exam 2 Flashcards
1
Q
thermodynamics
A
the branch of chemistry concerned with energy changes
2
Q
definition of energy
A
the capacity to do work
3
Q
what are the two states of energy
A
- kinetic
2. potential
4
Q
what is kinetic energy
A
energy of motion
5
Q
what is potential energy
A
stored energy
6
Q
forms of energy
A
mechanical, light, sound, heat, electrical, radioactivity
7
Q
most convenient way of measuring energy
A
heat
8
Q
what is one calorie
A
the heat required to raise 1 gram of water by 1 degree celcius
9
Q
where does energy flow from into the biological world?
A
the sun
10
Q
what captures the sun’s energy
A
photosynthetic organisms
11
Q
what is the energy from the sun stored as
A
stored as potential energy in chemical bonds
12
Q
oxidation
A
atom/molecule loses an electron
13
Q
reduction
A
atom/molecule gains and electron, higher level of energy than oxidized from
14
Q
redox reactions done in what
A
pairs
15
Q
first law of thermodynamics
A
energy cannot be created or destroyed
16
Q
what is the total amt of energy in the universe?
A
remains constant
17
Q
what happens to heat during each conversion
A
some energy is lost as heat
18
Q
second law of thermodynamics
A
energy always converts from a more ordered/less stable form to a less ordered/ more stable form
19
Q
entropy
A
disorder, continuously increasing
20
Q
disorder happens
A
spontaneously
21
Q
order requires
A
energy
22
Q
free energy equation
A
G = H - TS
23
Q
in G = H - TS, what does G stand for
A
energy available to do work
24
Q
in G = H - TS, what does H stand for
A
enthalpy
25
G = H - TS, what does T stand for
absolute temp
26
in G = H - TS, what does S stand for
entropy
27
what is enthalpy
energy in a molecules bond
28
what is entropy
unavailable energy
29
where do our photosynthetic organism reside?
algae, bacteria, eukaryotes in ocean, trees, mostly in water
30
how do humans capture energy
from plants, convert it to glucose
31
how is sunlight stored as potential energy
take carbon to fix them together, Carbon-Hydrogen bond is stored energy
32
role of reducing sugar
reduce other molecules
33
what is oxidation
atom or molecule loses an electron
34
what is reduction
atom or molecule gains and electron, higher level of energy than oxidized from
35
redox is always..
paired, to reduce you must oxidize must always be done at the same time
36
what is a big cause of disease in cells?
oxidation
37
energy states always go from..
more ordered and less stable state to a less ordered and more stable form (easier to keep room messy)
38
change in free energy equation
change in free energy = change in enthalpy - temperature x energy lost/not able to use
DeltaG = deltaH - TS
39
positive delta G
products have more free energy than reactants, H is higher and S is lower, not spontaneous, requires energy input, endergonic
40
negative dela G
products have less free energy than reactants, H is lower or S is higher o both, spontaneous, but may not be instantaneous, exergonic
41
what is extra energy required to do
destabilize existing bonds and initiate a chemical reaction
42
exergonic reaction rate depends on
activation energy required
43
larger activation energy proceeds more
slowly
44
how can activation energy rate be increased
1. increasing energy of reacting molecules (heating)
| 2. lowering activation energy (enzymes- catalysts)
45
what happens to activation energy without catalysts
its a lot longer
46
what are catalysts
substances that influence (destabilize) chemical bonds in a way that lowers activation energy
47
catalysts do not and cannot do what
cannot violate laws of thermodynamics, cannot make endergonic reaction spontaneous, do not alter the proportion of reactant turned into product
48
what is ATP
adenosine triphosphate, chief "currency" all cells use
49
what is ATP composed of
ribose - 5 carbon sugar, adenine, chain of 3 phosphates
50
ATP 3 chain phosphates, describe
1. key to energy storage
2. bonds are unstable
3. ADP - 2 phosphates
4. AMP - 1 phosphate (lowest energy form)
51
What happens in the ATP breakdown
ATP ---> ADP (diphosphate) ---> AMP (monophosphate) --> usually converts to ---> cAMP
52
what is cAMP?
cyclic AMP(monophosphate), signal molecules that tells the cell its low in energy
53
fats or carbs store longer term energy
fats
54
how do animals store energy
store gylcogen in muscles, break down into glucose, which breaks down in ATP
55
what drives endergonic reactions
ATP hydrolosis, coupled reactions in net -delta G )exergonic and spontaneous
56
how long do cells store ATP
only a few seconds
57
what are enzymes
most are proteins, based on amino acid structures, helix and sheet folding, disulfide bond, ionic interaction, globular structure, enzymes change shape of bond and not destroyed or used up, not changed or consumed in reaction
58
what does the shape of an enzyme do
stabilizes a temporary association between substrates
59
carbonic anhydrase with and without enzymes
without - 200 molecules of carbonic acid per hour made
| with - 600,000 molecules formed per second with enzyme
60
look at enzyme, substrate, active site diagram
ch. 6, page 8
61
what is the active site
pockets or clefts for substrate binding, forms enzyme- substrate complex, precise fit of substrate into the active site, applies stress to distort particular bond to lower energy
62
what is induced fit
enzyme can work on bonds and give a product
63
better the fit,
better the activation, the quicker the activation will take place
64
where would enzymes be found
suspended in the cytoplasm or attached to cell membranes and organelles
65
multienzyme complexes
subunits that work together to form a molecular machine, the product can be easily delievered to the next enzyme, unwanted side reactions are prevented, all reactions ar controlled as a unit
66
where are proteins found
in lipid bilayer, cytoplasm
67
rate of enzyme-catalyzed reactions depends on
concentration of substrate and enzyme
68
what conditions affect the enzymes 3D shape and change the rate
optimum temp and pH
69
taq polymerase
works at high temps and helps finding DNA
70
what is an inhibitor
substance that binds to enzyme and decreases its activity
71
what is a competitive inhibitor
competes with substrate for active site
72
what is a noncompetitive inhibitor
binds to enzymes at a site other than an active site, causes shape change that makes enzyme ubable to bind to substrate
73
what can inhibitors bind to?
1. active site
| 2. allosteric site
74
what is an allosteric site
a site where an inhibitor binds to, other than active site
75
what happens when an inhibitor binds
causes a conformational change
76
allosteric enzymes
enzyme that have allosteric site, enzyme that exists in active and inactive forms
77
where do most noncompetitive inhibitors bind to
allosteric site - chemical on/off switch
78
what is an allosteric inhibitor
binds to allosteric site and reduces enzyme activity
79
what is an allosteric activator
binds to allosteric site and increases enzymes activity
80
what is a metabolism
total of all chemical reactions carred out by an organism
81
anabolic reactions/anabolism
expends energy to build up molecules
82
catabolic reactions/catabolism
harvest energy by breaking down molecules
83
what are biochemical pathways
reactions that occur in a sequence, product of one reaction is the substrate for the next, many steps take place in organelles, assembly line
84
what is a feedback inhibition
end-product of pathway binds to an allosteric site on enzyme that catalyses first reaction in pathway, shuts down pathway so raw materials and energy are not wasted
85
autotrophs
able to produce their own organic molecules thru photosynthesis
86
heterotrophs
live on organic compounds produced by other organisms
87
what do all organisms do to extract energy from organic molecules
cellular respiration
88
dehydrogenations
lost electrons are accompanied by protons (a H atom is lost (1 e and 1 p))
89
what is important in cellular respiration
redox
90
what is NAD +
an electron carrier, accepts 2 electrons and 1 proton to become NADH, reaction is reversible
91
in overall cellular energy harvest, what happens?
dozens of redox reacions take place, number of electron acceptors including NAD+, in end, high-energy electrons from initial chemical bonds have lost much of their energy, transferred to a final electron acceptor
92
what is the final electron acceptor
oxygen
93
why is this process of redox slow?
if it was released fast, energy would be lost as heat
94
aerobic respiration final electron acceptor
O2
95
anaerobic respiration final electron acceptor
is an inorganic molecule (not O2)
96
fermentation final electron acceptor
organic molecule
97
humans use anaerobic when
working out
98
aerobic respiration equation
C6H12O6 + 6O2 = 6CO2 + 6H2O
99
what are the carriers like?
soluable, membrane bound, move within the membrane
100
carriers can be easily
oxidized and reduced
101
what does NAD+ acquire to become NADH
2 electrons and a proton
102
how is endergonic reactions driven
ATP
103
2 mechanisms for ATP synthesis
1. substrate level phosphorylation
| 2. oxidative phosphorylation
104
what is substrate level phosphorylation
transfer phosphate group directly to ATP, during glycolysis, produces enzyme reactions
105
what is oxidative phosphorylation
ATP synthase uses energy from a proton gradient, O2 and H2 gradient ends of steps
106
what is a substrate
something that binds to an enzyme, enzyme converts it to speed up reaction
107
what are the steps of the oxidation of glucose
1. glycolosis
2. pyruvate oxidation
3. krebs cycle
4. electron transport chain and chemiosmosis
108
where does glycolosis happen
cytoplasm
109
where does pyruvate oxidation, krebs cycle, electron transport chain and chemiosmosis happen
mitochondria
110
why is glucose a carbon 6
each point is a carbon
111
what is glycolosis
converts 1 glucose (6 carbon) to 2 pyruvate (3 carbon), 10-step biochemical pathway, occurs in cytoplasm, net production of 2 ATP molecules by substrate-level phosphorylation, 2 NADH produced by reduction of NAD+
112
end of glycolosis has what
2 pyruvate molecules, 2 net ATP molecules, 2 molecules of NADH per one glucose
113
how must glycolysis continue?
NADH must be recycled to NAD+ by either:
1. aerobic respiration (produces significant amt of ATP)
2. fermentation (occurs when O2 isnt avaliable)
114
what is the fate of pyruvate after glycolysis
when O2 is present: oxidized to acetyl-CoA, which enters the Krebs cycle (aerobic respiration)
w/out O2: pyruvate reduced in order to oxidize NADH back to NAD+ (fermentation)
115
what is pyruvate oxidation
occurs in mitochondria in eukaryotes, catalyzed by multienzyme complex called pyruvate dehydrogenase. occurs at plasma membrane in prokaryotes
116
what does 3 carbon pyruvate do
removes CO2 and H2 and makes acetyl- CoA
117
products of pyruvate oxidation
for each 3 carbon pryruvate molecule:
1 CO2 removed - decarboxylation by pyruvate dehydrogenase
generates 1 NADH
1 acetyl-CoA which consists of 2 carbons from pyruvate attached to coenzyme A (acetyl-CoA proceeds to Krebs cycle)
118
what is pyruvate when it is oxidized
acetyl-CoA
119
first molecule made in the krebs cycle
citric acid
120
krebs cycle occurs and how
occurs in the matrix of the mitochondria, biochemical pathway of 9 steps in 3 segments
121
3 segments of krebs cycle
1. acetyl-CoA + oxaloacetate = citrate
2. citrate rearrangement and decarboxylation
3. regeneration of oxaloacetate
122
what must be regenerated in the krebs cycle and why
oxaloacetate or cycle will not continue in krebs cycle
123
for each acetyl - CoA entering krebs cycle, what is released and reduced, and produced
1. release: 2 molecules of CO2
2. reduce: 3 NAD+ to 3 NADH
3. reduce: 1 FAD (electron carrier) to FADH2
4. Produce 1 ATP
5. regenerates oxoacetate
124
what is electron transport chain
a series of membrane-bound electron carriers, embedded in the inner mitochondrial membrane, electrons from NADH and FADH2 are transferred to complexes of the ETC
125
each complex in the ETC
a proton pump creating a proton gradient, transfers electrons to the next carrier.
126
where does FADH and NADH accepted in ETC
NADH gives electrons an H, opening pump allowing 3 H to flow,1 FADH skips a pump, only creates 2 ATP while 1 NADH creates 3 ATP
127
theoretical energy yield per glucose for bacteria
38 ATP
128
theoretical energy yield per glucose for eukaryotes
36 ATP
129
actual energy yield per glucose for eukaryotes
30 ATP
130
why is the actual yield reduced?
leaky inner membrane, use of proton gradient for purposes other than ATP synthesis
131
2 key control points of feedback inhibiton
1. in glycolysis - phosphofructokinase is allosterically inhibited by ATP and/or citrate
2. in pyruvate oxidation - pyruvate dehydrogenase inhibited by high levels of NADH, citrate sunthetase inhibited by high levels of ATP
132
oxidation without O2
1. anaerobic respiration - many prokaryotes use sulfur, nitrate, carbon dioxide or even inorganic metals as final electron acceptor
2. fermentation - organic molecules final electron acceptor
133
methanogen anaerobic respiration
CO2 is reduced to CH4 (methane), found in diverse organisms including cows
134
sulfur bacteria anaerobic respiration
inorganic sulphate (SO4) is reduced to hydrogen sulfide (H2S), early sulfate reducers set the stage for evolution of photosynthesis
135
fermentation reduces what
organic molecules in order to regenerate NAD+
136
where does ethanol fermentation occur?
in yeast, CO2, ethanol, and NAD+ are produced
137
lactic acid fermentation occurs where?
animal cells (especially muscles), electrons are transferred from NADH to pyruvate to produce lactic acid
138
catabolism of protein - what do amino acids undergo
deamination to remove amino group, remainder of th amino acid is converted to a molecule that enters glycolysis or the Krebs cycle
139
alanine (protein) is converted to what
pyruvate
140
aspartate (protein) is converted to what
oxaloacetate
141
catobolism of fat - fats are broken down
to fatty acids and glycerol, fatty acids are converted to acetyl groups by B-oxidation, oxygen-dependent process
142
respiration of a 6-carbon fatty acid yields how much more energy than 6-carbon glucose
20% more energy
143
evolution of metabolism
1. ability to store energy in atp
2. evolution of glycolysis
3, anaerobic photosynthesis (using H2S)
4. Use of H2O photosynthesis (not H2S)
5. evolution of nitrogen fixation
6. aerobic respiration evolved most recently
144
how do we get energy from glucose
breaking down glucose slowly and producing ATP through chemiosmosis
145
formula for photosynthesis
6CO2 + 12H2O = C6H12O6 + 6H2O + 6O2
146
how is oxygenic photosynthesis carried out
cynobacteria, 7 groups of algae, all land plants-chloroplasts, more from water than land bc more water than land
147
chloroplasts structure contains
1. thylakoid membrane
2. grana
3. stroma lamella
4. stroma
148
what is the thylakoid membrane
interal choloroplasts membrane, contains chloryphyll and other photosynthetic pigments, pigments clustered into photosystems
149
what is grana
stacks of flattened sacs of thylakoid membrane
150
what is stroma lamella
connect grana
151
what is stroma
semiliquid surrounding thylakoid membranes
152
2 types of reactions of photosynthesis
1. light-dependent reactions
| 2. light independent reactions
153
who was Jan Baptista van Helmont
1550-1644, demonstrated that the substance of the plant was not produced only from the soil, 1st scientist to understand a plant was doing something, watched plant grow
154
Joseph Priestly
1733-1804, living vegetation adds something to the air, candle in jar experiment
155
CB van Niel
1897-1985, found purple bacteria do not release O2 but accumlate sulfur, proposed general formula for photosynthesis, later researchers found O2 produced comes from water
156
what are pigments
molecules that abosorb light energy in the visible range
157
what is a photon
particle of light
158
what does photons do
acts as a discrete bundle of energy, energy content of a photon is inversely proportional to the wavelength of the light
159
what is the photoelectric effect
removal of an electron from a molecule by light
160
how is color shown?
visible light hits pigments and reflects color
161
what happens when a photon strikes a molecule
energy is either lost as heat or absorbed by the electrons of the molecule (boosts electrons into higher energy levels)
162
what is the absorption spectrum
range and efficency of photons molecule is capable of absorbing
163
2 general types of pigments used in green plant photosynthesis
chlorophylls and carotenoids
164
two types of chlorphyll
chlorophyll a and b
165
what is chlorophyll a
main pigments in plants and cyanobacteria, only pigment that can act directly to convert light energy to chemical energy, absorbs violet-blue and red light
166
what isn't in chlorophyll
chloroplasts
167
what is chlorophyll b
accessory pigment or secondary pigment absorbing light wavelength that chlorophyll a does not absorb
168
what are pigments used for
dyes in clothing and photosynthesis in chloroplasts
169
what is the structure of chlorophyll
porphyrin ring
170
describe a porphyrin ring
complex ring structure with alternating double and single bonds, magnesium ion at the center of the ring in chlorophyll, has H-C tail and ring
171
what also has a porphyrin ring
hemoglobin
172
effect of photons on the clorophyll porphyrin ring
photons excite the electrons in the ring, electrons are shuttled away from the ring
173
what is the action spectrum
relative effectiveness of different wavelengths of light in promoting photosynthesis, corresponds to the absorption spectrum for chlorophylls
174
what are carotenoids
carbon rings linked to chains with alternating single and double bonds, can absorb photons with a wide range of energies, also scavenge free radicals (antioxidants-protective role)
175
importance of phycobiloproteins
low-light in ocean areas
176
what is the photosystem organization
-antenna complex and reaction center
177
what is the antenna complex
hundreds of acessory pigment molecules, gather photons and feed the captured light energy to the reaction center, also called light-harvesting complex
178
what do the antenna complexes do
capture photons from sunlight and channels them to the reaction center chlorophylls
179
what do light-harvesting complexes do in chloroplasts
consist of web of chlorophyll molecules linked together and held tightly in the thylakoid membrane by a matrix of protiens
180
what is the reaction center
transmembrane protein-pigment complex, when a chlorophyll in the reaction center absorbs a photon of light, and electron is excited to a higher energy level, light-energized electron can be transferred to the primary electron acceptor, reducing it, oxidized chlorophyll then fills its electron "hole" by oxodizing a donor molecule
181
what happens in the reaction center
e- gets to a higher energy level, leaves a hole, water is e- donor, is split, donates e- to electron center to fill the hole that was left
182
what are the steps in the light-dependent reactions
1. primary photoevent
2. charge separation
3. electron transport
4. chemiosmosis
183
what happens during the primary photoevent
photon of light is captured by a pigment molecule, light excites a pigment
184
what happens during charge separation
energy is transferred to the reaction center, an excited electron is transferred to an acceptor molecule, excited, passed onto another pigment (acceptor molecule)
185
what happens during electron transport
electrons move thru carriers to reduce NADP+
186
what happens during chemiosmosis during light dependent reactions
produces ATP
187
what is cyclic photophosphorylation
in sulfur bacteria, only 1 photosystem used, generates ATP via electron transport, anoxygenic photosynthesis, excited electron passed to electron transport chain, generates a proton gradient for ATP synthesis
188
where does The actual step that converts light energy into chemical energy takes place
in a multiprotein complex called the photosystem
189
what happens in the photosystem one
bacteria, light excites pigment, passed onto enyzyme, electron lost to NADPH, moves onto something else, splitting H2O in PSII to keep passing electrons onto PSI
190
what kind of photosystems do chloroplasts have
PSI (p700) and PSII (p680)
191
oxygenic photosynthesis indicates
2 photosystems linked together
192
what happens in photosystem two
can generate an oxidation potential high enough to oxidize water, creates higher energy potential
193
what do the 2 photosystems do
they carry out a noncyclic transfer of electrons that is used to generate both ATP and NADPH
194
where are 2 photosystems found
in chloroplasts and eukaryotic cells
195
what does PSI makes
transfers electrons ultimately to NADP+ and produces NADPH
196
what happens to the electrons lost from PSI
they are replaced by electrons from PSII
197
what does PSII do to water
oxidizes it to replace electrons transferred to the PSI
198
how are photosystems connected
by cytochrome/ b6-f complex
199
what is noncyclic photophosphorylation
plants using PSI and PSII in series to produce ATP and NADPH, path of electrons is not a circle, photosystems replenished with electrons pbtained by splitting water. Z diagram!
200
what type of photosystems do prokaryote use
they use only photo I, they recycles electrons
201
what type of photosystems do eukaryotes use
undergo PSI and PSII (trees, grass, etc)
202
what is PSII
resembles the reaction center of purple bacteria, core of 10 reansmembrane protein subunits with electron transfer components and 2 P680 chlorophyll, reactions center differs from purple bacteria in that it also contains four manganese atoms
203
what is the purpose of four manganese atoms
essential for the oxidation of water in PSII
204
what is the B6-f complex
proton pump embedded in thylakoid membrane
205
describe reaction center of PSI
consists of a core transmembrane complex consisitng of 12 to 14 protein subunits with 2 bound p700 chlorophyll molecules
206
how do humans make energy
take glucose from plants
207
what do chloroplasts have
ATP synthase enzymes in the thylakoid membrane which allows protons into the stroma
208
what does the stroma contains
enzymes that catalyze the reactions of carbon fixation - calvin cycle reactions
209
what happens in the stroma
ATP, NADH, electron fixes CO2 and produces glucose
210
what does noncyclic photophosphorylation generate
NADPH and ATP, but building organic molecules takes more than energy than that alone
211
what is cyclic photophosphorylation used to do if not enough h2o around
used to produce additional ATP, short circuit PSI to make a larger proton gradient to make more ATP
212
what happens in the calvin cycle
carbon fixation, takes CO2 and fix it to RUBP, rubisco is the enzyme used to form PGA
