure of a beta adrenergic receptor

A

integral protein, 7 transmembrane helices of 20 to 28 AA

129
Q

What is an alternative name for receptors with 7 transmembrane helices

A

heptahelical receptors

130
Q

What does the binding of epinephrine to the receptor result in

A

a conformation change

131
Q

Where does the conformational change occur

A

to the intracellular domain

132
Q

What does the conformational change to the intracellular domain result in

A

promotes dissociation of GDP and binding of GTP

133
Q

What occurs to the g protein subunit

A

it separates into complexes

134
Q

What two complexes

A

beta gamma and then alpha

135
Q

Which complex moves away to activate the next step

A

the GalphaS

136
Q

What does the GalphaS complex activated

A

adenyly clyclase

137
Q

What is adenyly cyclase catalize

A

cAMP

138
Q

What is cAMP catalyzed from

A

ATP

139
Q

What does cAMP do

A

activates protein kinase A

140
Q

What does protein kinase A do

A

regulates downstream effects

141
Q

G proteins that are composed of three parts are what

A

trimeric

142
Q

What is the stimulatory protein for the G protein complex

A

alpha subunit

143
Q

What is the structure of adenyly cyclase

A

integral protein of plasma membrane

144
Q

How does GalphaS attach to the membrane

A

via covalently attached palmitoyl groups

145
Q

What inactivates the G alpha unity

A

intrinsic GTPase

146
Q

What does intrinsic GTPase do

A

self limits

147
Q

What does Protein Kinase A do

A

phosphorylate Ser or Thr residues of target proteins

148
Q

In its inactive state, what does protein kinase A structure

A

two catalytic subunitys and two regulatory subunits

149
Q

When bound together, what is the strucure of PKA like

A

auto inhibitory domain of each subunit occupies the substrate binding cleft of catalytic domains

150
Q

when cAMP binds to PKA R subunitys, what occurs

A

R moves out of catalytic domain and dissociates R and C subunits

151
Q

What is a consensus sequence

A

neighboring residues needed to make Ser or Thr residue for phosphorylation

152
Q

What are the 3 mechanisms that cause G protein termination

A

concentration of epinephrine
hydrolysis of GTP bound to G alpha subunit
remove 2nd messenger

153
Q

How does the concentration of epinephrine lead to termination of G protein complex

A

when epinephrine drops belows Kd, the hormone dissociates from the receptor and resumes inactive conformation

154
Q

How does inactivation through hydrolysis of GTP bound to G alpha subunit occur

A

GTPase activity occurs and GTP becomes GDP

155
Q

How does removing the 2nd messenger inactivate complex

A

hydrolysis of cAMP to 5’AMP

156
Q

What causes the hydrolysis of cAMP to 5’AMP

A

cyclic nucleotide phosphodiesterase

157
Q

What does desensitization cause

A

dampening the response even when the signal persists

158
Q

What mediates densitization

A

protein kinase that phosphorylates receptor on intracellular domain

159
Q

What does Beta ARK do

A

phosphorylate Ser residues

160
Q

What does BARK function

A

creates a binding site for Beta arrestin

161
Q

What does beta arrestin do

A

prevents further interaction of receptor and G-protein

facilitates receptor sequestration removal of receptors from membranes into vesicles

162
Q

Can PKA move into the nucleus

A

yes

163
Q

When PKA moves into the nucleus what does it do

A

phosphorylates CREb

164
Q

What are adaptor proteins

A

proteins that hold together other protein molecules

165
Q

What is the receptor tyrosine kinase family

A

large family of plasma membrane receptors with intrinsinc protein kinase activity

166
Q

How do tyrosin kinase family receptors transduce extracellular signals

A

via the ligand binding domain and enzyme

167
Q

Where is the ligand binding domain on the receptor

A

on extracellular side

168
Q

Where is the enzyme domain on the receptor

A

intracellular side

169
Q

How are the ligand binding domain and enzyme connected

A

by a single transmembrane segment

170
Q

What is the enzyme of the tyrosine kinase family do

A

phosphorylate Tyr residues in specific target proteins

171
Q

What is the type of enzyme in tyrosine kinase family

A

tyrosine kinase

172
Q

What is the function of insulin

A

regulates metabolic enzymes and gene expression

173
Q

Does insulin enter the cells

A

no

174
Q

What does insulin do to change gene expression

A

initiates a signal that travels a branched pathway from PM to insulin sensitive enzymes in cytosol and nucleus

175
Q

The units that make up the extracellular receptor are what

A

identical alpha subunits

176
Q

What are the units that make up the intracellular receptor

A

identical beta subunits

177
Q

the tyrosine receptor is made up of what

A

two alpha/beta monomers to make a dimer

178
Q

which subunit has insulin binding domain

A

alpha

179
Q

which subunit has kinase activity

A

beta

180
Q

What does the tyrosine kinase do

A

transfers phosphate from ATP to hydroxyl group of tyrosine residues

181
Q

each beta subunit phosphorylates what

A

3 tyrosine residues in beta subunit

182
Q

What type of phosphorylation is this

A

autophosphorylation

183
Q

What does autophosphorylation cause

A

opens up the active site so the enzyme can phosphorylate tyrosine residues of other target proteins

184
Q

In the insulin what occurs first

A

autophosphorylation of INSR occurs

185
Q

What is the target of INSR

A

insulin receptor substrate 1

186
Q

What does INSR do to INRS-1

A

phosphorylates on several tyrosine residues

187
Q

What occurs to the activated IRS1 molecule

A

becomes point of nucleation for complex of proteins that carry message from insulin receptor to targets in cytosol and nucleus

188
Q

What does the phosphorylate tyrosine domain of IRS1 bind

A

SH2 domain of Grb2 protein

189
Q

What is Grb2 protein

A

an adaptor protein

190
Q

What does Grb2 protein have

A

SH3 domain

191
Q

What does the SH3 domain bind

A

proline rich SOS that acts as guanosine nucleotide exchange factor

192
Q

What does the guanosine nucleotide exchange factor do

A

replace bound GDP with GTP on Ras, a G-protein

193
Q

What is Ras

A

a small family of G-proteins

194
Q

What does Ras do

A

activates Raf-1

195
Q

What is Raf-1

A

protein kinase

196
Q

What does Raf1 do

A

activates MEK

197
Q

What does MEK do

A

activates ERK

198
Q

How are MEK and ERK activated

A

phosphorylation of both threonine and tyrosine residues

199
Q

What does ERK do

A

enters nucleus and phosphorylates transcription factors

200
Q

What does ERK phosphorylate

A

Elk1

201
Q

What does Elk1 do

A

modulates 100 insulin regulated genes

202
Q

What does insulin act as

A

growth factor

203
Q

What family does ERK belong to

A

MAPK

204
Q

What does MAPK stand for

A

mitogen activated protein kinase

205
Q

What is mitogen

A

extracellular signals that induce mitosis and cell division

206
Q

What family does MEK belong to

A

MAPKK

207
Q

What family does Raf1 belong to

A

MAPKKK

208
Q

What do MAPK, MAPKK, MAPKKK make up

A

the MAPK cascade

209
Q

What functions as a branch in the insulin signaling pathway

A

PIP3 pathway

210
Q

Where does the PIP3 pathway branch in the insulin signaling pathway

A

where the insulin receptor substrate 1 is phosphorylated

211
Q

What interacts with IRS1 through its SH2 domain

A

PI3K

212
Q

What does PI3K do

A

convert PIP2 to PIP3

213
Q

What does the charged phosphorylated head protrude into

A

the cytoplasmic side

214
Q

What attaches to PIP3

A

protein kinase B

215
Q

What occurs to PKB when attached to PIP3

A

phosphorylated by PDK1

216
Q

What occurs once PKB is phosphorylated

A

it phosphorylates Serine and threonine residues of glycogen synthase kinase 3

217
Q

when phosphorylated by PKB is glycogen synthase kinase3 inactive or active

A

inactive

218
Q

What does PKB trigger

A

clathrin aided movement of glucose transports from internal vesicles to PM

219
Q

What terminates PI3K activity

A

PIP3 specific phosphatase

220
Q

What type of kinase activity does the JAK STAT signaling system involve

A

tyrosine

221
Q

In the JAK STAT signaling system, is there always kianse activity

A

no

222
Q

When is there JAK STAT signaling system when is there kinase activity

A

when the ligand binds

223
Q

When the ligand binds, what binds to give the receptor kinase activity

A

tyrosine kinase

224
Q

Whay is a cytokine for JAK STAT system

A

erythropoeitin

225
Q

Where is erythropoeitin produced

A

in kidneys

226
Q

When the tyrosine kinase binds what occurs to the receptor

A

receptor dimerizes and activates JA kinase

227
Q

What is the function of the JA kinase

A

phosphorylates Tyr residues in cytoplamic domains of EPO receptor

228
Q

What are STATs

A

collection of transcription factors that are targets of JAK

229
Q

STATs bind what

A

phosphorylate tyroside residues in EPO receptor

230
Q

phosphorylates STATS move where

A

into the nucleus

231
Q

What do phosphoylated STATs moving into the nucleus result in

A

transcription of specific genes

232
Q

What can JAK also trigger

A

MAPK cascade

233
Q

What are the general features of a receptor protein of enzyme

A

ligand binding domain or active site

transmembrane segment

234
Q

Under what conditions is insulin released

A

when blood glucose levels are high

235
Q

What does signal transduction mean

A

converting information into a chemical signal to result in cellular responses

236
Q

What is a hormone

A

a small chemcial molecule produced by various tissue types that bind to receptor to stimulate cell response. Hormones are produced by one cell and act upon another

237
Q

What is the end product of most signals

A

phosphorylation for enzyme activation and inhibition

238
Q

How do gated ion channels work

A

open or close in response to concentrations of signal ligand

239
Q

How do receptor enzymes work

A

ligand binding to extracellular domain stimulates enzyme activity in intracellular domain

240
Q

How do serpentine receptors work

A

external ligand binding to receptor activates GTP binding protein which regulates an enzyme

241
Q

What is receptor with no intrinsic enzymatic activity work

A

interacts with cytosolic protien kinase which activates a gene regulating protein to change gene expression

242
Q

How do adhesion receptors work

A

binds molecules in extracellular matrix and changes conformation thus altering its interaction with cytoskeleton

243
Q

How do steroid receptors work

A

steroid binding to a nuclear receptor protein allows the receptor to regulate the expression of specific genes

244
Q

What does a smaller Kd mean

A

has greater affinity for ligand and receptor

245
Q

How is glycogen phosphorylase b activated by epinephrine

A

epinephrine binds
activates G protein
activates adenyly cyclase to produce cAMP
cAMP activates protein kinase A
PKA phosphorylates phosphorylase b
phosphoylase b phosphoylates glycogen phosphorylase b to become active

246
Q

How is PKA regulated by cAMP

A

allosterically by binding at a site other than active site

247
Q

WHat enzyme is responsible for the degradation of cAMP

A

cyclic nucleotide phosphodiesterase

248
Q

What does cAMP become

A

5’AMP

249
Q

What allows beta arrestin to bind

A

after Barr phosphorylates Serine residues of the carboxyl terminus of the receptor

250
Q

When arrestin is bound to the receptor what occurs

A

the receptor enters cell via endocytosis

251
Q

In the inactive state of the insulin receptor what is its arrangement and structure

A

an unphosphorylated tyrosine domain keeps the activation loop in a position that blocks substrate binding site

252
Q

In active state what is structure of receptor

A

the negative aspartate groups nearby the phosphorylate tyrosine cause conformational change that moves the activation loop to move making room for target protein in substrate to bind

253
Q

What is the signaling pathway for insulin

A

insulin binds to receptor
receptor undergoes autophosphorylation
receptor phosphorylates IRS-1 on Tyr residues
SH2 domain of Grb2 binds to IRS1, SOS binds to Grb2 and then to Ras
causes GDp release and GTP binding to Ras
Ras binds to Raf1/activates it
Raf1 phosphorylates MEK on serine residues
MEK phosphoryles ERK on threonine residues
ERK moves into nucleus
ERK phosphorylates Elk1
Elk1 joins SRF to stimulate the transcription of genes

254
Q

What is the signaling pathway for glycogen synthesis

A

IRS1 activates PI3K (binds to SH2 domain)
PI3K converts PIP2 to PIP3
PKB bound to PIP3 is phosphorylated by PDK1
PKB inactivates GSK3
GSK3 cannot convert glycogen synthase to inactive form
synthesis of glycogen is accelerated
PKB stimulates movement of glucose transporter to PM

255
Q

What is PIPs

A

cell membrane lipids

Biochem 2 (2 decks)

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