Exam 3 Flashcards

(361 cards)

1
Q

flow of energy

A
  • thermodynamics

- Cells are governed by the laws of physics and chemistry

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2
Q

thermodynamics

A

Branch of chemistry concerned with energy changes

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3
Q

energy

A

Capacity to do work

  • 2 states: kinetic & potential
  • Many forms (mechanical, heat, sound, electric current, light, or radioactivity)
  • Heat is the most convenient way of measuring energy
    a) calories
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4
Q

2 states of energy

A

1) kinetic

2) potential

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5
Q

kinetic energy

A

energy of motion

ex: going down the slide

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6
Q

potential energy

A

stored energy

ex: climbing up the slide

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7
Q

what are some of the many forms of energy?

A
mechanical
heat
sound
electric current
light
radioactivity
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8
Q

__ is the most convenient way of measuring energy

A

heat

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9
Q

1 calorie =

A

heat required to raise 1 g of water 1ºC

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10
Q

calorie of food labels is actually a __

A

kilocalorie

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11
Q

energy flow

A
  • flows into the biological world thru the sun
  • photosynthetic organisms capture this e
  • stored as PE in chem bonds
  • breaking bonds requires e
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12
Q

energy flows into the biological world through the __

A

sun

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13
Q

__ __ capture the energy flow to the world

A

photosynthetic organisms

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14
Q

e in chemical bonds is __ __

A

potential e

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15
Q

redox rxns

A
  • oxidation (atoms or molecules LOSE an e-)
  • reduction (atoms or molecules GAIN an e-)
  • higher level of e than oxidized form
  • oxidation reduction rxn (AKA redox rxn)
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16
Q

oxidation

A

atoms or molecules LOSE an e-

*BECOMES POSITIVE

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17
Q

reduction

A

atoms or molecules GAIN an e-

*BECOMES NEGATIVE

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18
Q

1st law of thermodynamics

A

e cannot be created nor destroyed

  • e can only change from 1 form to another
  • total amnt of e in universe remains constant
  • during each conversion, some e is lost at heat
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19
Q

2nd law of thermodynamics

A

entropy (disorder) is continuously increasing
- Energy transformations proceed spontaneously to convert matter from a more ordered/less stable form to a less ordered/ more stable form

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20
Q

organization requires __

A

energy

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21
Q

disorder happens __

A

spontaneously

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22
Q

free energy

A
G = H – TS
G = Energy available to do work (free e)
H = enthalpy, energy in a molecule’s chemical bonds
T = absolute temp 
S = entropy, unavailable energy
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23
Q

ΔG = ΔH – TS

A

ΔG = change in free energy

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24
Q

positive ΔG

A
  • Products have more free energy than reactants
  • H is higher or S is lower
  • Not spontaneous, requires input of energy
  • Endergonic
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25
negative ΔG
- Products have less free energy than reactants - H is lower or S is higher or both - Spontaneous (may not be instantaneous) - Exergonic
26
endergonic rxn
energy in products > energy in reactants | *e is absorbed
27
exergonic rxn
energy in reactants > energy in products | *e is released
28
activation e
- Extra energy required to destabilize existing bonds and initiate a chemical reaction - Exergonic reaction’s rate depends on the activation energy required a) Larger activation energy proceeds more slowly - Rate can be increased 2 ways
29
a larger activation e proceeds more __
slowly
30
2 ways reaction rate can be increased
1. Increasing energy of reacting molecules (heating) | 2. Lowering activation energy
31
catalysts
- Substances that influence chemical bonds in a way that lowers activation energy - Cannot violate laws of thermodynamics a) Cannot make an endergonic reaction spontaneous - Do not alter the proportion of reactant turned into product
32
ATP
Adenosine triphosphate - Chief “currency” all cells use - Composed of: a) Ribose (5 carbon sugar) b) Adenine c) Chain of 3 phosphates*
33
what is ATP composed of?
- Ribose (5 carbon sugar) - Adenine - Chain of 3 phosphates
34
in ATP, what is the key to e storage?
chain of 3 phosphates - Bonds are unstable (meaning they break off easily bc they want to repel each other) - ADP: 2 phosphates - AMP: 1 phosphate (lowest e form)
35
ATP cycle
- ATP hydrolysis drives endergonic reactions a) Coupled reaction results in net –ΔG (exergonic and spontaneous) - ATP not suitable for long-term energy storage a) Fats and carbohydrates better b) Cells store only a few seconds worth of ATP
36
enzymes: biological catalysts
- most enzymes are protein a) some are RNA (called ribozymes) - shape of enzyme stabilizes a temporary association between substrates - enzyme not changed or consumed in rxn
37
Carbonic anhydrase ex
- 200 molecules of carbonic acid per hour made without enzyme - 600,000 molecules formed per second with enzyme
38
active site
- Pockets or clefts for substrate binding - Forms enzyme–substrate complex - Precise fit of substrate into active site - Applies stress (energy/pressure) on bonds to distort particular bond to lower activation energy a) induced fit
39
forms of enzymes
- Enzymes may be 1) suspended in the cytoplasm (inter-) or 2) attached to cell membranes and organelles (intra-) - multi enzyme complexes
40
multi enzyme complexes
subunits work together to form molecular machine - Product can be delivered easily to next enzyme - Unwanted side reactions prevented - All rxns can be controlled as a unit
41
nonprotein enzymes
- ribozymes - 1981 discovery that certain reactions catalyzed in cells by RNA molecule itself - 2 kinds 1) Intramolecular catalysis 2) Intermolecular catalysis
42
Intramolecular catalysis
catalyze reaction on RNA molecule itself
43
intermolecular catalysis
RNA acts on another molecule
44
enzyme function
- Rate of enzyme-catalyzed reaction depends on concentrations of substrate and enzyme - Any chemical or physical condition that affects the enzyme’s 3D shape can change rate a) optimum temp b) optimum pH
45
inhibitor
substance that binds to enzyme and decreases its activity
46
competitive inhibitor
Competes with substrate for active site
47
noncompetitive inhibitor
- Binds to enzyme at a site other than active site | - Causes shape change that makes enzyme unable to bind substrate
48
allosteric enzymes
enzymes exist in active and inactive forms - Most noncompetitive inhibitors bind to allosteric site (chemical on/off switch) - allosteric inhibitor - allosteric activator
49
allosteric inhibitor
binds to allosteric site and reduces enzyme activity
50
allosteric activator
binds to allosteric site and increases enzyme activity
51
metabolism
Total of all chemical reactions carried out by an organism - anabolism - catabolism
52
Anabolic reactions/anabolism
Expend energy to build up molecules
53
Catabolic reactions/catabolism
Harvest energy by breaking down molecules
54
biochemical pathways
- rxns occur in a sequence - Product of one rxn is the substrate for the next - Many steps take place in specific organelles
55
feedback inhibition
- End-product of pathway binds to an allosteric site on enzyme that catalyzes first reaction in pathway - Shuts down pathway so raw materials and energy are not wasted
56
Most noncompetitive inhibitors bind to __ __
allosteric site
57
allosteric site
chemical on/off switch
58
2 kinds of nonprotein enzymes
1) Intramolecular catalysis | 2) Intermolecular catalysis
59
what chemical/physical condition(s) can change rate of enzyme-catalyzed rxn?
a) optimum temp | b) optimum pH
60
A covalent bond between two atoms represents what kind of energy?
Potential energy
61
During a redox reaction the molecule that gains an electron has been
reduced and now has a higher energy level
62
An endergonic reaction has the following properties
+∆G and the reaction is not spontaneous.
63
A spontaneous reaction is one in which
the reactants have a higher free energy than the products
64
What is activation energy?
The energy required to initiate a chemical reaction
65
Which of the following is NOT a property of a catalyst?
A catalyst lowers the free energy of the reactants.
66
Where is the energy stored in a molecule of ATP?
In the bonds connecting the two terminal phosphate groups
67
Cells use ATP to drive endergonic reactions because
energy released by ATP hydrolysis makes ∆G for coupled reactions more negative.
68
Which of the following statements is NOT true about enzymes?
Enzymes make ∆G for a reaction more negative.
69
ATP hydrolysis has a ∆G of–7.4kcal/mol. Can an endergonic reaction with a ∆G of 12 kcal/mol be “driven” by ATP hydrolysis?
No, the overall ∆G is still positive.
70
An online auction site offers a perpetual-motion machine. You decide not to bid on this because
the Second Law says that energy loss due to entropy will not allow for perpetual motion.
71
Enzymes have similar responses to both changes in temperature and pH. The effect of both is on the
three-dimensional shape of the enzyme.
72
Feedback inhibition is an efficient way to control a metabolic pathway because the
first enzyme in a pathway is inhibited by the end-product of the pathway.
73
respiration
organisms can be classified based on how they obtain e - autotrophs - heterotrophs - all organisms use cell reps to extract e from organic molecules
74
autotrophs
able to produce their own organic molecules thru psyn
75
heterotrophs
live on organic compounds produced by other organisms
76
all organisms use __ __ to extract energy from organic molecules
cellular respiration
77
cellular respiration
- a series of rxns - oxidized - reduced - dehydrogenation
78
oxidized rxns
loss of e-
79
reduced rxns
gain of e-
80
dehydrogenation
lost e- are accompanied by protons | - a H+ atom is lost (1 e-, 1 proton)
81
redox rxns
- e- cary e from one molecule to another - NAD+ - dozens of these rxns take place - number of e- acceptors including NAD+ - in the end, high e e- from initial chm bonds have lost much of their e - transferred to a final e- acceptor
82
NAD+
nicotinamide adenosine dinucleotide - an e- carrier - accepts 2 e- and 1 proton to become NADH - rxn is reversible
83
oxidation-reduction rxn
2 e- and 1 proton are transferred to NAD+ to form NADH | - a second proton is donated to the solution
84
e- acceptors
final e- acceptors are... - aerobic resp: oxygen (O2) - anaerobic resp: inorganic molecule (not O2) - fermentation: organic molecule
85
aerobic resp
C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O - free e: -686 kcal/mol of glucose a) can be even higher than this in a cell b) amnt of e must be released in small steps rather than all at once
86
e- carriers
- many types of carriers used a) soluble, membrane-bound, move within membrane - all carriers can be reversibly oxidized and reduced - some carry just e-, some e- and protons - NAD+ acquires 2 e- and a proton to become NADH
87
ATP
- cells use ATP to drive endergonic rxns a) ∆G (free energy) of hydrolyzing terminal phosphate = -7.3 kcal/mol - 2 mechanisms for synthesis a) substrate-level phosphorylation b) oxidative phosphorylation
88
substrate-level phosphorylation
- transfers phosphate group directly to ADP | - during glycolysis
89
oxidative phosphorylation
- ATP synthase uses e from a proton gradient
90
oxidation of glucose
the complete oxidation of glucose proceeds in stages: 1) glycolysis 2) pyruvate oxidation 3) Krebs cycle 4) ETC & chemiosmosis
91
glycolysis
- converts 1 glucose (6-C) to 2 pyruvate (3-C) - 10 step biochemical pathway - occurs in cytoplasm - net production of 2 ATP molecules by substrate-level phosphorylation - 2 NADH produced by reduction of NAD+
92
NADH must be __
recycled
93
for glycolysis to continue, NADH must be recycled to NAD+ by either __ __ or __
aerobic resp; fermentation
94
aerobic resp
- oxygen is available as the final e- acceptor | - produces significant amnt of ATP
95
fermentation
- occurs when oxygen is not available | - organic molecule is the final e- acceptor
96
fate of pyruvate
- when O2 is present: pyruvate is oxidized to acetyl-CoA which enters the Krebs cycle * aerobic resp - no O2: pyruvate is reduced in order to oxidize NADH back to NAD+
97
the fate of pyruvate depends on __ availability
oxygen
98
pyruvate oxidation
- in the presence of oxygen, pyruvate is oxidized - occurs in the mitochondria in eukaryotes a) pyruvate dehydrogenase catalyzes the rxn - occurs at the plasma membrane in prokaryotes
99
products of pyruvate oxidation
- for each 3-C pyruvate molecule: a) 1 CO2 - decarboxylation by pyruvate dehydrogenase b) 1 NADH c) 1 acetyl-CoA - consists of 2-C from pyruvate attached to CoA - proceeds to Krebs Cycle
100
Krebs cycle
- oxidized acetyl group from pyruvate - occurs in mitochondrial matrix - biochemical pathway of 9 steps in 3 segments
101
3 segments of Krebs Cycle
1) acetyl-CoA + oxaloacetate -> citrate 2) citrate rearrangement and decarboxylation 3) regeneration of oxaloacetate
102
Krebs cycle yield
- for each Acetyl-CoA entering: 1) releases 2 molecules of CO2 2) reduce 3 NAD+ to 3 NADH 3) reduce 1 FAD (e- carrier) to FADH2 4) produce 1 ATP 5) regenerate oxaloacetate
103
glucose yield after Krebs cycle
Glucose has been oxidized to: - 6 CO2 - 4 ATP - 10 NADH - 2 FADH2 a) NADH and FADH2 proceed to ETC b) e- transfer has released 53 kcal/mol of e by gradual e extraction c) e will be put to use to manufacture ATP
104
electron transport chain (ETC)
a series of membrane-bound e- carriers - Embedded in the inner mitochondrial membrane - E- from NADH and FADH2 are transferred to complexes of the ETC - Each complex in the chain operates as a proton pump, driving protons to the intermembrane space - E- move from protein complex to protein complex
105
chemiosmosis
Accumulation of protons in the intermembrane space drives protons into the matrix via diffusion, but this occurs slowly since the membrane is relatively impermeable to ions - most protons can only reenter matrix thru ATP synthase a) uses e of gradient to make ATP from ADP + Pi
106
ATP synthase
ATP synthesis carried out by a tiny rotary motor driven by proton gradient - F0 membrane-bound complex - F1 complex (stalk and knob) has enzymatic activity - Protons travel through F0 channel, which causes F0 to rotate - Mechanical e changes confirmation of catalytic domain in F1
107
energy yield of resp
- theoretical e yield a) 32 ATP per glucose for bacteria b) 30 ATP per glucose for eukaryotes - P/O ratio (phosphate-to-oxygen ratio) is the amnt of ATP synthesized per O2 molecule - theoretical and direct calc of P/O has been contentious and has changed over time
108
regulation of resp
- ex of feedback inhibition - 2 key control points 1) in glycolysis - Phosphofructokinase is allosterically inhibited by ATP and/or citrate 2) in pyruvate oxidation/ Krebs cycle - Pyruvate dehydrogenase inhibited by high levels of NADH - Citrate synthetase inhibited by high levels of ATP
109
oxidation without O2
1) anaerobic resp - Use of inorganic molecules (other than O2) as final e- acceptor - Many prokaryotes use sulfur, nitrate, carbon dioxide or even inorganic metals 2) fermentation - use of organic molecules as final e- acceptor
110
anaerobic resp
- methanogens | - sulfur bacteria
111
methanogens
- CO2 is reduced to CH4 (methane) | - Found in diverse organisms including cows
112
sulfur bacteria
- Inorganic sulfate (SO4) is reduced to hydrogen sulfide (H2S) - Early sulfate reducers set the stage for evolution of photosynthesis
113
fermentation
reduces organic molecules in order to regenerate NAD+ - ethanol fermentation - lactic acid fermentation
114
ethanol fermentation
- occurs in yeast | - CO2, ethanol and NAD+ are produced
115
lactic acid fermentation
- occurs in animal cells (especially muscles) | - e- are transferred from NADH to pyruvate to produce lactic acid
116
catabolism of protein
- amino acids undergo deamination to remove amino group - remainder of amino acid is converted to a molecule that enters glycolysis or the Krebs cycle a) alanine is converted to pyruvate b) aspartate is converted to oxaloacetate c) glutamate is converted to Ketoglutarate
117
in catabolism of protein, alanine is converted to __
pyruvate
118
in catabolism of protein, aspartate is converted to __
oxaloacetate
119
catabolism of fat
- fats are broken down to fatty acids and glycerol a) fatty acids are converted to acetyl groups by ß-oxidation - resp of a 6-C fatty acid yield 20% more e than 6-C glucose
120
The respiration of a 6-carbon fatty acid yields __ more energy than 6-carbon glucose.
20%
121
evolution of metabolism
- hypothetical timeline 1) Ability to store chm e in ATP 2) Evolution of glycolysis - Pathway found in all living organisms 3) Anoxygenic psyn (using H2S) 4) Use of H2O in psyn (not H2S) - Begins permanent change in Earth’s atmosphere 5) Evolution of nitrogen fixation 6) Aerobic resp evolved most recently
122
An autotroph is an organism that
does both a and b a. extracts energy from organic sources. b. converts energy from sunlight into chemical energy
123
Which of the following processes is (are) required for the complete oxidation of glucose?
all of the choices are correct a. The Krebs cycle b. Glycolysis c. Pyruvate oxidation
124
Which of the following is NOT a product of glycolysis?
CO2
125
Glycolysis produces ATP by
substrate-level phosphorylation
126
What is the role of NAD+ in the process of cellular respiration?
It functions as an electron carrier
127
The reactions of the Krebs cycle occur in the
matrix of the mitochondria
128
The electrons carried by NADH and FADH2 can be
moved between proteins in the inner membrane of | the mitochondrion
129
Which of the following is NOT a true statement regarding cellular respiration?
Electrons have a higher potential energy at the end | of the process.
130
The direct source of energy for the ATP produced by ATP synthase comes from
a proton gradient
131
Anaerobic respiration
yields less energy than aerobic respiration because other final electron acceptors have lower affinity for electrons than O2
132
What is the importance of fermentation to cellular metabolism?
It oxidizes NADH to NAD+ in the absence of O2
133
The link between electron transport and ATP synthesis
is a proton gradient.
134
A chemical agent that makes holes in the inner membrane of the mitochondria would
stop ATP synthesis.
135
Yeast cells that have mutations in genes that encode enzymes in glycosides can still grow on glycerol. They are able to utilize glycerol because it
can feed into the Krebs cycle and generate ATP via e- transport and chemiosmosis.
136
Energy for all life on Earth ultimately comes from __
photosynthesis
137
formula for psyn
6CO2 + 12H2O -> C6H12O6 + 6H2O + 6O2
138
Oxygenic photosynthesis is carried out by
- Cyanobacteria - 7 groups of algae - All land plants - chloroplasts
139
stages: light-dependent rxns
Require light 1. Capture energy from sunlight 2. Make ATP and reduce NADP+ to NADPH
140
stages: light-independent rxns/ carbon fixation rxns
–Does not require light | 3.Use ATP and NADPH to synthesize organic molecules from CO2
141
chloroplast
- thylakoid membrane - grana - stroma lamella - stroma
142
thylakoid membrane
internal membrane - Contains chlorophyll and other photosynthetic pigments - Pigments clustered into photosystems
143
grana
stacks of flattened sacs of thylakoid membrane
144
stroma lamella
connect grana
145
stroma
semiliquid surrounding thylakoid membranes
146
Jan Baptista van Helmont (1580–1644)
Demonstrated that the substance of the plant was not produced only from the soil
147
Joseph Priestly (1733–1804)
Living vegetation adds something to the air
148
Jan Ingenhousz (1730–1799)
Proposed plants carry out a process that uses sunlight to split carbon dioxide into carbon and oxygen (O2 gas)
149
F.F. Blackman (1866–1947)
- Came to the startling conclusion that psyn is in fact a multistage process, only one portion of which uses light directly - Light vs dark reactions - Enzymes involved
150
C. B. van Niel (1897–1985)
Found purple sulfur bacteria do not release O2 but accumulate sulfur - Proposed general formula for psyn •CO2 + 2 H2A + light energy → (CH2O) + H2O + 2 A - Later researchers found O2 produced comes from water
151
Robin Hill (1899–1991)
demonstrated Niel was right that light energy could be harvested and used in a reduction reaction
152
pigments
Molecules that absorb light energy in the visible range •Light is a form of energy •Photon •Photoelectric effect
153
photon
particle of light - Acts as a discrete bundle of energy - Energy content of a photon is inversely proportional to the wavelength of the light
154
light is a form of __
energy
155
photoelectric effect
removal of an electron from a molecule by light
156
Absorption spectrum
range and efficiency of photons molecule is capable of absorbing
157
When a photon strikes a molecule, its energy is either
- Lost as heat - Absorbed by the e- of the molecule •Boosts electrons into higher energy level
158
pigments in psyn
- Organisms have evolved a variety of different pigments - Only two general types are used in green plant photosynthesis a) Chlorophylls b) Carotenoids - In some organisms, other molecules also absorb light energy
159
Chlorophyll a
- Main pigment in plants and cyanobacteria - Only pigment that can act directly to convert light energy to chemical energy - Absorbs violet-blue and red light
160
chlorophyll b
Accessory pigment or secondary pigment absorbing light wavelengths that chlorophyll a does not absorb
161
structure of chlorophyll
- Porphyrin ring - Photons excite electrons in the ring - Electrons are shuttled away from the ring
162
Porphyrin ring
- Complex ring structure with alternating double and single bonds - Magnesium ion at the center of the ring
163
action spectrum
- Relative effectiveness of different wavelengths of light in promoting photosynthesis - corresponds to the absorption spectrum for chlorophylls
164
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- antioxidant •Protective role
165
Phycobiloproteins
Important in low-light ocean areas
166
Photosystem organization
Light is captured by photosystems, each of which consists of two components 1) Antenna complex 2) Reaction center
167
antenna complex
- Hundreds of accessory pigment molecules - Gather photons and feed the captured light e to the rxn center - aka light-harvesting complex - Captures photons from sunlight & channels them to the rxn center chlorophylls - In chloroplasts, light-harvesting complexes consist of a web of chlorophyll molecules linked together & held tightly in the thylakoid membrane by a matrix of proteins
168
reaction center
- 1 or more chlorophyll a molecules - Passes excited electrons out of the photosystem - transmembrane protein–pigment complex •When a chlorophyll in the rxn center absorbs a photon of light, an e- is excited to a higher e level •Light-energized e- can be transferred to the primary electron acceptor, reducing it •Oxidized chlorophyll then fills its electron “hole” by oxidizing a donor molecule
169
light-dependent rxns
1. Primary photoevent 2. Charge separation 3. Electron transport 4. Chemiosmosis
170
Primary photoevent
Photon of light is captured by a pigment molecule
171
charge separation
Energy is transferred to the reaction center; an excited electron is transferred to an acceptor molecule
172
Electron transport
Electrons move through carriers to reduce NADP+
173
chemiosmosis
produces ATP
174
cyclic photophosphorylation
- In sulfur bacteria, only one photosystem is used - Generates ATP via electron transport - Anoxygenic photosynthesis - Excited electron passed to electron transport chain - Generates a proton gradient for ATP synthesis
175
chloroplasts have 2 connected photosystems
- Oxygenic photosynthesis - Photosystem I (P700): Functions like sulfur bacteria - Photosystem II (P680): Can generate an oxidation potential high enough to oxidize water - Working together, the two photosystems carry out a noncyclic transfer of e- that is used to generate both ATP and NADPH
176
photosystem I and II
- Photosystem I transfers e- ultimately to NADP+, producing NADPH - E- lost from photosystem I are replaced by e- from photosystem II - Photosystem II oxidizes water to replace the e- transferred to photosystem I - 2 photosystems connected by cytochrome/ b6-f complex
177
noncyclic phosphorylation
- Plants use photosystems II and I in series to produce both ATP and NADPH - Path of electrons not a circle - Photosystems replenished with e- obtained by splitting water - Z diagram
178
photosystem II
- Resembles the reaction center of purple bacteria •Core of 10 transmembrane protein subunits with e- transfer components & two P680 chlorophyll molecules - Reaction center differs from purple bacteria in that it also contains four manganese atoms a) Essential for the oxidation of water - b6-f complex a) Proton pump embedded in thylakoid membrane
179
photosystem I
- Rxn center consists of a core transmembrane complex consisting of 12 to 14 protein subunits with two bound P700 chlorophyll molecules - Photosystem I accepts an e- from plastocyanin into the “hole” created by the exit of a light-energized e- - Passes electrons to NADP+ to form NADPH
180
chemiosmosis
- Electrochemical gradient can be used to synthesize ATP - Chloroplast has ATP synthase enzymes in the thylakoid membrane a) Allows protons back into stroma - Stroma also contains enzymes that catalyze the reactions of carbon fixation-the Calvin cycle reactions
181
production of additional ATP
•Noncyclic photophosphorylation generates NADPH and ATP •Building organic molecules takes more energy than that alone •Cyclic photophosphorylation used to produce additional ATP –Short-circuit photosystem I to make a larger proton gradient to make more ATP
182
carbon fixation- calvin cycle
``` To build carbohydrates cells use: – Energy •ATP from light-dependent reactions •Cyclic and noncyclic photophosphorylation •Drives endergonic reaction – Reduction potential •NADPH from photosystem I •Source of protons and energetic electrons ```
183
calvin cycle
Named after Melvin Calvin (1911–1997) •Also called C3 psyn •Key step is attachment of CO2 to RuBP to form PGA •Uses enzyme ribulose bisphosphate carboxylase/oxygenase or rubisco
184
3 phases of the calvin cycle
1. Carbon fixation 2. Reduction 3. Regeneration of RuBP
185
calvin cycle: carbon fixation
RuBP + CO2 → PGA
186
calvin cycle: reduction
PGA is reduced to G3P
187
calvin cycle: regeneration of RuBP
–PGA is used to regenerate RuBP •3 turns incorporate enough carbon to produce a new G3P •6 turns incorporate enough carbon for 1 glucose
188
output of calvin cycle
``` Glucose is not a direct product of the Calvin cycle •G3P is a 3 carbon sugar –Used to form sucrose •Major transport sugar in plants •Disaccharide made of fructose and glucose –Used to make starch •Insoluble glucose polymer •Stored for later use ```
189
energy cycle
Psyn uses the products of respiration as starting substrates •Resp uses the products of psyn as starting substrates •Production of glucose from G3P even uses part of the ancient glycolytic pathway, run in reverse •Principal proteins involved in e- transport & ATP production in plants are evolutionarily related to those in mitochondria
190
photorespiration
Rubisco has 2 enzymatic activities –Carboxylation –Photorespiration •CO2 and O2 compete for the active site on RuBP
191
carboxylation
* Addition of CO2 to RuBP | * Favored under normal conditions
192
photorespiration
* Oxidation of RuBP by the addition of O2 | * Favored when stoma are closed in hot conditions •Creates low-CO2 and high-O2
193
types of psyn
• C3 –Plants that fix carbon using only C3 photosynthesis (the Calvin cycle) • C4 and CAM –Add CO2 to PEP to form 4 carbon molecule –Use PEP carboxylase –Greater affinity for CO2, no oxidase activity –C4: spatial solution –CAM: temporal solution (time difference)
194
C4 plants
- Corn, sugarcane, sorghum, and a number of other grasses - Initially fix carbon using PEP carboxylase in mesophyll cells - Produces oxaloacetate, converted to malate, transported to bundle-sheath cells - Within the bundle-sheath cells, malate is decarboxylated to produce pyruvate and CO2 - Carbon fixation then by rubisco and the Calvin cycle
195
C4 pathway
- it overcomes the problems of photorespiration - does have a cost - To produce a single glucose requires 12 additional ATP compared with the Calvin cycle alone - C4 psyn is advantageous in hot dry climates where photorespiration would remove more than half of the carbon fixed by the usual C3 pathway alone
196
CAM plants
•Many succulent (water-storing) plants, such as cacti, pineapples, and some members of about two dozen other plant groups •Stomata open during the night & close during the day – Reverse of that in most plants •Fix CO2 using PEP carboxylase during the night and store in vacuole •When stomata closed during the day, organic acids are decarboxylated to yield high levels of CO2 •High levels of CO2 drive the Calvin cycle and minimize photorespiration
197
C4 and CAM
- Both use both C3 and C4 pathways •C4: two pathways occur in different cells •CAM: C4 pathway at night and the C3 pathway during the day
198
the light-dependent rxns of psyn are responsible for the production of
ATP and NADPH
199
Which region of a chloroplast is associated with the capture of light energy?
Thylakoid membrane
200
The colors of light that are most effective for photosynthesis are
red, blue, and violet
201
During noncyclic photosynthesis, photosystem I functions to ___________, and photosystem II functions to ______________.
reduce NADP+; oxidize H2O
202
How is a reaction center pigment in a photosystem different from a pigment in the antenna complex?
The reaction center pigment loses an electron when it absorbs light energy.
203
The ATP and NADPH from the light reactions are used
during the reactions of the Calvin cycle to produce glucose.
204
The carbon fixation reaction converts
inorganic carbon into an organic acid.
205
C4 plants initially fix carbon by
incorporating CO2 into oxaloacetate, which is converted to malate.
206
The overall flow of electrons in the light reactions is from
H2O to NADPH.
207
If you could measure pH within a chloroplast, where would it be lowest?
In the lumen of the thylakoid
208
The excited electron from photosystem I
Both a and c are correct. a. can be returned to the reaction center to generate ATP by cyclic photophosphorylation. c. is replaced by an electron from photosystem II.
209
If the Calvin cycle runs through six turns
enough carbon will be fixed to make one glucose, but they will not all be in the same molecule.
210
Which of the following are similarities between the structure and function of mitochondria and chloroplasts?
Both a and c are correct. a. They both create internal proton gradients by electron transport. reactions. c. They both have a double membrane system.
211
Given that the C4 pathway gets around the problems of photorespiration, why don’t all plants use it?
It also has an energetic cost.
212
if the thylakoid membrane became leaky to ions, what would you predict to be the result on the light reactions?
It would stop ATP production.
213
the overall process of photosynthesis
results in the reduction of CO2 and the oxidation of H2O.
214
the optimum temp for human enzyme is at __
42ºC
215
at 50ºC, the enzyme will be __
degraded
216
optimal temp for humans
37ºC
217
optimum temp for enzyme from hot springs prokaryote
72ºC
218
competitve inhibition
substrate binds to block
219
allosteric inhibition (noncompetitive)
allosteric binds somewhere else to give off a lock to block it
220
anaerobic vs aerobic
anaerobic: no oxygen, undergoes fermentation aerobic: oxygen present, undergoes cell resp in the mitochondria
221
the longer the wavelength the __ the energy; the shorter the wavelength the __ the energy
lower; higher
222
plants use the visible wavelengths of light to...
capture e
223
colors on the wavelength spectrum: ROYGBIV
``` red orange yellow green blue indigo violet ```
224
chlorophyll __ green light
reflects
225
carotenoids absorb __ lights
green, yellow, orange, red
226
the Calvin cycle is also known as __
light independent reactions
227
Communication between cells requires
- Ligand - Receptor protein - Interaction of these two components initiates the process of signal transduction, which converts the information in the signal into a cellular response
228
ligand
signaling molecule
229
receptor protein
molecule to which the receptor binds
230
types of cell signaling
four basic mechanisms for cellular communication: 1) Direct contact 2) Paracrine signaling 3) Endocrine signaling 4) Synaptic signaling - Some cells send signals to themselves (autocrine signaling)
231
direct contact
- Molecules on the surface of one cell are recognized by receptors on the adjacent cell Important in early development - Gap junctions
232
paracrine signaling
- Signal released from a cell has an effect on neighboring cells - Important in early development - Coordinates clusters of neighboring cells - Signaling between immune cells
233
endocrine signaling
- Hormones released from a cell travel through circulatory system to affect other cells throughout the body - Both animals and plants use this mechanism extensively
234
synaptic signaling
- Occurs in animals - Nerve cells release the signal (neurotransmitter) which binds to receptors on nearby cells - Association of neuron and target cell is a chemical synapse
235
signal transduction
- Events within the cell that occur in response to a signal - When a ligand binds to a receptor protein, the cell has a response - Different cell types can have similar response to the same signal a) Glucagon example - Different cell types can respond differently to the same signal a) Epinephrine example
236
phosphorylation
- Addition of phosphate group - A cell’s response to a signal often involves activating or inactivating proteins - Phosphorylation is a common way to change the activity of a protein - Protein kinase - Phosphatase
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protein kinase
an enzyme that adds a phosphate to a protein
238
phosphatase
an enzyme that removes a phosphate from a protein
239
receptor types
- Receptors can be defined by their location 1) Intracellular receptor 2) Cell surface receptor or membrane receptor
240
intracellular receptor
located within the cell - bind to hydrophobic ligands - bind non polar ligands - steroid hormones
241
Cell surface receptor or membrane receptor
- located on the plasma membrane to bind a ligand outside the cell - bind polar ligands a) Transmembrane protein in contact with both the cytoplasm and the extracellular environment
242
3 Subclasses of membrane receptors
1) Chemically gated ion channels 2) Enzymatic receptors 3) G protein-coupled receptor
243
Chemically gated ion channels
channel-linked receptors that open to let a specific ion pass in response to a ligand
244
enzymatic receptors
receptor is an enzyme that is activated by the ligand | a) almost all are protein kinases
245
G protein-coupled receptor
a G-protein (bound to GTP) assists in transmitting the signal from receptor to enzyme (effector)
246
steroid hormones
- Common nonpolar, lipid-soluble structure - Can cross the plasma membrane to an intracellular steroid receptor - Binding of the hormone to the receptor causes the complex to shift from the cytoplasm to the nucleus - Act as regulators of gene expression
247
steroid hormone receptors
- 3 functional domains 1) Hormone-binding domain 2) DNA-binding domain 3) Domain that interacts with coactivators to affect level of gene transcription - In its inactive state, the receptor typically cannot bind to DNA because an inhibitor protein occupies the DNA binding site - Binding of ligand changes conformation
248
coactivators
- Target cell’s response to a lipid-soluble cell signal can vary enormously, depending on the nature of the cell - Even the same type of cell may have different responses - Depends on coactivators present - Estrogen has different effects in uterine tissue than mammary tissue a) Regulation is not by presence or absence of receptor b) Instead presence or absence of coactivator
249
intracellular receptors as enzymes
- Intracellular receptors can act as enzymes - Nitric oxide (NO) is a small gas molecule that can diffuse in and out of cells - NO binds to guanylyl cyclase, enabling it to catalyze the synthesis of cyclic guanosine monophosphate (cGMP) - cGMP is an intracellular messenger molecule that relaxes smooth muscle cells
250
Paracrine signaling is characterized by ligands that are
secreted by neighboring cells
251
signal transduction pathways
include the intracellular events stimulated by an extracellular signal
252
the function of a __ is to add phosphates to proteins, whereas a __ functions to remove the phosphates
protein kinase, protein phosphatase
253
which of the following receptor types is NOT a membrane receptor a. channel-like receptor b. enzymatic receptor c. G protein-coupled receptor d. steroid hormone receptors
steroid hormone receptors
254
how does the function of an intracellular receptor differ from that of a membrane receptor?
the intracellular receptor binds DNA
255
signaling through receptor tyrosine kinases often
leads to the activation of a cascade of kinase enzymes
256
what is the function of Ras during tyrosine kinase cell signaling?
it links the receptor protein to the MAP kinase pathway
257
which of the following best describes the immediate effect of ligand binding to a G protein-coupled receptor?
the G protein trimer releases a GDP and binds a GTP
258
the action of steroid hormones is often longer-lived than that of peptide hormones. this is because they
they turn on gene expression to produce proteins that persist in the cell
259
the ion Ca2+ can act as a second messenger because it is
normally at a low level in the cytoplasm
260
different receptors can have the same effect on a cell. one reason for this is that
signal transduction pathways intersect- the same pathway can be stimulated by different receptors
261
in comparing small G proteins like Ras and GPCR proteins, we can say that
both proteins have intrinsic GTPase activity that stops signaling & both proteins are active bound to GTP
262
the same signal can have different effects in different cells because there
a. are different receptor subtypes that initiate different signal transduction pathways. b. may be different coactivators in different cells. c. may be different target proteins in different cells’ signal transduction pathways.
263
The receptors for steroid hormones and peptide hormones are fundamentally different because
peptides are hydrophilic and steroids are hydrophobic
264
what are the intermediates of the Krebs cycle?
“Can I Keep Selling Substances For Money, Officer?” oxaloacetate (4C) and acetyl-CoA work to make citrate (6C) -> isocitrate (6C) -> a-Ketoglutarate (5C) -> succinyl-CoA (4C) -> succinate (4C) -> fumarate (4C) *FADH to FAD -> malate (4C) *H2O -> oxaloacetate (4C) ``` “Can I Keep Selling Substances For Money, Officer?” Citrate Isocitrate Ketoglutarate Succinyl CoA Succinate Fumarate Malate Oxaloacetate ```
265
doorbell and finger example
ligand is finger receptor is the doorbell push button, signal transduction takes place door bell ringing, stimulating the signal to go off
266
phosphorylation
how response is regulated | -kinase
267
dephosphorylation
phosphatase removes phosphate from protein
268
steroids are __
lipids
269
receptor kinases
- protein kinases phosphorylate proteins to alter protein function - receptor tyrosine kinases (RTK)
270
RTKs
- Influence cell cycle, cell migration, cell metabolism, and cell proliferation a) Alteration to function can lead to cancer - Membrane receptor - Plants possess receptors with a similar overall structure and function - have 3 domains - When a ligand binds, dimerization and autophosphorylation occur - Cellular response follows – depends on cellular response proteins
271
RTKs deal with what 3 amino acids?
Ser Thr Tyr
272
kinases __
phosphorylate
273
what are the 3 domains of RTKs
- a single transmembrane domain a) Anchors them in membrane - Extracellular ligand-binding domain - Intracellular kinase domain a) Catalytic site of receptor acts as protein kinase
274
insulin receptor
- Activated receptor has phosphorylated sites that allow docking - Insulin binds to an RTK; insulin response protein binds to the phosphorylated receptor and is itself phosphorylated; signal is transmitted downstream to lower blood sugar
275
insulin
a hormone that helps to maintain a constant blood glucose level
276
kinase cascade
series of proteins that phosphorylate other proteins | - Mitogen-activated protein (MAP) kinases
277
Mitogen-activated protein (MAP) kinases
- class of cytoplasmic kinases - mitogen stimulates cell division - Activated by signaling module called a phosphorylation cascade/kinase cascade - Series of protein kinases that phosphorylate each other in succession - Amplifies the signal because a few signal molecules can elicit a large cell response
278
signal amplification
signal -> receptor -> activator -> kinase cascade -> response proteins -> cell responses
279
scaffold proteins
- bind series of kinases on 1 protein - goes very quickly; leads to rapid response/transfer - Thought to organize the components of a kinase cascade into a single protein complex - Binds to each individual kinase such that they are spatially organized for optimal function - Benefit in efficiency - Disadvantage in reducing amplification effect
280
Ras proteins
- Small GTP-binding protein (G protein) - Link between the RTK and the MAP kinase cascade - is mutated in many human tumors, indicative of its central role in linking growth factor receptors to their cell response - is active when bound to GTP - inactive when bound to GDP - Ras switch is flipped by exchanging GDP for GTP (stimulated by GEFs) and by Ras hydrolyzing GTP to GDP. - Activated Ras activates the first kinase in the MAP kinase cascade - Ras can regulate itself – stimulation by growth factors is short-lived
281
G protein-coupled receptors (GPCRs)
- Single largest category of receptor type in animal cells - Receptors act by coupling with a G protein - G protein provides link between receptor that receives signal and effector protein that produces cellular response - All G proteins are active when bound to GTP and inactive when bound to GDP - Effector proteins are usually enzymes
282
effector proteins are usually __
enzymes
283
second messengers
stimulate the activation of processes in the cell - Often, the effector proteins activated by G proteins produce a second messenger - 2 common effectors 1) Adenylyl cyclase 2) Phospholipase C
284
adenylyl cyclase
- Produces cAMP - cAMP binds to and activates the enzyme protein kinase A (PKA) - PKA adds phosphates to specific proteins
285
phospholipase C
- PIP2 is acted on by effector protein phospholipase C - Produces IP3 plus DAG a) IP3 leads to produce calcium - Both act as second messengers
286
Inositol Phosphates and calcium
- Ca^(2+) serves widely as second messenger - Intracellular levels normally low - Extracellular levels quite high - IP3 binds to receptors on the ER, signals the release of Ca^(2+) - Ca^(2+) initiates some cellular responses by binding to calmodulin
287
response to second messengers
- Different receptors can produce the same second messengers - Hormones glucagon and epinephrine can both stimulate liver cells to mobilize glucose a) Different signals, same effect b) Both act by same signal transduction pathway
288
epinephrine
boosts u up
289
receptor subtypes
- Single signaling molecule can have different effects in different cells - Existence of multiple forms of the same receptor (subtypes or isoforms) - Receptor for epinephrine has 9 isoforms a) Encoded by different genes b) Sequences are similar but differ in their cytoplasmic domains - Different isoforms activate different G proteins leading to different signal transduction pathways
290
GPCRs and RTKs can activate same pathways
- RTKs and GPCRs can both activate the MAP kinase cascade - RTKs and GPCRs can both activate phospholipase C - Cross-reactivity provides cells with flexibility
291
non polar __ pass thru the phospholipid bilayer
can
292
3 things that happen when an RTK is stimulated
1. ligand binds to RTK 2. RTK will dimerize 3. dimerized form will autophosphorylate each other 4. phosphorylated form will phosphorylate other proteins and those proteins will do the same throughout cell
293
coupled receptor
- not gonna be directly responding | - activated which will then result in activating effector proteins to respond
294
example of an RTK
insulin receptor
295
end process of insulin receptor
taking glucose out of circulatory system and forming glycogen, a stored form
296
unlike insulin, glucagon and epinephrine..
stimulate breakdown of glycogen to release glucose into the system
297
every time u lose an carbon,
energy is released and captured by e- carrier
298
purpose of cell resp is to produce
ATP
299
NAD+
accepts e- and becomes reduced to NADH
300
glycolysis
Occurs in the cytosol of the cell Begins cell resp by breaking glucose into 2 molecules of a 3-C compound called pyruvate begins w a single molecule of glucose and concludes w/ 2 molecules of pyruvate Glucose has 6-C, same 6-C end up in 2 molecules of pyruvate
301
pyruvate oxidation in krebs cycle
Takes place within the mitochondria Pyruvate is oxidized to a 2-C compound The citric acid cycle then completes the breakdown of glucose to CO2 The cell makes a small amnt of ATP during glycolysis and the citric acid cycle Main function of first 2 stages is to supply the 3rd stage of resp w/ e-
302
oxidative phosphorylation
happens in inner mito membrane Involves e- transport and chemiosmosis Most of ATP produced by cell resp is generated here The e- are finally passed to O2, which becomes reduced to H2O As e- are passed down the e staircase, the ETC also pumps H+ ions across the inner mitochondrial membrane into narrow intermembrane space Result is a conc gradient of H+ across the membrane In chemiosmosis, the PE of this conc gradient is used to make ATP
303
substrate level phosphorylation
an enzyme transfers a phosphate group from a substrate molecule to ADP, forming ATP ATP is also generated by this in the citric acid cycle
304
does pyruvate enter the Krebs cycle?
no
305
parts of the mitochondria
- outer membranes - intermembrane space - inner membranes (oxidative phos) - matrix (citric acid cycle)
306
NADH and FADH2 go thru the __
ETC
307
carbon cycle
C cycles from CO2 to glucose and back to CO2; uses the high e molecules to make glucose from CO2
308
pyruvate is a _C molecule
3
309
products of glycolysis
2 net ATP, 2 NADH, 2 pyruvates
310
products of the citric acid cycle
ATP, NADH, and FADH2, CO2
311
products of oxidative phosphorylation
2 pyruvates, 2 H2O, 2 ATP, 2 NADH, and 2 (H+)
312
cell resp equation
C6H12O6 + 6O2 → 6CO2 + 6H2O (glucose + oxygen -> carbon dioxide + water)
313
psyn equation
6CO2 + 6H2O + light energy = C6H12O6 + 6O2
314
products of grooming pyruvate
NADH, CO2, acetyl Co-A
315
energy in glucose must be converted into __, which is very reactive and can be used by cells
ATP
316
main point of chemiosmosis
H+ moves down conc gradient, use ATP synthase, and make ATP
317
main point of ETC
put e- in protein to pump H+ protons from mito matrix to inner membrane
318
main purpose of light rxn
ATP and NADPH; use light e to convert low to high e molecules
319
main purpose of dark rxn
make CO2 into glucose
320
psyn
Plants make glucose & O2 from e in sunlight, CO2, and H2O In chloroplasts
321
chlorophyll
a light-absorbing pigment in the chloroplasts that plays a central role in converting solar e to chem e
322
2 membranes in chloroplast
thylakoids and stroma
323
which way do e- move in psyn?
Water is split, and its e- are transferred along w/ H+ ions to CO2, reducing it to sugar. The PE of e- increases as they move from H2O to CO2. the light e captured by chlorophyll molecules in the chloroplast provides this e boost
324
e- acceptor of psyn
NADP+
325
NADPH
temporarily stores e- and provides “reducing power” to the calvin cycle
326
sugar isn't made in psyn until ____
Calvin cycle
327
Calvin cycle
occurs in the stroma of chloroplast; a cyclic series of rxns that assembles sugar molecules using CO2 and the e rich products of the light rxns; sometimes referred to as “dark rxns” or “light-independent rxns” bc none of the steps requires light directly
328
carbon fixation
the incorporation of C from CO2 into organic compounds | After carbon fixation, the carbon compounds are reduced to sugars
329
In the stroma, the enzyme __ combines CO2 with RuBP
rubisco
330
ATP and NADPH are used to reduce a 3C intermediate to__
G3P
331
the more ordered something is the __ energy it has
less
332
example for ordered
less ordered room to a more ordered room, u put in energy to get ur room clean. therefore, the energy is released
333
disorder happens __
spontaneously
334
- ΔG
products have less free e - exergonic - spontaneous
335
+ ΔG
products have more free e - endergonic - ordered
336
shape of enzymes affects the _ of the rxn
rate
337
in catabolism of protein, glutamate is converted to __
Ketoglutarate
338
competitive vs non-competitive inhibition
competitive: - binds to the site of the substrate - it inhibits the substrate from binding - decreases activity of enzyme * competes for active site non-competitive: - binds to an allosteric site or site on another part of the enzyme - changes the SHAPE of enzyme - substrate doesn't match the shape - aka allosteric inhibition
339
allosteric inhibition is an __
on/off switch
340
active vs inactive inhibition
``` active: - allosteric activator - increases enzyme activity - products formed inactive: - allosteric inhibitor - decreases enzyme activity - no products formed ```
341
the glycolytic pathway
glucose -> glucose 6-phosphate -> fructose 6-phosphate -> fructose 1, 6-biphosphate ** separates into 2 1) dihydroxyacetone phosphate 2) glyceraldehyde 3-phosphate (G3P) - 1, 3- diphosphoglycerate (BPG) - 3- phosphoglycerate (3 PG) - 2- phosphoglycerate (2 PG) - phosphoenolpyruvate (PEP) - pyruvate
342
enzymes of the Krebs cycle
Acetyl-CoA + oxolacetate -> citrate synthase, -> citrate -> aconitase, ->isocitrate -> isocitrate dehydrogenase, --> Ketoglutarate -> Ketoglutarate dehydrogenase, -> succinyl-CoA -> succinyl CoA synthase, -> succinate -> succinate dehydrogenase, -> fumarate -> fumarase, -> malate -> malate dehydrogenase -> oxolacetate
343
products of the Krebs cycle
- 3 NADH net: 6 - 2 CO2 net: 4 - 1 ATP net: 2 - 1 FADH2 net: 2
344
net means
x 2 to get overall #
345
c4 plants diagram
mesophyll vs bundle sheath -mesophyll: O2 + PEP = 5C -> oxolacetate -> malate (4C) -> *enters bundle sheath shell* -> 1) pyruvate 2) CO2 -> enters Calvin cycle -> G3P -> glucose
346
CAM plants diagram
night vs day night: CO2 -> C4 -> CO2 -> Calvin cycle -> G3P
347
What oxidizing agent is used to temporarily store high energy electrons harvested from glucose molecules in a series of gradual steps in the cytoplasm?
NAD+
348
an exergonic rxn occurs __
spontaneously
349
what is activation e?
The energy required to initiate a chemical reaction.
350
NADPH is made by
the passing of electrons from photosystem I to an electron transport chain.
351
in aerobic respiration, chemiosmotic generation of ATP is driven by:
a difference in H+ concentration on the two sides of the inner mitochondrialmembrane.
352
For photosynthesis in green plants, the electron donor for the light dependent reaction is
water
353
What color of light is least strongly absorbed by chlorophyll?
green
354
ATP hydrolysis drives __ reactions
endergonic
355
Visible light has a wavelength range of
400-740 nanometers.
356
What happens to the oxygen that is used in cellular respiration?
its reduced to make water
357
Most enzymes are composed of ___
proteins
358
what are the common monosaccharides?
glucose and fructose
359
what are the common disaccharides?
sucrose, lactose, and maltose
360
what are the common polysaccharides?
starch and glycogen
361
The Krebs Cycle is an __ pathway, while the Calvin cycle is an ___ pathway
Amphibolic ; anabolic