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biochem > biochem lecture 4 pt 1 > Flashcards

biochem lecture 4 pt 1 Flashcards

1
Q

what serves as a major energy source in organisms

A

glucose

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2
Q

what are different sources of glucose

A

from glycogen stores, directly from diet

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3
Q

how can glucose be stored

A

glycogen, starch, sucrose

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4
Q

one way glucose can be used

A

oxidation into ribose-5-phosphate via pentose phosphate pathway

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5
Q

another way glucose can be used

A

oxidized into pyruvate via glycolysis

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6
Q

what does glycolysis mean

A

“sweet splitting”

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7
Q

what cells is glucose catabolism carried out in

A

all cells

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8
Q

what is glycolysis basically

A

glucose catabolism

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9
Q

where does glycolysis take place

A

in cytoplasm

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10
Q

what is glycolysis to certain cells

A

only source of metabolic energy

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11
Q

how many reactions in glycolysis

A

10 reactions

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12
Q

is glycolysis same or different in all cells

A

same

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13
Q

what are products of glycolysis?

A

pyruvate, ATP, NADH

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14
Q

what are the three possible fates for pyruvate

A

aerobic oxidation, anaerobic glycolysis (lactate), anaerobic fermentation (ethanol)

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15
Q

what does glycolysis involve/entail

A

breakdown of glucose (6 C molecule) into 2 molecules of pyruvate/pyruvic acid (3 C molecule)

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16
Q

describe the aerobic fate for pyruvate

A

complete oxidation of pyruvate thru rest of cell respiration; TCA cycle, and reducing power from TCA cycle is fed into ETC, which drives ox phos or ATP synthesis

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17
Q

what happens to pyruvates generated at end of glycolysis in cell respiration

A

we produced CO2

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18
Q

what happens in aerobic fate of pyruvate in glycolysis

A

6 carbons of glycolysis will undergo complete oxidation; some in TCA cycle, some in end of cell respiration

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19
Q

what is anaerobic metabolism

A

fermentation

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20
Q

what happens in anaerobic metabolism

A

any form of oxidation where you don’t have O2 as final electron acceptor

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21
Q

what is the final electron acceptor in cell respiration /aerobic respiration

A

O2

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22
Q

when do organisms use anaerobic respiration

A

lack of oxygen, or if oxygen is toxic to them

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23
Q

is glycolysis well conserved

A

yes

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24
Q

what does a well conserved process imply

A

implies that there is a high level of utility of this pathway across species barriers

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25
Q

what does pyruvate produced at end of glycolysis represent

A

only a partial oxidation of glucose

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26
Q

how much energy do we generate at end of glycolysis

A

2 ATPs, 2 NADHs per glucose molecule

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27
Q

is there still more E to be extracted from pyruvate at end of glycolysis?

A

yes

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28
Q

does glycolysis generate a lot or a little energy

A

only a little bit

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29
Q

how do we generate ATP in glycolysis

A

substrate-level phosphorylation

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30
Q

where do we generate more ATP from (what other process)

A

complete oxidation of glucose

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31
Q

when is ATP production via glycolysis important

A

anaerobic conditions (oxygen is lacking or toxic to them)

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32
Q

what are the 3 main catabolic fates of pyruvate

A

aerobic respiration, anaerobic processes [ethanol fermentation and lactic acid fermentation]

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33
Q

describe aerobic process / complete oxidation of glucose

A

there is complete oxidation of glucose through TCA, and transfer of electrons from reduced electron carriers generated in TCA cycle to completely oxidized glucose’s carbons, through ETC and ox phos

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34
Q

what type of organisms go thru TCA cycle, ETC, and ox phos

A

aerobic

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35
Q

why don’t anaerobic organisms go thru TCA cycle, ETC, and ox phos

A

because there is no oxygen to serve as the final electron acceptor

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36
Q

so how do they extract E from glucose

A

have to find another way; via ethanol or lactic acid fermentation

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37
Q

who does lactic acid fermentation

A

humans

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38
Q

who does ethanol fermentation

A

yeast

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39
Q

what are the 2 end products for these 2 anaerobic pathways

A

ethanol and lactic acid

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40
Q

what is Ethanol fermentation

A

when we convert pyruvates into ethanol molecules

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41
Q

what is lactic acid fermentation

A

when we convert pyruvates into lactic acid molecules

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42
Q

what is net energy yield of glycolysis

A

2 ATP, 2 NADH per glucose

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43
Q

what is big picture of glycolysis

A

1 molecule of glucose (6 C) is degraded to make 2 molecules of pyruvate (3 C)

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44
Q

describe thermodynamics of glycolysis

A

irreversible & exergonic

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45
Q

how does ATP synthesis in glycolysis occur

A

strictly thru substrate-level phosphorylation

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46
Q

why do we invest a bit of ATP early on

A

to set the stage for more ATP production later

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47
Q

does glycolysis have input of ATP

A

yup; it’s like investing

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48
Q

is ATP synthesis exergonic or endergonic

A

endergonic; input of E

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49
Q

where does the E needed to make ATP come from

A

from partial oxidation of glucose into 2 pyruvates

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50
Q

what is delta G for conversion of glucose –> pyruvate

A

large and negative (exergonic)

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51
Q

what does this exergonic delta G do

A

offsets the positive (endergonic) delta G for synthesis ATP

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52
Q

what is glycolysis overall

A

exergonic, but there are endergonic reactions embedded

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53
Q

how do we do ATP synthesis in glycolysis

A

substrate level phosphorylation

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54
Q

what kind of intermediates do we have

A

high energy intermediates

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55
Q

what are two phases of glycolysis

A

preparatory phase and payoff phase

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56
Q

what happens in prep phase

A

phosphorylation of glucose & conversion to glyceraldehyde - 3 phosphate (basically glucose –> GAP)

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57
Q

how many steps in prep phase

A

4 (5 if you count DHAP –> GAP)

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58
Q

what does prep phase do/convert

A

converts 6 C sugar to 2 3C sugars

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59
Q

how much ATP used in prep phase

A

2 ATP

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60
Q

what is prep phase

A

investment phase (we use ATP)

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61
Q

what is payoff phase

A

oxidative conversion of GAP to pyruvate, and coupled formation of ATP and NADH

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62
Q

how many steps in payoff phase

A

6 (or 5)

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63
Q

what is converted in payoff phase

A

converts two 3C sugars to 2 pyruvates

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64
Q

how much ATP is made in payoff phase

A

4 ATP (2 from each 3 C sugars)

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65
Q

what do we do after step 5

A

we multiply everything by 2, because DHAP –> GAP means 2 GAPs

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66
Q

what is yielded in payoff phase

A

the energy invested in the two priming rxns in prep phase yield our 2 examples of high E intermediates

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67
Q

what are 1,3-BPG and PEP

A

high E intermediates

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68
Q

what does it mean when we see these high E intermediates

A

something important is gonna happen (high E compounds are gonna be used in substrate-level phosphorylation)

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69
Q

where is ATP generated (what steps)

A

7 and 10

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70
Q

when are priming reactions

A

prep phase

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71
Q

what happens when we see a high E intermediate

A

ATP production

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72
Q

what is step 1

A

phosphorylation of glucose to glucose-6-phosphate

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73
Q

what enzyme catalyzes step 1

A

hexokinase

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74
Q

what is our first priming rxn

A

step 1

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75
Q

where do we invest our first ATP

A

step 1

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76
Q

what is kinase

A

enzyme that utilizes ATP as phosphate donor; transfers phosphate group from ATP to a substrate (in this case glucose)

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77
Q

what is the point of phosphorylating glucose in step 1

A

we trap glucose in the cell; glucose will remain in cell, used in glycolysis

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78
Q

what do you do to G6P when you have lot of ATP and don’t need to do glycolysis

A

G6P can be redirected to glycogen synthesis or hexose phosphate pathway

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79
Q

step 2

A

conversion of glucose-6-P to fructose-6-P

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80
Q

what kinda reaction is in step 2

A

isomerization reaction

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81
Q

what enzyme catalyzes step 2

A

phosphohexose isomerase

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82
Q

ddscribe delta G

A

positive but very small –> reversible rxn

83
Q

is step 2 reversible or irreversible

A

reversible

84
Q

what is step 3

A

phosphorylation of fructose-6-p to fructose-1,6-bisphosphate (f6p to f-1,6-bp)

85
Q

when is. second priming reaction

A

step 3

86
Q

what is first committed step of glycolysis

A

step 3

87
Q

describe step 3

A

second priming reaction, first committed step of glycolysis

88
Q

what enzyme is in step 3

A

phosphofructokinase-1 (PFK-1)

89
Q

why do we call step 3 first committed step

A

fructose-1,6-bisphosphate is only targeted for glycolysis; its dedicated to glycolysis and is gonna be directed thru glycolysis exclusively at this point

90
Q

describe step 3s delta G

A

negative; allows rxn to occur

91
Q

what kinda reaction is step 3

A

phosphate group transfer reaction involving ATP

92
Q

how is PFK activity regulated and influenced

A

by ATP levels

93
Q

describe PFK activity when [ATP] is low

A

activity is high

94
Q

describe PFK activity when [ATP] is high

A

activity is low

95
Q

what does a lot of ATP mean

A

energy state is high, things are good

96
Q

what does high ATP serve as an inhibitor of

A

PFK-1 activity

97
Q

describe the inhibitor effect on PFK in presence of little ATP

A

not as pronounced effect; steeper slope

98
Q

what happened to graph when we add ATP

A

activity curve shifts to the right

99
Q

what does it mean when we see a rightward shift in activity curve

A

indicates something is reducing activity of that enzyme

100
Q

what does ATP do to enzyme

A

lowers/reduces activity of enzyme

101
Q

how does ATP reduce activity of PFK-1

A

ATP binds to an allosteric site on PFK-1, lowering the activity

102
Q

describe curve with ATP mixed with a bit of AMP

A

curve shifts back to the left partially

103
Q

what is ATP indicator of

A

high E state in the cell

104
Q

what does AMP an indicator of

A

low E state in the cell

105
Q

why is AMP an indicator of low E state

A

more AMP means less ATP, so less E

106
Q

what does adding AMP with ATP do

A

shifts the curve a little bit; we don’t have as high activity as we would w/ no inhibitor, but we’ve reinstated a significant level of activity in presence of AMP

107
Q

what does AMP does to the effect of ATP

A

antagonizes the effect of ATP

108
Q

what is allosteric regulator of PFK-1

A

ATP (AMP?)

109
Q

what else is PFK/AMP an example of

A

feedback inhibition

110
Q

what is step 4

A

cleavage of fructose 1,6 BP into DHAP and GAP

111
Q

what enzyme is for step 4

A

aldolase

112
Q

why is it called aldolase

A

cuz it carries out an aldol condensation reaction

113
Q

what kinda reaction is step 4

A

cleavage reaction

114
Q

what are DHAP and GAP to each other

A

isomers

115
Q

where do carbons in DHAP come fro

A

first 3 Cs in glucose (C1 to C3)

116
Q

what do carbons 4-6 correspond to

A

GAP

117
Q

what happens to DHAp

A

dead end compound, can’t continue for rest of glycolysis

118
Q

what do we need in order for all the PE stored in glucose to be utilized

A

DHAP has to be isomerized to GAP

119
Q

how did we figure out what Cs in DHAP and what in GAP

A

radioactive labeling

120
Q

what is step 5

A

conversion of DHAP to GAP

121
Q

why do we need to convert DHAP to GAP

A

only GAP can be directly degraded to pyruvate

122
Q

what enzyme in step 5

A

triose phosphate isomerase

123
Q

specifically what does triose phosphate isomerase do

A

takes ketone form of DHAP and isomerizes it into an aldehyde and we get GAP

124
Q

what happens from this point on

A

2 molecules of GAP, so multiply everything w/ 2

125
Q

summarize phase one/prep phase

A

4/5 steps, converts one 6C sugar into 2 3C sugars, uses 2 ATPw

126
Q

what kinda reactions are in prep phase

A

the 2 priming rxns

127
Q

what do priming reactions involve

A

investment of ATP at each step AND phosphoryl group transfer reactions

128
Q

what other rxns in prep phase

A

isomerization reaction, cleavage reactions, another isomerization reaction that generates 2 molecules of GAP

129
Q

what is step 6

A

oxidation of gAP to 1,3-bisphosphoglycerate (1,3-BPG)

130
Q

what is produced in step 5

A

a high energy intermediate (1,3BPG)

131
Q

what else is made in step 6

A

NADH

132
Q

basically what 2 things are done in step 6

A

generate NADH, and our first high E intermediate 1,3-BPG

133
Q

what enzyme does step 6

A

glyceraldehyde 3-phosphate dehydrogenase

134
Q

what is a dehydrogenase

A

involved in redox reactions

135
Q

what’s being reduced in step 6

A

NAD+ to NADh

136
Q

what is NADH

A

money in the bank, can be used in ETC, other stuff

137
Q

how do we produce our first high E intermediate 1,3- BPG

A

dehydrogenase uses inorganic phosphate

138
Q

do we invest more ATP to make 1,3-BPG?

A

no, doesn’t make sense to use ATP to eventually get an ATp

139
Q

describe the availability of the inorganic phosphate

A

readily available in the cell

140
Q

basically what are we doing in step 6

A

using a non-ATP phosphate source (inorganic phosphate) to generate ATP in the next step (step 7) thru substrate level phosphorylation

141
Q

basically

A

we’re using inorganic phosphate to produce ATP in the next step

142
Q

what is step 7

A

phosphoryl transfer from 1,3-BPG to ADP (to make ATP), and we make 3-PG (3-phosphoglycerate)

143
Q

where does the phosphate group go

A

is transferred from 1,3-BPG to ADP to make ATP, and we’re left with 3-PG

144
Q

what enzyme for step 7

A

phosphoglycerate kinase

145
Q

why is it a kinase in step 7

A

because of its ability to catalyze the reverse reaction (to phosphorylate 3-phosphoglycerate and make 1,3-BPG) in gluconeogenesis

146
Q

when is our first substrate level phosphorylation reactoin

A

step 7 (1,3-BPG converted to 3-PG)

147
Q

what makes 1,3BPG a high E compound

A

how readily the phosphate group can be transferred from 1,3-BPG to a molecule of ADP

148
Q

if we have something involved in substrate level phosphorylation, what is necessary

A

group transfer rxn potential of that high E compound has to be higher than ATP

149
Q

what would happen if ATP’s rxn potential was higher than high E intermediate

A

reverse rxn occurs, with ATP transferring its phosphate to 3-PG to make 1,3-BPG

150
Q

describe delta G values in step 7

A

higher and more negative for 1,3-BPG and PEP compared to ATP hydrolysis (basically phosphoryl group transfer potential of 1,3-BPG is higher than ATP) –> rxn is favored

151
Q

what steps are coupled

A

6 and 7

152
Q

describe free E change in step 6

A

conversion of GAP to 1,3-BPG is endergonic

153
Q

how do we make step 6 go

A

couple it to step 7, exergonic

154
Q

how are steps 6 and 8 coupled

A

thru a common intermediate: a thioester bond formed b/w a cysteine in GAP dehydrogenase enzyme and GAP

155
Q

what does GAP DH have in its active site

A

a catalytically relevant cysteine and histidine

156
Q

what happens to enzyme GAP DH first

A

will form a covalent complex w/ substrate in form of a thioester bond

157
Q

what kinda bond is a thioester bond

A

a high energy bond

158
Q

what happens when you break a thioester bond / high E bond

A

release E

159
Q

basically how do you drive the otherwise endergonic step of GAP being converted to 1,3-BPG

A

formation of a thioester linked enzyme substrate intermediate

160
Q

what can happen to thioester linkage

A

can be hydrolyzed, some of that free E released as a result of hydrolysis is gonna be enough E to generate a high E compound 1,3-BPG

161
Q

what is steps 6 and 7 an example of

A

energy coupling; basically taking PE stored in thioester bond to form the first high E intermediate

162
Q

what happens with the dehydrogenase enzyme

A

forms a high E intermediate form of the substrate within the cysteine residue within the active site of the enzyme

163
Q

what does the dehydrogenase enzyme have

A

a thiol group (SH)

164
Q

what is SH gonna be a part of

A

the thioester linked enzyme-substrate intermediate

165
Q

what happens when the thioester linkage is cleaved

A

the free E that’s released will be enough to transfer this inorganic phosphate group from GAP to 1,3-BPG

166
Q

what happens to free E if there is no thioester intermediate

A

large activation E

167
Q

what happens to E with thioester intermediate (enzyme substrate thioester linked intermediate)

A

lower activation E barrier to overcome, easier

168
Q

what makes this reaction of GAP to 1,3-BPG

A

formation of thioester intermediate

169
Q

what is step 8

A

conversion of 3PG to 2PG

170
Q

what happens after step 7, after substrate-level phosphorylation

A

we are left with ATP and 3PG (de-phosphorylated compound)

171
Q

what happens in step 8

A

isomerize 3PG to 2PG

172
Q

what enzyme in step 8

A

phosphoglycerate mutase

173
Q

are mutase same or different from isomerase

A

different catalytic mechanism

174
Q

what’s interesting about phosphoglycerate mutase

A

it has catalytically important histidine residue in its active site

175
Q

what’s up w/ phosphoglycerate mutase

A

one nitrogen on the imidazole ring of histidine undergoes phosphorylation

176
Q

what is phosphorylation of N on imidazole ring of histidine important for

A

isomerization of 3PG to 2PG

177
Q

what is a mutase

A

catalyze transfer of a functional group from one position to another on a molecule (in this case phosphoryl from C3 to C2)

178
Q

what does phosphoglycerate mutase have

A

unique phosphorylated HIstidine in its active site

179
Q

what is step 9

A

dehydration of 2PG to PEP

180
Q

what enzyme in step 9

A

enolase

181
Q

what does enolase do in this step

A

catalyzes conversion of 2PG to PEP via elimination

182
Q

what does enolase do basically

A

rearranges 2PG to form (PEP) from which more E can be released

183
Q

why do we dehydrate 2PG to PEP

A

to create a high E compound capable of driving synthesis of ATP

184
Q

what is free E for hydrolysis of 2PG

A

too low to make ATP; so we need to convert to a high E intermediate

185
Q

what is step 10

A

phosphoryl transfer from PEP to ADP, to make pyruvate and ATP

186
Q

what kinda rxn is step 10

A

substrate level phosphorylation

187
Q

what is made in step 10

A

2nd ATP and pyruvate

188
Q

what enzyme in step 10

A

pyruvate kinase

189
Q

why is enzyme name pyruvate kinase confusing

A

b/c it’s named for the reverse reaction that we see in gluconeogenesis (pyruvate to PEP)

190
Q

how many ATPs do we make

A

2 x 2 is 4, but we use 2 so net gain is 2

191
Q

summarize payoff phase or phase 2

A

5 steps, converts GAP to pyruvate, makes 2 ATP and 1 NADH (per gap)

192
Q

how many net NADH produced

A

2 NADH (1 per gap)

193
Q

can we extract more E from pyruvate

A

yes

194
Q

when do we oxidize the rest of E from pyruvate

A

in TCA cycle when oxidize pyruvate to CO2 and make more reducing power

195
Q

what else do we make in TCA cycle

A

more reducing power

196
Q

where does reducing power we make in cell respiration come from

A

TCA cycle

197
Q

what is net gain in glycolysis

A

2 ATP, 2 NADH, 2 pyruvates

198
Q

what happens as glucose is oxidized

A

2 NAD+ are reduced to NADH

199
Q

how many fates for pyruvate at end of glycolysis

A

3 fates, divided in anaerobic and aerobic

200
Q

what’s up w/ pyruvate and NADH in aerobic conditions

A

NADH is reoxidized in ETC and makes ATP in ox-phos. pyruvate enters TCA

201
Q

what’s up w/ pyruvate and NADH in anaerobic conditions

A

NADH reoxidized to NAD+, provides more NAD+ for more glycolysis. pyruvate converted to lactate (muscles) or ethanol (yeast)

202
Q

describe pyruvate conversion to lactate

A

lactic acid fermentation, in muscles

203
Q

describe pyruvate conversion to ethanol

A

ethanol fermentation, in yeast

biochem (15 decks)

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