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Biochemistry 441B > Photosynthesis > Flashcards

Photosynthesis Flashcards

1
Q

What are the energy sources on the basic metabolic map?

A

Primarily, it will come from carbohydrates and lipids

Secondary, proteins will come after

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2
Q

How is the basic metabolic map separated?

A

Separated into two discrete groups of pathways:

  1. Energy conversion
    Metabolite synthesis/degradation
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3
Q

What are the energy conversion pathways?

A

Glycolysis, Citrate cycle, Oxidative phosphorylation, Photosynthesis and Carbon Fixation (Calvin cycle)

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4
Q

What are the synthesis and degradation pathways?

A

Pentose phosphate pathway, Gluconeogenesis, Glycogen degradation and synthesis, Fatty acid degradation and synthesis, Nitrogen fixation and assimilation, Urea cycle

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5
Q

What is Photosynthesis?

A

Production of energy from the sun

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6
Q

What is another term for the Calvin cycle?

A

Carbon fixation; incorporation of atmospheric CO2 into an organic compound

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7
Q

What is converted in photosynthesis?

A

Converts sunlight energy, CO2, and H2O

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8
Q

What are the products of photosynthesis?

A

Chemical energy (ATP, NADPH), O2, and glyceraldehyde-3-phosphate

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9
Q

Why is photosynthesis essential to life on earth?

A

Provides metabolic fuel to non-photosynthetic organisms such as ourselves

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10
Q

What are photosynthetic autotrophs?

A

They use solar enmergy to oxidize H2O and produce O2, generating chemical energy in the form of glucose (C6H12O6).

The plants uses this glucose at night for metabolic fuel to sustain aerobic respiration.

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11
Q

What are photosynthetic heterotrophs?

A

They cannot convert solar energy into chemical energy directly and therefore depend on photosynthetic autotrophs to generate the O2 and glucose needed for aerobic respiration and to provide those essential nutrients required for life that heterotrophs cannot synthesize themselves.

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12
Q

What is the daily recycling of O2 and CO2?

A

The sun provides light energy to autotrophs, such as plants, which undergo photosynthesis where O2 + Carbohydrates will be given to heterotrophs, such as animals, which will then undergo respiration of CO2 + H2O to under photosynthesis again and repeat.

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13
Q

What two processes do photosynthesis consist of?

A

Light-dependent reactions and Carbon-assimilation/fixation reactions (Calvin cycle).

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14
Q

What are light-dependent reactions?

A

Generate energy-rich NADPH and ATP at the expense of solar energy

Photons are absorbed by chlorophyll molecules

Electrons transport establishes a proton gradient

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15
Q

What are carbon-assimilation/fixation reactions?

A

ATP and NADPH are used to reduce CO2 to form triose phosphates, starch and sucrose.

Enzymes of Calvin cycle use NADPH and ATP to drive carbon fixation

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16
Q

When is the best time of the day for these two reactions?

A

These reactions preform best when exposed to light so during the day.

During the night, these use mitochondrial energy.

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17
Q

Photosynthetic machinery in eukaryotic plant cells is contained within organelles called ________

A

Chloroplasts

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18
Q

How many chloroplasts per cell?

A

10-500 chloroplasts/cell

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19
Q

Do chloroplasts contain their own DNA?

A

Yes

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20
Q

Do mitochondria contain their own DNA?

A

Yes

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21
Q

Name all parts of the anatomy of a chloroplast.

A

Thylakoid membrane, Thylakoids, Thylakoid lumen, Lamella, Stroma, Granum, outer membrane, inner membrane

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22
Q

How many membranes do chloroplast have and what are they?

A

3 membranes: outer, inner, thylakoid membrane

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23
Q

Which membrane of the chloroplast is permeable?

A

Outer membrane

Permeable = lets things across easily

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24
Q

Which membrane of the chloroplast are impermeable?

A

Inner membrane and thylakoid membrane

Impermeable = crossing through membrane is hard

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25
Q

What is the thylakoid lumen?

A

aqueous chamber enclosed by thylakoid membrane

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26
Q

What is the stroma?

A

aqueous phase outside the thylakoid

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27
Q

What is the granum?

A

a stack of thylakoid structures

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28
Q

What is the lamella?

A

an unstacked region of thylakoid membrane

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29
Q

Where is the electron transfer system (chain) located?

A

On the thylakoid membrane

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30
Q

What does electron transfer accompany from the stroma to the thylakoid lumen?

A

H+ translocation

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31
Q

What is the final electron acceptor for photosynthesis and what does it do?

A

NADP+ which generates NADPH in the stroma

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32
Q

What is the ultimate donor and ultimate acceptor in photosynthesis?

A

ultimate donor = water

ultimate acceptor = NADP+

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33
Q

Where does photon absorption take place?

A

PS II and PSI

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34
Q

What creates the uneven pH in photosynthesis?

A

Cyt b6f

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35
Q

Is the increase of protons directly proportional to pH?

A

No, it is inversely proportional as protons increase, the pH decreases

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36
Q

Where does H+ flow out through and what does this lead to?

A

ATP synthase which leads to ATP synthesis in the stroma

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37
Q

Calvin cycle enzymes located in the stroma use _____ and _____ to produce ______ from _____.

A

use NADH and ATP to produce glyceraldehyde-3-phosphate (GAP) from CO2.

38
Q

Where can glyceraldehyde-3-phosphate (GAP) be used?

A

GAP can be used either in the stroma or transported to cytosol.

39
Q

What is Chemiosmotic theory?

A

movement of ions across a semipermeable membrane down their electrochemical gradient

40
Q

For mitochondria, where is the low pH region and the high pH region?

A

Low pH = inter-membrane space
High pH = mitochondrial matrix

Low pH High pH

High [H+] Low [H+]
High positive charge low positive charge

41
Q

For chloroplast, where is the low pH region and the high pH region?

A

High pH = stroma
Low pH = lumen

High pH Low pH

Low [H+] High [H+]
Low positive charge High positive charge

42
Q

What are chromophores?

A

a special molecule that absorbs the light energy

43
Q

What are chromophores associated with?

A

Chromophores are associated with the membrane proteins of photosynthetic organisms

44
Q

What is the most important chromophore?

A

Chlorophyll which is present in PSI and PSII

45
Q

What is chlorophyll?

A

Polycyclic planar structures that resembles heme

Chl molecules have a Mg2+ ion coordinated to the ring nitrogens

An extended hydrophobic side chain, which anchors it to the protein

46
Q

Are chlorophylls highly effective photoreceptors? Why or why not?

A

Yes, the heterocyclic 5-ring system has an extended polyene structure with alternating single and double bonds

They have strong absorption in the visible region of spectrum (where solar output reaching earth is maximal)

Chlorophylls have unusually high molar extinction coefficient

Well-suited for absorbing visible light during photosynthesis

47
Q

What is the most important energy conversion process on Earth?

A

Turning atmospheric CO2 into metabolic fuel

48
Q

What accomplishes the most important energy conversion process on Earth?

A

The Calvin Cycle

49
Q

What is the Calvin Cycle?

A

Carbohydrate biosynthesis in plants

Uses chemical energy (ATP and NADPH) to convert CO2 into triose phosphates

50
Q

Where does the Calvin Cycle take place?

A

Stroma of chloroplasts

51
Q

What are the three stages of the Calvin Cycle?

A
  1. Fixation
  2. Reduction
  3. Regeneration
52
Q

Describe stage 1 of the Calvin Cycle.

A

Stage 1 - CO2 Fixation

This fixation is catalyzed by an enzyme called Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)

3 Ribulose 1,5-bisphosphate + 3CO2 –> 6 3-phoshpglycerate

53
Q

What does Rubisco do in carbon fixation (stage 1)?

A

Rubisco is able to fix oxygen

54
Q

Describe stage 2 of the Calvin Cycle.

A

Stage 2 - Reduction of 3-Phosphoglycerate

3-Phosphoglycerate is REDUCED to Glyceraldehyde-3-phosphate (G3P aka GAP) using NADPH and ATP from the light dependent reactions.

This reduction is catalyzed by 3-Phosphoglycerate kinase and Glyceraldehyde-3-phosphate dehydrogenase
(These are also seen in glycolysis which occurs in the cytosol)

55
Q

Describe stage 3 of the Calvin Cycle.

A

Stage 3 - Regeneration of Ribulose 1,5-bisphosphate

In stage 3, ATP is used to regenerate ribulose-1,5-bisphosphate so that the Calvin cycle can go another round.

56
Q

What is the greenhouse effect?

A

The process by which atmospheric gases, such as CO2, capture and recycle thermal energy radiated by Earth, thus further warming the surface of Earth

57
Q

What important strategies are used to reduce global warming and climate change with the increase of the greenhouse effect?

A

Decreased global production of CO2 and preservation of photosynthetic capacity in tropical rain forests

58
Q

A cyanobacterium absorbs 2856 photons. How many molecules of ATP are produced?

A

For every 8 photons (4 photons PSII and 4 in PSI), 3 ATP are produced where it will be used in the Calvin cycle along with NADPH to produce glyceraldehyde 3-phosphate (GAP, G3P) from CO2.

(2856 photons)(3 ATP/8 photons) = 1071 ATP produced.

59
Q

When a leaf on an oak tree absorbs 15,440 photons, how many glyceraldehyde-3-phosphate molecules can be produced by the Calvin cycle?

A

Using the Calvin cycle reaction:

(15440 photons) (3 ATP/8 photons) = 5790 ATP

For every 9 ATP, 1 G3P is made:

(5790 ATP)(1 G3P/9 ATP) = 643 G3Ps are made

60
Q

In the same oak leaf that absorbed 15,440 photons, how many CO2 molecules are fixed to produce the glyceraldehyde-3-phosphate molecules that are used as building blocks for hexose sugars?

A

Using Calvin cycle reaction:
For every 3 CO2, 1 G3P is produced.

(643 G3P) (3CO2/1G3P) = 1930 CO2 are fixed.

61
Q

In a chloroplast, ATP synthase releases newly synthesized ATP into ______

A

stroma

Generated in the lumen and released out into the stroma

62
Q

What are the three possible outcomes of photon absorption?

A

Fluorescence
Photooxidation
Resonance energy transfer

63
Q

What consequence does fluorescence have on photosynthesis?

A

Energy is wasted as there is no useful work in photosynthesis is accomplished

64
Q

What consequence does photooxidation have on photosynthesis?

A

Important in redox-based energy conversion

Energy transduction occurs in reaction centers, resulting in photoinduced charge separation

65
Q

What consequence does resonance energy transfer have on photosynthesis?

A

Important in “harvesting” light energy

This would make the 2nd electron excited, then the 3rd, and so on.

66
Q

Compare and contrast the structural differences and similarities of chlorophyll and heme.

A

Chlorophyll and heme are both chromophores due to their chemical structures.

Their light-absorbing properties are due to the presence of delocalized electrons above and below the planar ring of single and double bonds.

Each molecule contains a coordinated metal ion in the center of the porphyrin ring: Fe2+ in most hemes and Mg2+ in chlorophyll.

The long hydrophobic tail found in chlorophyll anchors it to pigment proteins.

67
Q

What is the role of most chlorophyll molecules in a photosynthetic membrane?

A

to serve as light-harvesting antennae

Chlorophyll molecules associate with chromophore proteins that are organized into light-harvesting complexes (LHCs). There are two types of LHCs: LHC I and LHC II. The LHCs collect photons and pass them via resonance energy transfer from one chromophore to the next until they reach the specialized chlorophyll molecules in the reaction centers.

68
Q

What are the most abundant proteins in the thylakoid membrane?

A

Light-harvesting complexes (LHCs) which are proteins containing these chromophore molecules that participate in energy transfer reactions (rather than photooxidation)

69
Q

What are the major components and reactions of the photosynthetic Z scheme?

A

PSII:
2H2O –> O2 + 4H+
P680

PSI:
P700

Then:
2 NADP+ –> 2NADPH

The Z scheme represents the flow of electrons through the photoactivated electron transport system found in chloroplasts of plants and in cyanobacteria.
Two different reaction center complexes, photosystems PSII and PSI, are activated by photons. Specifically, PSII absorbs light energy at a wavelength of 680 nm, while PSI absorbs light energy at 700 nm.
A specialized chlorophyll molecule, called P680, located in the PSII reaction center is excited by photon absorption. Excited P680 is oxidized when it transfers its electron to pheophytin, and oxidized P680 is reduced by electrons donated when H2O is oxidized to O2.
PSI contains a pair of chlorophyll molecules, known as P700, that absorb photons and initiate electron flow.
The terminal electron acceptor in the Z scheme is NADP+, which is reduced to NADPH.

70
Q

How do the electrons flow in photosystem I?

A

Electrons enter PSI from electron carriers in the thylakoid lumen and exit PSI via electron carriers in the stroma.

All electron carriers in PSI are embedded in the thylakoid membrane.

71
Q

For every 5,100 protons that move through the chloroplast ATP synthase, how many molecules of ATP are produced?

A

12 protons move through chloroplast ATP synthase producing 3 ATP.

(5100 protons (H+)) (3 ATP / 12 protons) = 1275 ATP produced

72
Q

In the same cell, 5,100 other protons pass through the mitochondrial ATP synthase. How many molecules of ATP are produced?

A

1 ATP is produced for every 3 protons that pass through the mitochondrial ATP synthase.

(5100 protons (H+)) (1 ATP / 3 protons) = 1700 ATP produced

73
Q

When NADPH levels in the stroma are higher than stromal ATP levels, ferredoxin transfers its electron to _________?

A 
plastoquinone PQB 
(not plastoquinone PQA as that happens before PQB)

Since this does not go back to PSII, no oxygen (O2) will be produced.

74
Q

Why is cyclic photophosphorylation an efficient alternative pathway for plant chloroplasts?

A

It restores the 3:2 ratio of ATP to NADPH needed in the stroma for the Calvin cycle to operate.

Increased ATP production at the cost of less reduction of NADP+

75
Q

When PQBH2 levels are high compared to levels of PQB, LHC II complexes are phosphorylated, causing them to redistribute to the ________?

A

Thylakoid lamellae, which leads to increased rates of cyclic photophosphorylation.

When PQBH2 levels are high, an LHC II kinase is activated, resulting in LHC II phosphorylation and movement of LHC II-P from the stacked to unstacked regions of the thylakoid membrane. This causes increased rates of PSI photooxidation and cyclic photophosphorylation.

76
Q

What are the inputs and outputs of the Calvin cycle?

A

Inputs:
CO2, ATP, NADPH

Outputs:
NADP+, ADP + Pi, Triose phosphates

77
Q

Which inputs of the Calvin cycle are produced from the light reactions of photosynthesis and which are produced from the air?

A

From the light reactions:
ATP + NADPH

From the air:
CO2

78
Q

During which stages of the Calvin cycle are NADPH and ATP consumed?

A

stages 2 and 3

In stage 2, the conversion of 3-phosphoglycerate to glyceraldehyde-3-phosphate requires energy in the form of ATP hydrolysis and a reducing agent, in this case, NADPH.
In stage 3, ATP is used to regenerate ribulose-1,5-bisphosphate so that the Calvin cycle can go another round.

79
Q

What are the three mechanisms that control the activity of Calvin cycle enzymes in response to light intensity?

A

There are several light-driven mechanisms that regulate the Calvin cycle so that it operates during the day and is inhibited at night.

TLDR: Enzyme inhibitors (CA1P) active at night, Rubisco and fructose-1,6-bisphosphatase more active when stromal pH and Mg2+ are elevated (daytime means pH increases from pH 7 to pH 8), reduced thioredoxin is available during the daytime (inactive at night).

  1. Several enzyme inhibitors, such as CA1P, bind to enzymes like rubisco and block their activity. These inhibitors are active at night and are inactive during the day.
  2. Rubisco and fructose-1,6-bisphosphatase are more active when stromal pH and Mg2+ are elevated. The light-activated electron transport chain moves protons into the lumen and thus raises the stromal pH to 8. In response to the drop in lumenal pH, Mg2+ ions are pumped out of the lumen into the stroma to balance the charge.
  3. Several Calvin cycle enzymes contain cysteine residue pairs, whose redox state controls the enzymes’ activity. These cysteine pairs spontaneously oxidize, a state that inhibits enzyme activity. When the light-activated electron transport chain is operating, reduced ferredoxin keeps a pool of thioredoxin in a reduced state, which in turn reduces the oxidized cysteine pairs in these Calvin cycle enzymes. When the cysteines are reduced, the enzymes are active.
80
Q

The net change in stage 3 of the Calvin cycle can be represented as?

A

5 C3 → 3 C5

In the carbon shuffle reactions, the total number of carbons does not change, only their distribution does.
Five 3-carbon molecules of glyceraldehyde-3-phosphate and its isomer dihydroxyacetone phosphate are ultimately converted to three 5-carbon molecules of ribulose-1,5-bisphosphate.

81
Q

In stage 2 of the Calvin cycle, phosphoglycerate kinase, triose phosphate isomerase, and glyceraldehyde-3-phosphate dehydrogenase convert 3-phosphoglycerate to dihydroxyacetone phosphate. Which of the three enzymes catalyze reversible reactions?

A

phosphoglycerate kinase, triose phosphate isomerase, and glyceraldehyde-3-phosphate dehydrogenase

The free energy change of the reactions catalyzed by these three enzymes is close to zero in each case. This means that all three of the reactions are reversible.

82
Q

Phosphoglycerate kinase transfers a phosphate group between ATP and 3-phosphoglycerate. In which of the following three pathways does the phosphoglycerate kinase reaction generate ATP?
(Glycolysis, gluconeogenesis, or Calvin cycle?)

A

Glycolysis for energy conversion

In glycolysis, phosphoglycerate kinase transfers a phosphate group from 1,3-bisphosphoglycerate in a substrate-level phosphorylation transfer that yields ATP and 3-phosphoglycerate. This is one of the ATP-producing reactions in the “second half” of glycolysis.
Gluconeogenesis and the Calvin cycle are both anabolic pathways that use phosphoglycerate kinase, but to catalyze the addition of a phosphate group to 3-phosphoglycerate.

83
Q

Where does the conversion of triglycerides to fatty acids take place?

A

lipid stores

84
Q

Where is the location of isocitrate lyase and malate synthase?

A

glyoxysomes

85
Q

Where does the formation of glyoxylate and succinate from isocitrate occur?

A

glyoxysomes

86
Q

Where does the conversion of fatty acids to acetyl-CoA occur?

A

glyoxysomes

87
Q

Where does the hydration of fumarate to form malate occur?

A

mitochondria

88
Q

Where is the site of gluconeogenesis?

A

cytoplasm

89
Q

Where does the conversion of oxaloacetate to phosphoenolpyruvate occur?

A

cytoplasm

90
Q

What is the Glyoxylate Cycle?

A

Converts lipids into carbohydrates in plants

Provides a mechanism for fats stored in seeds to be converted to glucose

Metabolic pathway that converts acetyl CoA molecules into succinate, which serves as the carbon source for glucose biosynthesis

91
Q

What serves as the carbon source for glucose biosynthesis?

A

The Glyoxylate cycle which is a metabolic pathway that converts acetyl CoA molecules into succinate (which takes place in glyoxysomes)

Biochemistry 441B (10 decks)

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