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biochem > biochem lecture 2 pt 1 > Flashcards

biochem lecture 2 pt 1 Flashcards

1
Q

are pathways interconnected or do they exist in isolation

A

interconnected, often serve as feeders

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2
Q

what are feeders

A

intermediates can be siphoned off into other pathways

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3
Q

metabolism

A

sum of all chemical transformations taking place in cell/organism

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4
Q

what are 2 subdivisions of biochemical pathways

A

catabolism and anabolism

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5
Q

what is catabolism

A

degradative pathways

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6
Q

what is anabolism

A

biosynthesis pathways

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7
Q

how do metabolic reactions occur

A

through enzyme catalyzed reactions

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8
Q

what does each step in a metabolic pathway bring about

A

specific, small chemical change (removal, transfer, addition of atom/functional group, etc.)

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9
Q

how are percursors converted into products

A

through series of metabolic intermediates

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10
Q

metabolites

A

metabolic intermediates

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11
Q

intermediary metabolism

A

combined activities of all metabolic pathways for low molecular weight compounds

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12
Q

are DNA/protein synthesis examples of intermediary metabolism

A

no, those are macromolecular structures

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13
Q

is there intelligence behind these biochemical processes

A

no; just happened through evolution

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14
Q

describe metabolism

A

highly coordinated set of activities within the cell

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15
Q

goals of metabolism

A

to obtain chemical E from environment (light organic molecules and food, etc.)

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16
Q

another goal of metabolism

A

convert nutrient molecules into cellular components (precursors of macromolecules like AAs nucleotides)

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17
Q

yet another goal of metabolism

A

polymerize monomeric precursors into macromolecules (proteins, nucleic acids)

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18
Q

aaandddddd another goal of metabolism

A

synthesize & degrade biomolecules needed for specialized functions (membrane lipids, intracellular messengers, lipids)

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19
Q

what would happen without chemical energy

A

cell/organism can’t perform functions needed to survive

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20
Q

describe catabolism

A

degradative; breaks down larger molecules to smaller ones

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21
Q

what does catabolism do/release

A

releases energy

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22
Q

what does catabolism create

A

ATP, NADH, NADPH, FADH2

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23
Q

what does catabolism do by breaking down stuff

A

releases energy, some E can be captured and harnessed

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24
Q

anabolism

A

can use electrons to build structures

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25
Q

why does anabolism need electron source

A

building stuff, need to form covalent bonds, needs electron source

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26
Q

where does this reducing power/electron source come from

A

NADH, FADH2, etc.

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27
Q

how are electron carriers used

A

in catabolism as source of electron flow and ATP production; in anabolism, reducing power provides electron source to form bonds and build structures

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28
Q

how are both types of metabolism (catabolic and anabolic) connected

A

ATP/chemical energy cycle

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29
Q

basically describe catabolic pathways

A

start w/ E rich compounds, degrade and break them down, generate reducing power and ATP

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30
Q

what can ATP be used as

A

E source to drive anabolic processes

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31
Q

what can the reducing power be used in

A

formation of chemical bonds to build structures

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32
Q

what can happen to the energy depleted products/byproducts of what was used in anabolic processes

A

can be recycled and fed back into catabolic processes

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33
Q

is catabolism oxidative or reductive

A

oxidative

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34
Q

oxidation

A

removal or stripping off electrons from things

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35
Q

describe oxidation in a metabolic context

A

those electrons that are stripped off are transferred to something else

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36
Q

what happens to NAD/ FAD, etc. in catabolism

A

become reduced

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37
Q

what is redox

A

something is oxidized, electrons are transferred to something else, other thing is reduced

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38
Q

describe catabolism

A

oxidative, means that electrons being stripped off from E rich compounds are gonna be transferred to other things

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39
Q

what are the electrons that are stripped off being used for

A

to generate reducing power, ATP, proton motive force etc.

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40
Q

describe anabolism

A

reductive; adding electrons to build chemical bonds

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41
Q

is the synthesis of precursors (AAs, fatty acids) reductive or oxidative

A

reductive b/c you’re building chemical structures

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42
Q

where is this input of electrons coming from

A

some comes from this reducing power

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43
Q

generally, sum this up

A

anabolism is reductive, catabolism is oxidative

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44
Q

do all organisms obtain E the same way (same energy source)?

A

no

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45
Q

what else is important to sustain life besides E

A

carbon

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46
Q

why is carbon important

A

we are carbon-based life forms; chem structures are carbon based; glucose, fats, proteins/AA are carbon based structures

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47
Q

organic molecule

A

C and H

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48
Q

inorganic molecule

A

just C, no H (like CO2)

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49
Q

what is CO2

A

waste product

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50
Q

when is CO2 generated

A

at the end of catabolic processes

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51
Q

Co2 fixation

A

CO2 can be recycled; take CO2 from air and reincorporate it into organic structure

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52
Q

what does calvin cycle do

A

involves fixation of CO2, takes CO2 from air and fixes/incorporates it into other structure

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53
Q

what can the C that’s taken from CO2 in the air be used for

A

synthesis of carbohydrate precursors, used for glucose synthesis down the road (but needs E)

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54
Q

where do autotrophs get carbon from

A

carbon from air (CO2)

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55
Q

where do autotrophs get energy from

A

sunlight

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56
Q

what do autotrophs make

A

O2, H2O

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57
Q

what are autotrophs

A

plants

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58
Q

where do heterotrophs get carbon from

A

food

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59
Q

where do heterotrophs get energy from

A

degradation (of molecules)

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60
Q

what do heterotrophs make

A

CO2, H2O

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61
Q

what are heterotrophs

A

animals

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62
Q

why do autotrophs use sun as an E source

A

in order to do Co2 fixation, carry out calvin cycle (synthesis of carbohydrates) need E

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63
Q

where do autotrophs get the E needed for carbon fixation

A

ATP, but need another E source to synthesize ATP

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64
Q

where do autotrophs get that other E source

A

sunlight

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65
Q

another word for autotroph

A

phototroph

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66
Q

what does autotroph refer to

A

what the carbon source is

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67
Q

what does phototrophy refer to

A

what the E source is

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68
Q

what are most autotrophs in nature

A

also phototrophs

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69
Q

why/how are most autotrophs phototrophs

A

able to utilize CO2 and incorporate into organic structures; utilize E from the sun to do that

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70
Q

what does photoautotroph do

A

combines their energy source and carbon source

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71
Q

example of phototrophs

A

plants, photosynthetic bacteria, algae, etc.

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72
Q

what are organisms that prefer utilizing organic forms of carbon

A

heterotrophs

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73
Q

what do heterotrophs utilize as an energy source

A

organic structures (rather than CO2, which is inorganic)

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74
Q

chemotrophy

A

use of specific chemical comppunds as a source of energy

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75
Q

chemoheterotroph

A

combines chemotroph and heterotroph

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76
Q

how do we (heterotrophs) derive energy

A

use carbon from food, derive ATP energy from degradation of carbon structures that are E rich (carbs, fats, etc.)

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77
Q

what are waste products for heterotrphs

A

CO2, H2O, etc.

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78
Q

can CO2 be recycled

A

yes

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79
Q

who can recycle CO2 and H2O

A

autotrophic organisms / photoautotrophs

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80
Q

what do photoautotrophs generate as a byproduct

A

O2 (oxygen)

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81
Q

how much of atmosphere is Nitrogen

A

Nitrogen makes up 80% of earth’s atmosphere

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82
Q

what requires nitrogen

A

all living things

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83
Q

why do living things need nitrogen

A

for DNA, RNA, proteins, etc.

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84
Q

is nitrogen biochemically useful or no

A

no, it’s biochemically inert

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85
Q

can diff life species utilize nitrogen gas in biochemical processes

A

no

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86
Q

so what do soil bacteria do

A

nitrogen fixing

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87
Q

what is nitrogen fixing

A

reduction of atmospheric nitrogen

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88
Q

describe nitrogen fixing

A

start off w/ N2 gas, end up producing a reduced form of nitrogen called ammonia (NH3+)

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89
Q

what is ammonia

A

gateway compound for nitrogen

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90
Q

what can ammonia be used for

A

fed into the rest of this nitrogen cycle

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91
Q

why is ammonia a gateway compound

A

because reduced form of ammonia is what we need to get to in order to incorporate it into organic structures like AAs, nucleotides, etc.

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92
Q

what does nitrogen fixing start off with

A

N2 gas

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93
Q

what does nitrogen fixing end up with

A

ammonia

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94
Q

what occurs in nitrogen fixing

A

converts N2 into a reduced form, ammonia (NH3+)

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95
Q

can atmospheric nitrogen be incorporated into organic structures

A

no

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96
Q

what is process of nitrogen fixation important for

A

assimilation of N into organic structures and living things

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97
Q

what plays a huge role in this nitrogen cycle

A

bacteria

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98
Q

what role do bacteria play besides nitrogen fixing

A

take ammonia, oxidize it into nitrates and nitrites

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99
Q

what are these bacteria called

A

nitrifying bacteria

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100
Q

who utilizes ammonia w/ these nitrates and nitrites

A

plants

101
Q

what does this process of nitrogen fixation occur in symbiosis with

A

specific plants

102
Q

where is this conversion occuring

A

N2 gas that’s reduced to ammonia by nitrogen fixing bacteria occurs in structures within root systems of plants

103
Q

what is this symbiosis important for

A

how nitrogen gets into the rest of the food chain, b/c animals eat these plants and consume nitrogen

104
Q

how do animals get this nitrogen in their system

A

by consuming plants that have bacteria which do nitrogen fixing

105
Q

what happens when these animals die

A

release waste products that include N, converted back to ammonia, continue the cycle etc.

106
Q

what is carbon cycle

A

how carbon flows through biosphere

107
Q

is there a lot of carbon that cycles between photo-autotrophs and heterotrophs?

A

YES; tons and tons annually

108
Q

what does this carbon cycle and mass cycle of carbon need to occur

A

microorganisms

109
Q

three types of nonlinear metabolic pathways

A

converging catabolic, diverging anabolic, cyclic

110
Q

what is the main cyclical pathway (most ppl think about)

A

TCA cycle

111
Q

what is TCA cycle (besides a cyclical pathway)

A

amphibolic pathway

112
Q

what is an amphibolic pathway

A

has intermediates used for both catabolic and anabolic pathways

113
Q

what are intermediates in TCA cycle also used for

A

precursors for hella synthesis reactions (biosynthetic pathways, nucleotide synthesis pathways, etc.)AND ALSO in catabolic pathways

114
Q

what happens to these intermediates in a cyclical process

A

can siphon them to other pathways AND regenerate them

115
Q

in cyclical pathways what do you need to do in order to keep pace w/ consumption/level of demand

A

need to regenerate or produce more of that intermediate/byproduct

116
Q

what is TCA cycle very much dependent on

A

levels of oxaloacetate & other intermediates

117
Q

why is TCA cycle dependent on oxaloacetate

A

b/c its last step of TCA cycle ANDDD you need it in order to feed acetyl-coA units to keep this pathway going

118
Q

what stuff is common in cyclical pathways

A

feeder pathways that go into the cycle, pathways that produce these intermediates that are then siphoned off into other pathways

119
Q

catabolic converging pathways

A

bunch of diff energy source but all converge into a common intermediate

120
Q

example of a common intermediate that diverging energy sources converge into

A

acetyl coA

121
Q

describe different E sources that converge to acetyl coA

A

carbons that come from carbs, fat, proteins, etc.

122
Q

what is acetyl coA also known as

A

a common currency

123
Q

what happens to acetyl coA regardless of its source

A

fed into TCA cycle

124
Q

most oxidized form of carbon in nature

A

CO2

125
Q

in catabolic mode what happens to carbons from acetyl coA

A

undergo complete oxidation to CO2

126
Q

what does CO2 produced indicate

A

complete oxidation

127
Q

why is CO2 most oxidized

A

hella electronegative oxygens bonded to C, withdraw electron density from the C making it more oxidized

128
Q

what is acetyl coA

A

a common intermediate

129
Q

why is acetyl coA a common intermediate

A

because you can produce it regardless of the initial E source (carbs, fats, etc).)

130
Q

why is it a useful strategy

A

b/c regardless of the carbon source used to generate acetyl coA, it can be fed into this common hub (TCA cycle)

131
Q

what else can acetyl coA be used as

A

a precursor in biosynthesis reactions

132
Q

what is another kind of nonlinear pathway

A

diverging anabolic processes

133
Q

describe diverging anabolic processes

A

take common precursors/intermediates, diversify or split off and synthesize different things

134
Q

example of different things you can synthezie

A

fats, components of phospholipids, cholesterol, vitamins, bile, etc.

135
Q

what is the idea w/ converging and diverging processes

A

can go from converging catabolic processes to common intermediate and then diverging pathways

136
Q

what are the 3 types of metabolic pathways

A

converging catabolic, diverging anabolic, cyclical pathways

137
Q

what is delta G standard linked to

A

reaction equilibrium

138
Q

endergonic

A

absorbs energy, positive delta G, KEQ < 1

139
Q

KEQ less than 1 indicates

A

unfavorable reaction

140
Q

exergonic

A

releases energy, negative delta G, KEQ > 1

141
Q

positive KEQ indicates

A

favorable reaction

142
Q

is endergonic favorable or unfavorable

A

unfavorable

143
Q

is exergonic favorable or unfavorable

A

favorable

144
Q

energy coupling

A

taking something unfavorable/endergonic and coupling it to an exergonic or favorable reaction

145
Q

when do you get a release of energy w/ ATP

A

ATP donating phosphate group to glucose

146
Q

what can you use that energy generated from releasing p from ATP

A

to transfer that p to a glucose

147
Q

why is ATP a useful source of E

A

b/c it can participate in these rxns

148
Q

what happens when you couple an exergonic and endergonic reaection

A

overall reaction is endergonic

149
Q

are free energy changes additive

A

yes; can add up delta G values

150
Q

what is needed in order to make an endergonic process occur

A

need to have a more exergonic process coupled to it

151
Q

how much E is released w/ ATP when you release a phosphate group

A

30 kJ/mol so (-30 kJ/mol)

152
Q

what do metabolic pathways couple

A

endergonic and exergonic steps

153
Q

what do you put energy into

A

making high E intermediate compounds that can be broken down to drive rxns that produce ATP, NADH, etc.

154
Q

basically what are you doing

A

Couple endergonic rxns (like synthesis, etc.) to exergonic reaction like hydrolysis of ATP

155
Q

is transfer of electrons b/w compounds exergonic or endergonic

A

exergonic (favorable, releases E)

156
Q

oxidation

A

loss of electrons

157
Q

in oxidation, what is the substance that loses electrons called

A

reducing agent

158
Q

reduction

A

gain of electrons (reduction of charge)

159
Q

in reduction what is the substance that gains the electron called

A

oxidizing agent

160
Q

what is catabolism overall

A

oxidative

161
Q

why is catabolism oxidative

A

b/c substrates start reduced and become oxidized

162
Q

what is anabolism overall

A

reductive

163
Q

why is anabolism reductive

A

substrates start oxidized and become reduced

164
Q

what are redox reaections

A

transfer of electrons between compounds

165
Q

why are redox reactions so prevalent

A

typically some amount of Energy is released in that process

166
Q

example of releasing energy in form of heat and light

A

when you set wood on fire, it oxidizes carbs in cellulose and glucose; chem bonds are heated, break, and release E

167
Q

when do humans release heat energy

A

when we biochemically breakdown glucose in cell respiration; E can be utilized

168
Q

where does the E that is used to synthesize ATP come from

A

PE stored in E rich molecules

169
Q

how much E is required to make ATP

A

+30 kJ/mol

170
Q

what does hydrolysis of ATP lead to

A

release of energy

171
Q

why does making ATP take energy instead of releasing it

A

trying to stick negatively charged p (phosphate group) to already negative ADP molecule, requires in put of E due to repulsion

172
Q

where does the E we use to make ATP come from

A

tarnsfer of electrons; energy coupling –> coupling exergonic process w/ this endergonic process (ATP synthesis)

173
Q

is ATP synthesis exergonic or endergonic

A

endergonic

174
Q

how can we make ATP if process requires input of energy

A

we have a source of E (oxidizing energy rich compounds like glucose, fats, etc.)

175
Q

what is a source of E to help make ATp

A

oxidizing energy rich compounds like glucose, fats, etc.

176
Q

is burning wood the same way as biochemical processes?

A

no; wood burning is one single step and release HELLA energy in one step

177
Q

are biochemical pathways one step

A

no; this is biochemically useless AND dangerous

178
Q

why are there many steps in biochemical pathways

A

incremental release of small amounts of energy which can be used for AYP synthesis

179
Q

what happens to electrons when something is oxidized

A

transferred to something; that’s why we call it redox

180
Q

when a compound is oxidized, what does it lead to

A

something else being reduced (due to those electrons being transferred)

181
Q

what gets reduced in catabolism

A

electron carriers like NAD and FAD

182
Q

what do NAD and FAD get reduced to in catabolism

A

NADH and FADH

183
Q

why are electron carriers important

A

can serve as currency which can be cashed in to provide E to make ATP

184
Q

example of electron transfer in mitochondria

A

provides energy to establish proton motive force

185
Q

what are you coupling when you establish the proton motive force

A

couple E derived from facilitated diffusion of protons through enzyme complex (ATP synthase) which drives production of ATP

186
Q

is ATP synthesis exergonic or endergonic

A

enderogonic

187
Q

what are you coupling with synthesis of ATP to make it happen

A

free energy available from the flow of protons through AYP synthase

188
Q

what do you do in catabolism (why is it oxidative)

A

take reduced substrates, strip electrons from them (when you break them down), they become oxidized

189
Q

what do you do in anabolism (why is it reductive)

A

you put in electrons into oxidized compounds to synthesize them, become reduced

190
Q

what are important biological electron carriers and coenzymes

A

NADH and NADPH

191
Q

what is oxidized form of NAD

A

NAD+

192
Q

what is reduced form of NAD

A

NADH

193
Q

what is NAD

A

nicotinamide adenine dinucleotide

194
Q

where is NAD derived from

A

niacin

195
Q

what is niacin

A

vitamin

196
Q

what are NADH etc.

A

electron carriers

197
Q

can NAD get reused

A

yes; cycles b/w oxidized and reduced forms and gets reused

198
Q

what is the process when NADH goes to NAD+

A

reduced to oxidized –> oxidation

199
Q

can electron carriers get reused/recycled

A

yes

200
Q

what is niacin deficiency

A

pellagra

201
Q

what is pellagra

A

rough skin

202
Q

is pellagra still there

A

mostly eradicated

203
Q

where do we see pellagra

A

in alcoholics, developing countries

204
Q

where is niacin derived from

A

tryptophan (amino acid)

205
Q

what is FAD

A

flavin adenine nucleotide

206
Q

where is flavin adenine nucleotide derived from

A

riboflavin

207
Q

what do FAD/FADH2 and FMN/FMNH2 act as

A

coenzymes in several types of enzyme-catalyzed redox reactions

208
Q

what is riboflavin

A

vitamin

209
Q

what does FAD serve as

A

electron carriers

210
Q

what can FAD and NAD become

A

oxidized and reduced

211
Q

how many Hs can FAD accept (as opposed to…)

A

one or 2 hydrogens, as opposed to NAD

212
Q

who is involved in more types of reactions

A

FAD (more than NAD or NADP)

213
Q

what is NADP

A

phosphorylated form of NAD

214
Q

what is NADPH

A

reduced form of NADP

215
Q

what is NADPH an important source of

A

reducing power, source of electrons in synthesis

216
Q

is NADH also an electron source

A

yes

217
Q

what is more common NADH or NADPH

A

NADPH in biosynthesis reactions

218
Q

what are redox reactions catalyzed by

A

dehydrogenases

219
Q

is there a net consumption or production of NAD+/NADH

A

no net consumption/production

220
Q

what do dehydrogenases do

A

transfer electrons from one compound to another

221
Q

what are we talking about in catabolism (in terms of transfer of e-)

A

transfer of e- from NAD+ to reduce it to NADH (b/c other thing gets oxidized)

222
Q

NAD+ reduced to NADH will invariable involve what

A

dehydrogenase

223
Q

what is cellular ratio

A

NAD+&raquo_space;> NADH

224
Q

what does it favor

A

hydride transfer to NAD+ (degradation)

225
Q

what is NAD+ being reduced to NADH+ more common in

A

catabolism

226
Q

what is 1st step in NAD/NADH redox reaction

A

substrate undergoes oxidation –> dehydrogenation

227
Q

what occurs during dehydrogenation

A

loses 2 H atoms (2 protons and 2 e-s)

228
Q

what is 2nd step in NAD/NADH redox reaction

A

oxidized form of NAD accepts a hydride ion (1 proton and 2 e-), becomes reduced

229
Q

what is hydride ion

A

1 proton, 2 e-

230
Q

what does transfer of e- from reduced substrate to NAD+ to oxidized form of NAD result in

A

reduction of NAD to NADH, and oxidation of compound that initially carried those electrons [catabolic]

231
Q

describe reduction/anabolism for NAD/NADH step 1

A

NADH donates a hydride ion to oxidized substrate

232
Q

is there a net of hydrogen atoms transferred/lost from reduced compound?

A

yes

233
Q

describe step 2 reduction of nad/nadh

A

substrate becomes reduced

234
Q

what do dehydrogenases cattalyze

A

both reduction of NAD+ to NADH but also oxidation of NADH to NAD+

235
Q

what is more common to see in anabolic processes

A

oxidation; transfer of e- from reduced electron carrier to something else

236
Q

describe what happens to that something else in reduction

A

that something else starts off oxidized and becomes reduced, NADH is oxidized to NAD+

237
Q

real life redox reaction example

A

oxidation of ethanol

238
Q

describe oxidation of ethanol by NAD+

A

ethanol is oxidized to an aldehyde, NAD+ is reduced to NADH

239
Q

how is it redox

A

you’re coupling oxidation reaction with a reduction reaction; or removing electrons from one compound and transferring to another

240
Q

what does ethanol start off as

A

reduced substrate, gets oxidized; NAD+ is oxidized,gets reduced

241
Q

where are the electrons transferred from

A

electrons are removed from ethanol and transferred to NAD+, generates acetaldehyde

242
Q

what is more oxidized acetaldehyde or alcohol

A

acetaldehyde

243
Q

describe reduction of pyruvate by NADH

A

pyruvate is reduced to form lactic acid/lactate, NADH is oxidized to NAD+

244
Q

what does NADH do/carry out

A

NADH gets oxidized to NAD+, so it must carry out a reduction

245
Q

what does NAD+ do

A

NAD+ gets reduced to NADH, so it must carry out an oxidation

246
Q

describe oxidation of C-C bond to C=C bond by FAD/FADH

A

C-C bond is oxidized to C=C, while FAD is reduced to FADH2

247
Q

where are the electrons transferred

A

removed from hydrocarbon chain and transferred to FAD –> FADH2

248
Q
A

biochem (15 decks)

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