Metabolism and Assimilation

As we go through metabolism and assimilation, remember that the materials for building all of those fantastic structural components we've covered come from CO₂, H₂O, and a handful of soil minerals.

Also note: food = a carbon-containing molecule with calories; nutrient = inorganic mineral

These two processes have many things in common.
1. Both processes occur in organelles with complex internal membrane systems that are essential to the processes.
2. Both processes rely on existing molecules in cells to carry out the energy conversion reactions.
3. Both processes involve synthesis of ATP.
4. Photosynthesis and respiration are essentially the reverse of each other. Photosynthesis starts with CO₂ and converts the C to sugar; this conversion requires energy, which is obtained from light. Respiration starts with sugar and converts the sugar C to CO₂; this process releases energy some of which is collected as ATP. In order to get the chemicals needed to change CO₂to sugar, photosynthesis changes H₂O to O₂ and H (actually, H⁺ and electrons). Respiration uses H (actually, H⁺ and electrons) obtained from sugar to change O₂to H₂O.

------ energy input from light ----->
6 CO₂ + 12 H₂O ------------------------------------------ C₆H₁₂O₆ + 6 O₂ + 6 H₂O
<---- energy output as ATP and heat -------

Four Elements: earth, water, air, fire. The first two have weight; the second two do not.

"I took an earthenware pot, placed in it 200 lbs of earth dried in an oven, soaked this with water, and placed in it a willow shoot weighing 5 lbs. To prevent dust flying around from mixing with the earth, the top of the pot was kept covered with an iron plate coated with tin and pierced with many holes. After five years had passed, the tree growth therefrom weighed 169 lb and about 3 oz. I did not compute the weight of the deciduous leaves of the four autumns. Finally, I again dried the earth of the pot, and it was found to be the same 200 lb minus about 2 oz.

Successfully showed that plants don’t eat dirt; the paradigm of the time of four elements led van Helmont to only half of the answer as to where the increase in plant mass had come from.

1772: Joseph Priestly showed that a spring of mint could "restore" contaminated air, i.e. release O₂

1779: Jan Ingen-Housz showed that green plant parts and light were required to oxygenate air

1882: T. W. Engelmann demonstrated which parts of the visible light spectrum were required in order for plants to release oxygen

1930s: C. B. van Niel proposed that the O₂ released by plants in the light comes from H₂O (confirmed in 1941 by Ruben and Kamen)

Collection of light energy for photosynthesis requires pigments that can absorb blue and red light: chlorophyll a, chlorophyll b, and carotenoids (carotenes and xanthophylls. The pigments must be organized into photosystems located inside the chloroplasts.

1804: N. T. de Saussure found that approximately equal volumes of CO₂ and O₂ are exchanged during photosynthesis. (He also found that the weight that plants gained during photosynthesis could not be accounted for by the weight difference between CO₂ and O₂; he attributed the difference to the involvement of water as a reactant in photosynthesis.)

1864: Julius von Sachs demonstrated that only the parts of leaves exposed to light synthesized starch

1946-1953: Calvin, Benson, Bassham, and their associates used ¹⁴CO₂, Chlorella (unicellular green alga), and paper chromatography to discover how plants reduce CO₂ to sugar: the Calvin cycle

1950s: the molecules that connect the oxygen generation and sugar synthesis processes were discovered: NADP⁺/NADPH, ADP/ATP.

NADPH carries the electrons from the light energy collection reactions to the sugar synthesis reactions.

•ATP is an energy intermediate between light energy and stored energy (sugar).

Photosynthesis occurs in two sets of reactions that are linked by NADP⁺/NADPH and ADP/ATP. The two reactions go by several names. I'll be sticking to light reactions and Calvin cycle for what your textbook calls the light-dependent reactions and light-independent reactions, respectively.

Light energy is collected by pigments in the photosystems and used to excite electrons in chl a molecules. The excited electrons are given to NADP⁺ which converts it to NADPH.

How does a chloroplast replace the electrons that keep leaving the chl a molecules? By splitting water in a process called photolysis:
2 H₂O ---------> O₂ + 4 H⁺ + 4 e^-

Photolysis and the chloroplast structure also provide the means to capture light energy in a readily accessible chemical form, ATP.

In the first step of the Calvin cycle, carbon dioxide and RuBP (a 5C sugar) are combined to give two molecules of PGA (a 3C acid). The enzyme that catalyzes this reaction is abbreviated rubisco. ATP, electrons (from NADPH), and H+ are then used in a series of steps to change PGA to a 3C sugar, GA3P. Once you have lots of GA3P, it can be used to make glucose (6C sugar), fructose (6C sugar), sucrose (a dimer of glucose and fructose), and starch (a glucose polymer).

What the abbreviations stand for:
rubisco = RuBP carboxylase and oxygenase
RuBP = ribulose-1,5-bisphosphate
PGA = 3-phosphoglyceric acid
GA3P = glyceraldehyde-3-phosphate (also known as 3-phosphoglyceraldehyde or PGald)
ATP = adenosine triphosphate; ADP = adenosine diphosphate
NADP⁺/NADPH = nicotinamide adenine dinucleotide phosphate

Besides looking at photosynthesis as a chloroplast event, you need to remember that it is also a leaf event.

Recall that a leaf is composed of three tissues:
1. epidermis
        holes for gas exchange called stomata (guard cells open and close the holes)
        covered by a waxy layer called cuticle
2. vascular tissue
        xylem + phloem together in a vascular bundle (vein)
3. mesophyll (ground tissue)
        tightly packed layer of cells = palisade mesophyll
        loose cell layer with lots of air spaces = spongy mesophyll
(a review of leaf anatomy is recommended)

Most plants open their stomata during the day (light) so CO₂ enters the leaf for photosynthesis. Downside: water evaporates out of the stomata whenever they are open. Evaporation is fastest when the temperatures are highest, which would also be during the day. The stomata close at night when photosynthesis is not going on (no need to let in CO₂).

Some plants have a system that lets them open their stomata at night to collect and store CO₂. During the day, they can close their stomata to conserve water but still do photosynthesis. These plants are known as CAM plants. CAM == Crassulacean acid metabolism. CAM was first discovered in members of the Crassulaceae family. CAM has since been found in many angiosperm families (both monocots and eudicots), a seedless vascular plant (Isoetes), and a gymnosperm (Welwitschia).

CAM is generally associated with plants that live in xeric environments: deserts, as epiphytes. These types of CAM plants have at least some succulence (water storing). However, some CAM plants are aquatic. CAM enables these aquatic plants to collect carbon dioxide when competition with other photosynthesizers (like algae) for this resource is low (at night).

PEP = phosphoenolpyruvate, a 3C acid.
CO₂ can be attached to PEP by the enzyme PEP carboxylase.

At night, the stomata are open. Starch is broken down to produce PEP. PEP combines with CO₂ to form a 4C acid. This 4C acid is stored in the vacuole. During the day, the stomata close. The 4C acid is broken down to release CO₂ and a 3C acid. The 3C acid is converted back to starch. The CO₂ enters the Calvin cycle.

CAM is estimated to occur in ~10% of plant species. C3 photosynthesis (where the only carbon reactions are the Calvin cycle ones) occurs in ~89% of species. The remaining ~1% do C4 photosynthesis. Although C4 species are in the minority, C4 photosynthesis attracts a lot of study because (1) it is a highly efficient form of photosynthesis and (2) it accounts for the high productivity of such major crops as corn, sugar cane, sorghum, and millet.

The CO₂ lost because of the oxygenase reaction is called photorespiration. It is a problem under conditions of high temperature, high light intensity, and low water. Under these conditions, a C3 plant might lose 50% of its carbon via photorespiration.

How can you decrease photorespiration? Keep rubisco away from O₂. Some plants do this by engaging in C4 photosynthesis.

C4 plants have a distinctive leaf anatomy. There is a prominent ring of cells around the vascular bundles = the bundle sheath. The mesophyll cells form a ring that is tightly appressed to the bundle sheath cells. Kranz anatomy.

In a mesophyll cell, CO₂ and PEP combine to form a 4C acid. The 4C acid is sent to a bundle sheath cell. In the bundle sheath cell, the CO₂ is released from the 4C acid and enters the Calvin cycle. The 3C acid that remains goes back to the mesophyll cell, is made back into PEP, and is ready to carry more CO₂. (Rubisco is located only in the bundle sheath cells.) So, a CO₂ shuttle system delivers CO₂ to rubisco; the leaf anatomy keeps O₂ away from the bundle sheaths. Result ==> no photorespiration.

Downside to C4: the CO₂ shuttle is not a free ride. It adds 2 ATP to the standard 3 ATP (for the Calvin cycle) needed per CO₂. So C4 photosynthesis is only cost effective for plants in an environment (high temperature, high light intensity, and low water) where photorespiration is detrimental.

One final thing to remember about photosynthesis is that it is a whole plant event. The roots need to take in essential elements from the soil. Many of the chemical elements that plants require have some role in photosynthesis: sulfur, magnesium, iron, manganese, chlorine, nitrogen, copper, phosphorus. Potassium is needed to open the stomata to let in CO₂. There needs to be an adequate water supply coming in from the roots to keep the stomata open. Under conditions of water stress, the stomata will close (at least partly, if not completely) and photosynthetic yield goes down.

------ energy input from light ----->
6 CO₂ + 12 H₂O ------------------------------------------ C₆H₁₂O₆ + 6 O₂ + 6 H₂O
<---- energy output as ATP and heat -------

The overall reaction for cellular (aerobic) respiration is essentially photosynthesis in reverse. Basically, respiration involves converting sugar carbons to CO₂. This process releases energy, less than half of which is captured for cellular use as ATP. (The bulk of the energy released during respiration goes off as heat.) The most efficient use of the energy stored in the sugar needs O₂; in the process of energy conversion, O₂ will be converted to H₂O.

Respiration is strongly identified with the mitochondria, however, the starting reactions are in the cytosol. If oxygen is available, the mitochondria get involved with respiration, and the internal structure of the mitochondria is critical to the process.

The carbon oxidation takes place in two sets of reactions, glycolysis in the cytosol and the Krebs cycle in the mitochondria. Both glycolysis and the Krebs cycle occur in steps. Stepwise oxidation is important because it allows the cell to:
1. dissipate energy that is released as heat
2. generate intermediates ==> steps to start making amino acids, N-bases, other sugars for cell wall and nucleic acids, fatty acids, chlorophyll, anthocyanins, hormones, alkaloids, essential oils, etc.

Glycolysis
Glycolysis converts glucose or fructose (6C sugars) to pyruvate (3C acid). Some of the energy released during the process is captured as ATP. Electrons are released and held by NADH. Pyruvate is an organic acid. If the carbon is organic, there is energy (calories) available in pyruvate.

The Krebs Cycle
The Krebs cycle finishes the process of converting all of the carbons originally in the starting sugar (now in pyruvate) to CO₂. A little bit of ATP is made during the Krebs cycle. Most of the energy released during the Krebs cycle is associated with electrons that are held by more NADH molecules (with a few held by FADH₂).

Electron Transport Chain (ETC)
In the mitochondria, the electrons from NADH (and FADH₂) are passed to O₂ which is then converted to H₂O. As a result of the transport system to get electrons to O₂, ATP can be synthesized. How much ATP gets made? It depends on who is doing the counting. Most plants that convert the carbon atoms in one glucose molecule completely to six CO₂ molecules will get between 30 and 38 ATP from glycolysis, Krebs cycle, and ETC. The majority of that ATP (85-90%) comes from the ETC. The high end of ATP yield (35-38 ATP) represents about 40% of the energy that was available in a molecule of glucose. The remaining energy is given off as heat.

Some plants deliberately have an ATP yield in the mid-teens. Because the ATP yield is down, these plants release more heat. These plants are called thermogenic. They can raise the temperature in their microenvironment as much as 10^oC. This temperature increase volatilizes scents to attract pollinators more efficiently. The Titan Arum you saw at the end of "The Birds and the Bees" video is thermogenic, as is the dead horse Arum. For some thermogenic plants, the heat they produce during flowering is the reward for pollinators.

Fermentation
In the absence of oxygen, plants can still carry out glycolysis, but any reactions involving the mitochondria are not available. Without oxygen and the ETC, where can NADH dump off its electrons? Enter fermentation: a set of reactions that lets NADH unload electrons so glycolysis can continue. Most plants use alcohol (ethanol) fermentation. The most likely anaerobic scenario for plants ==> roots in water-logged soil.

Some plants (hydrophytes) are adapted to have their roots always in water, like anchored aquatic plants and emerged plants (water lilies, cattails, etc.) These plants have large air spaces in their ground tissue. These air spaces serve as passage ways to get O₂ to the roots.

Don't forget: The reactions of respiration, besides providing a means to change the stored calories of sugars into useable energy as ATP, let a cell start the process of converting carbons from carbohydrates produced during photosynthesis into a variety of molecules: amino acids, nucleotides, pigments, hormones, etc.

To be considered an essential element:
1. must be required for completion of life cycle
2. must be involved in some aspect of metabolism as part of a molecule, enzyme cofactor, ion for water balance, etc.
3. cannot be replaced by another element

14 of the essential elements are obtained as soil minerals. The other three are C, H, and O. C, H, and O are obtained from CO₂ and H₂O during photosynthesis.

The remaining 14 elements (the ones obtained as soil minerals) are divided into two groups, based on the quantity required by plants, macroelements (macronutrients) and microelements (micronutrients).

Macroelements: P (phosphorus), K (potassium), N (nitrogen), S (sulfur), Ca (calcium), Mg (magnesium)
all except Ca have some fairly direct role in photosynthesis
specific roles:
P      ATP, NAD, NADP, phospholipids, nucleic acids
K      regulation of the stomatal apparatus
N      amino acids/proteins, nucleotides/nucleic acids, chlorophyll
S       some amino acids (proteins)
Ca     complexes with pectin in the middle lamella to "glue" cells together
Mg    chlorophyll, enzyme activator

Microelements: Cu (copper), Zn (zinc), B (boron), Mn (manganese), Mo (molybdenum), Fe (iron), Cl (chlorine), Ni (nickel). In general, micronutrients act as enzyme activators.

When it comes to applying minerals to soils, three of the macronutrients are the ones that need to be supplemented most often: N, P, K. The other macronutrients and the micronutrients are generally adequate. (The main exception tends to be Fe.) Therefore, N, P, and K are sometimes known as primary nutrients as it is deficiency of one of these that is most likely to limit plant growth.

Fertilizer bags are always labeled with the percentage of N, P₂O₅, and K₂O by weight.
The label on a bag of fertilizer:
20-20-20 = 20% nitrogen, 20% P₂O₅, and 20% K₂O
The remaining 40% of the weight is usually other elements (like O with the N if it is nitrate = NO₃^-).

Some fertilizers might also have micronutrients (esp Fe as chelated Fe), herbicides (weed and feed), or insecticides.

•Producers

–autotrophs

–manufacture their own food by photosynthesis or chemosynthesis

•Consumers

–heterotrophs

–get food by eating producers or other consumers

–their “leftovers” still have nutritional value

•Decomposers

–heterotrophs

–get food by eating the remains of producers or other consumers

–break down organic matter to a form from which elements can be re-assimilated by the producers

•two (or more) different species living in close association

•The association could be:

– beneficial to both (mutualism)

– beneficial to one but harmful to the other (parasitism)

–beneficial to one with the other unaffected by the association (commensalism)

1. Ammonification
                                    decomposers
   organic N ------------------------------------> NH₄⁺
(urea, proteins, amino acids)

2. Nitrification
conducted by chemotrophic bacteria
              Nitrosomonas                     Nitrobacter
NH₄⁺ --------------------> NO₂^- ------------------> NO₃^-

3. Nitrogen Fixation
done by symbiotic or free-living N₂-fixing bacteria

N₂ ------------------> NH₄⁺

Symbiotic: Rhizobium + legume
A specific Rhizobium infects the roots of a specific legume, forming a structure called a nodule in which nitrogen fixation occurs.
The nodulation process:
1. Recognition between legume root and Rhizobium
2. Rhizobium bacteria attaches to the root hairs; root hairs curl
3. Formation of infection thread
4. Rhizobium bacteria enter cells of the root cortex and form nodules
5. Rhizobium bacteria convert to bacteroids and begin nitrogen fixation via the enzyme nitrogenase
6. Legume provides Rhizobium with organic carbon; Rhizobium provides legume with useable N
7. Legume provides leghemoglobin to maintain O₂-free environment for nitrogenase

Free-ling soil bacteria
Clostridium (anaerobic)
Azospirillum, Azotobacter: often found in the rhizosphere of tropical grasses, corn

Cyanobacteria: soils, aquatic
Heterocyst: 1 in every 10-20 cells. Nitrogen fixation occurs in heterocysts; can transform light energy to ATP energy, but does not split H₂O to evolve O₂.
Rest of the cells: full set of photosynthesis reactions
==> cell specialization and cooperation in a prokaryote

4. Denitrification

NO₃^- -----------------> N₂

5. N assimilation by plants

NO₃^- --------->    NO₂^-   ------------>   NH₄⁺ ------------> organic molecules
   ↑                                                                ↑
   ↑                                                                ↑
   ↑                                                                ↑
  soil                                                             soil

Mycorrhizae = "fungus root"

generally viewed as a mutualistic relationship
very common, could be present in as high as 90% of all plants: natural and agricultural conditions; seed plants, seedless vascular plants, and non-vascular plants

Endomycorrhizae
1. Orchids
usually basidiomycetes
seeds are minute; will not germinate unless fungus is present
fungi are saprobes, getting food from dead organic matter
the orchids depend on trehalose from the fungus
orchids grow as epiphytes; those without chlorophyll are dependent on fungus (mycotrophic)
2. Vesicular Arbuscular Mycorrhizae
zygomycetes; the association seems to be obligate for the fungus
enhance mineral uptake in general, phosphate uptake in particular
also seem to provide some stress protection for the plant

Ectomycorrhizae
mostly basidiomycetes; some ascomycetes (truffles, morels)
mostly found on woody plants (hardwoods and conifers) in temperate areas
branch and extend into soil for mineral collection
decomposers == break down leaf litter and pick up released mineral nutrients; some release proteases to mobilize N from decomposing leaf litter
plant makes specific sugars for the fungus (mannitol, trehalose)
increase the tree’s hardiness to cold and dry conditions (i.e., winter)

Carnivorous Plants
> 600 species are known. All are angiosperms (~300,000 species).
Have leaves modified to attract and trap small animals (insects), digest their prey (the soft tissues), and/or absorb and use small organic molecules.

Active trappers move to catch prey; passive trappers use sticky secretions and pitfalls to catch prey.

Venus flytrap
Active trapper. Insect touches trigger on leaf surface. The underside of the leaf rapidly enlarges. This causes the leaf to rapidly fold shut on the insect. Once the insect has been digested, the upper side of the leaf grows. This opens the leaf again and resets the trap.

Bladderwort
Active trapper. Aquatic. A bladder is under tension. Aquatic critter (usually insect larva) brushes against trigger at mouth of the bladder. The bladder opens, a vacuum pulls in the larva, along with a lot of water. Once the larva is digested, the water is removed from the bladder, and the trap is reset.

Pitcher plant
Passive trapper. The leave forms a cone. A solution of digestive enzymes is at the base of the cone. Insects fall into the cone, drown, and are digested.

Sundew
Passive trapper. Sticky, stalked glands cover the leaves. Insects get stuck and can't get away. Slowly, the stalks fold over the insects. Eventually, the entire leaf can curl around the insect. By having the leaf in close contact with the insect, you have more efficient digestion and uptake of nutrients.

Butterwort
Passive trapper. Flat sticky glands on leaf surface. Insects get stuck. Slowly, the leaf will curl around the insect for improved digestion and nutrient uptake.

Features of Carnivorous Plants
The carnivorous plants use a variety of features to attract insects: color, scent, nectar reward. These are the same features found in flowers to attract pollinators.
Glands for secretion and absorption ==> not unique to carnivorous plants.
Leaf modifications: common among plants. Even the parts of flowers (petals, sepals, pistils, stamens) are modified leaves.
Rapid movements. Some plants, like the sensitive plant, have rapid leaf movements that startle insects.

So the plant features found in carnivorous plants aren't unique to them. However, the carnivorous plants have put the features together in such a way that they can attract, catch, digest, and/or absorb prey.

Why practice carnivory? Does this make carnivorous plants heterotrophic? No. They have perfectly good photosynthetic rates. Where do you find carnivorous plants? mineral poor soils. Most plants can't live in these habitats. Carnivorous plants can because they can use insects and other small animals as a source of essential elements, notably nitrogen.
        Carnivorous plants don't necessarily capture insects as the source of N. Other materials that contain N are sometime collected in the traps:
                "vegetarian" carnivorous plants
                feces collecting

What do photosynthesis and respiration have in common? In what ways are they essentially the reverse of each other?

Besides looking at photosynthesis as a chloroplast event, you need to remember that it is also a leaf event. Inside of a leaf are three tissues: epidermis, vascular tissue, mesophyll (ground tissue). Be able to relate the leaf tissues to their roles in photosynthesis.

What are CAM plants? How do they manage to do photosynthesis if their stomata are closed during the day for water conservation? In what habitats do you find CAM plants?

Why do C4 plants attract so much attention? What is photorespiration? What is rubisco? How is it involved in photosynthesis? How is it involved in photorespiration?

C4 plants have Kranz anatomy. How does Kranz anatomy relate to C4 photosynthesis?

Be able to give at least two examples each of C3 plants, C4 plants, and CAM plants.

Why is it important that the conversion of sugar carbons to CO₂ occur in steps during respiration?
What is the importance of generating carbon intermediates during glycolysis and the Krebs cycle?

Electron Transport Chain (ETC)
Be able to briefly state what happens as a result of this process.

Element vs. Mineral Nutrient
What criteria must be met for an element to be considered essential for plants?
Be able to name (chemical name or symbol) the essential elements. Which three are not obtained as soil minerals? How do plants get these three elements? Be able to distinguish between macronutrients and micronutrients. Know the functions covered in class for each of the macronutrients. Be able to give a collective function for the micronutrients.

Which three essential elements are known as primary nutrients? Why are these three singled out? How are their amounts presented on a bag of fertilizer? What else might be in a fertilizer besides these three elements?

Know the trophic levels in ecosystems and the types of organisms found at each level: decomposers, consumers, producers.

Nitrogen cycle:
ammonification
nitrification
nitrogen fixation: symbiotic (Rhizobium in legume roots), free-living (cyanobacteria with heterocysts)
denitrification
N assimilation by plants
What roles do bacteria play in the different steps of the nitrogen cycle? In particular, address their roles in nitrogen fixation, ammonification, nitrification, and denitrification.

What are mycorrhizae? What is difference between endomycorrhizae and ectomycorrhizae?
Know the two types of endomycorrhizae presented in class: the fungi in each, the benefit to the plants, the benefit to the fungi. Know about the ectomycorrhizae: the fungi, the typical plants involved, the benefits to both organisms.

Be able to distinguish between active traps and passive traps. Be familiar with examples of each: Venus flytrap, bladderwort, sundew, butterwort, pitcher plants.
What features of carnivorous plants enable them to lure and capture prey? Are the individual features unique to the carnivorous plants? What abilities do the features provide that are the criteria for being carnivorous? In what sort of habitat do you find carnivorous plants? How does carnivory enable them to live in this habitat?