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Wednesday, September 14, 2016

THE LIGHT-DEPENDENT REACTIONS OF PHOTOSYNTHESIS

How can light be used to make food? When a person turns on a lamp, electrical energy becomes light energy. Like all other forms of kinetic energy, light can travel, change form, and be harnessed to do work. In the case of photosynthesis, light energy is converted into chemical energy, which photoautotrophs use to build carbohydrate molecules (Figure 1.1). However, autotrophs only use a few specific components of sunlight.

Figure 1.1 Photoautotrophs can capture light energy from the sun,  converting  it into the chemical energy used to build food molecules. (credit: Gerry Atwell)

What Is Light Energy?
The sun emits an enormous amount of electromagnetic radiation (solar energy). Humans can see only a fraction of this energy, which portion is therefore referred to as “visible light.” The manner in which solar energy travels is described as waves. Scientists can determine the amount of energy of a wave by measuring its wavelength, the distance between consecutive points of a wave. A single wave is measured from two consecutive points, such as from crest to crest or from trough to trough (Figure 1.2).
Figure  1.2  The wavelength of a single  wave  is the distance between two consecutive points  of similar position  (two crests or two troughs) along the wave.

Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun and other stars. Scientists differentiate the various types of radiant energy from the sun within the electromagnetic spectrum. The electromagnetic spectrum is the range of all possible frequencies of radiation (Figure 1.3). The difference between wavelengths relates to the amount of energy carried by them.
Figure   1.3   The  sun   emits   energy  in  the  form  of  electromagnetic  radiation.  This  radiation   exists   at  different wavelengths, each of which has  its own characteristic energy. All electromagnetic radiation, including visible light, is characterized by its wavelength.

Each type of electromagnetic radiation travels at a particular wavelength. The longer the wavelength (or the more stretched out it appears in the diagram), the less energy is carried. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of a piece of moving a heavy rope. It takes little effort by a person to move a rope in long, wide waves. To make a rope move in short, tight waves, a person would need to apply significantly more energy.
The electromagnetic spectrum (Figure 1.4) shows several types of electromagnetic radiation originating from the sun, including X-rays and ultraviolet (UV) rays. The higher-energy waves can penetrate tissues and damage cells and DNA, explaining why both X-rays and UV rays can be harmful to living organisms.
Absorption of Light
Light energy initiates the process of photosynthesis when pigments absorb the light. Organic pigments, whether in the human retina or the chloroplast thylakoid, have a narrow range of energy levels that they can absorb. Energy levels lower than those represented by red light are insufficient to raise an orbital electron to a populatable, excited (quantum) state. Energy levels higher than those in blue light will physically tear the molecules apart, called bleaching. So retinal pigments can only “see” (absorb) 700 nm to 400 nm light, which is therefore called visible light. For the same reasons, plants pigment molecules absorb only light in the wavelength range of 700 nm to 400 nm; plant physiologists refer to this range for plants as photosynthetically active radiation.
The visible light seen by humans as white light actually exists in a rainbow of colors. Certain objects, such as a prism or a drop of water, disperse white light to reveal the colors to the human eye. The visible light portion of the electromagnetic spectrum shows the rainbow of colors, with violet and blue having shorter wavelengths, and therefore higher energy. At the other end of the spectrum toward red, the wavelengths are longer and have lower energy (Figure 1.4).

Figure 1.4 The colors of visible light do not carry the same amount of energy. Violet has  the shortest wavelength and therefore carries the  most  energy, whereas red  has  the  longest wavelength and  carries the  least  amount of energy. (credit: modification of work by NASA)

Understanding Pigments
Different kinds of pigments exist, and each has evolved to absorb only certain wavelengths (colors) of visible light. Pigments reflect or transmit the wavelengths they cannot absorb, making them appear in the corresponding color.
Chlorophylls and carotenoids are the two major classes of photosynthetic pigments found in plants and algae; each class has multiple types of pigment molecules. There are five major chlorophylls: a, b, c and d and a related molecule found in prokaryotes called bacteriochlorophyll. Chlorophyll a and chlorophyll b are found in higher plant chloroplasts and will be the focus of the following discussion.
With dozens of different forms, carotenoids are a much larger group of pigments. The carotenoids found in fruit—such as the red of tomato (lycopene), the yellow of corn seeds (zeaxanthin), or the orange of an orange peel (β-carotene)—are used as advertisements to attract seed dispersers. In photosynthesis, carotenoids function as photosynthetic pigments that are very efficient molecules for the disposal of excess energy. When a leaf is exposed to full sun, the light-dependent reactions are required to process an enormous amount of energy; if that energy is not handled properly, it can do significant damage. Therefore, many carotenoids reside in the thylakoid membrane, absorb excess energy, and safely dissipate that energy as heat.
Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light, which is the absorption spectrum. The graph in Figure 1.5 shows the absorption spectra for chlorophyll a, chlorophyll b, and a type of carotenoid pigment called β-carotene (which absorbs blue and green light). Notice how each pigment has a distinct set of peaks and troughs, revealing a highly specific pattern of absorption. Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red), but not green. Because green is reflected or transmitted, chlorophyll appears green. Carotenoids absorb in the short-wavelength blue region, and reflect the longer yellow, red, and orange wavelengths.

Figure  1.5  (a)  Chlorophyll  a,  (b)  chlorophyll  b,  and  (c)  β-carotene are  hydrophobic organic   pigments found  in the  thylakoid  membrane. Chlorophyll  a and  b, which  are  identical  except for the  part  indicated in the  red  box,  are responsible for the green color of leaves. β-carotene is responsible for the orange color in carrots. Each  pigment  has (d) a unique  absorbance spectrum.

Many photosynthetic organisms have a mixture of pigments; using them, the organism can absorb energy from a wider range of wavelengths. Not all photosynthetic organisms have full access to sunlight. Some organisms grow underwater where light intensity and quality decrease and change with depth. Other organisms grow in competition for light. Plants on the rainforest floor must be able to absorb any bit of light that comes through, because the taller trees absorb most of the sunlight and scatter the remaining solar radiation (Figure 1.6).

 Figure  1.6  Plants that  commonly  grow  in the  shade have  adapted to low levels  of light by changing the  relative concentrations of their chlorophyll pigments. (credit: Jason Hollinger)

When studying a photosynthetic organism, scientists can determine the types of pigments present by generating absorption spectra. An instrument called a spectrophotometer can differentiate which wavelengths of light a substance can absorb. Spectrophotometers measure transmitted light and compute from it the absorption. By extracting pigments from leaves and placing these samples into a spectrophotometer, scientists can identify which wavelengths of light an organism can absorb. Additional methods for the identification of plant pigments include various types of chromatography that separate the pigments by their relative affinities to solid and mobile phases.

How Light-Dependent Reactions Work
The overall function of light-dependent reactions is to convert solar energy into chemical energy in the form of NADPH and ATP. This chemical energy supports the light-independent reactions and fuels the assembly of sugar molecules. The light-dependent reactions are depicted in Figure 1.7. Protein complexes and pigment molecules work together to produce NADPH and ATP.
 Figure  1.7  A photosystem consists of a  light-harvesting complex   and  a  reaction center. Pigments in the  light- harvesting complex  pass light energy to two special chlorophyll a molecules in the  reaction center. The  light excites an electron from the chlorophyll a pair, which passes to the primary electron acceptor. The excited  electron must  then be replaced. In (a) photosystem II, the electron comes from the splitting of water,  which releases oxygen  as a waste product.  In (b) photosystem I, the electron comes from the chloroplast electron transport chain discussed below.

The actual step that converts light energy into chemical energy takes place in a multiprotein complex called a photosystem, two types of which are found embedded in the thylakoid membrane, photosystem II (PSII) and photosystem I (PSI) (Figure 1.8). The two complexes differ on the basis of what they oxidize (that is, the source of the low-energy electron supply) and what they reduce (the place to which they deliver their energized electrons).
Both photosystems have the same basic structure; a number of antenna proteins to which the chlorophyll molecules are bound surround the reaction center where the photochemistry takes place. Each photosystem is serviced by the light- harvesting complex, which passes energy from sunlight to the reaction center; it consists of multiple antenna proteins that contain a mixture of 300–400 chlorophyll a and b molecules as well as other pigments like carotenoids. The absorption of a single photon or distinct quantity or “packet” of light by any of the chlorophylls pushes that molecule into an excited state. In short, the light energy has now been captured by biological molecules but is not stored in any useful form yet. The energy is transferred from chlorophyll to chlorophyll until eventually (after about a millionth of a second), it is delivered to the reaction center. Up to this point, only energy has been transferred between molecules, not electrons.
Figure  1.8  In the  photosystem II (PSII) reaction center, energy from sunlight  is used to extract  electrons  from water.  The electrons travel through  the chloroplast electron transport chain to photosystem I (PSI), which reduces NADP+ to NADPH. The electron transport chain moves protons across the thylakoid membrane into the lumen.  At the same time, splitting of water  adds protons to the lumen,  and  reduction of NADPH removes protons from the stroma. The net result  is a low pH in the thylakoid lumen,  and  a high pH in the stroma. ATP synthase uses this electrochemical gradient to make  ATP.

What is the initial source of electrons for the chloroplast electron transport chain?
a.   water
b.   oxygen
c.   carbon dioxide
d.   NADPH
The reaction center contains a pair of chlorophyll a molecules with a special property. Those two chlorophylls can undergo oxidation upon excitation; they can actually give up an electron in a process called a photoact. It is at this step in the reaction center, this step in photosynthesis, that light energy is converted into an excited electron. All of the subsequent steps involve getting that electron onto the energy carrier NADPH for delivery to the Calvin cycle where the electron is deposited onto carbon for long-term storage in the form of a carbohydrate.PSII and PSI are two major components of the photosynthetic electron transport chain, which also includes the cytochrome complex. The cytochrome complex, an enzyme composed of two protein complexes, transfers the electrons from the carrier molecule plastoquinone (Pq) to the protein plastocyanin (Pc), thus enabling both the transfer of protons across the thylakoid membrane and the transfer of electrons from PSII to PSI.
The reaction center of PSII (called P680) delivers its high-energy electrons, one at the time, to the primary electron acceptor, and through the electron transport chain (Pq to cytochrome complex to plastocyanine) to PSI. P680s missing electron is replaced by extracting a low-energy electron from water; thus, water is split and PSII is re-reduced after every photoact. Splitting one H2O molecule releases two electrons, two hydrogen atoms, and one atom of oxygen. Splitting two molecules is required to form one molecule of diatomic O2 gas. About 10 percent of the oxygen is used by mitochondria in the leaf to support oxidative phosphorylation. The remainder escapes to the atmosphere where it is used by aerobic organisms to support respiration.
As electrons move through the proteins that reside between PSII and PSI, they lose energy. That energy is used to move hydrogen atoms from the stromal side of the membrane to the thylakoid lumen. Those hydrogen atoms, plus the ones produced by splitting water, accumulate in the thylakoid lumen and will be used synthesize ATP in a later step. Because the electrons have lost energy prior to their arrival at PSI, they must be re-energized by PSI, hence, another photon is absorbed by the PSI antenna. That energy is relayed to the PSI reaction center (called P700). P700 is oxidized and sends a high- energy electron to NADP+ to form NADPH. Thus, PSII captures the energy to create proton gradients to make ATP, and PSI captures the energy to reduce NADP+ into NADPH. The two photosystems work in concert, in part, to guarantee that the production of NADPH will roughly equal the production of ATP. Other mechanisms exist to fine tune that ratio to exactly match the chloroplasts constantly changing energy needs.
Generating an Energy Carrier: ATP
As in the intermembrane space of the mitochondria during cellular respiration, the buildup of hydrogen ions inside the thylakoid lumen creates a concentration gradient. The passive diffusion of hydrogen ions from high concentration (in the thylakoid lumen) to low concentration (in the stroma) is harnessed to create ATP, just as in the electron transport chain of cellular respiration. The ions build up energy because of diffusion and because they all have the same electrical charge, repelling each other.
To release this energy, hydrogen ions will rush through any opening, similar to water jetting through a hole in a dam. In the thylakoid, that opening is a passage through a specialized protein channel called the ATP synthase. The energy released by the hydrogen ion stream allows ATP synthase to attach a third phosphate group to ADP, which forms a molecule of ATP (Figure 1.8). The flow of hydrogen ions through ATP synthase is called chemiosmosis because the ions move from an area of high to an area of low concentration through a semi-permeable structure.

Using Light Energy  to Make Organic  Molecules
After the energy from the sun is converted into chemical energy and temporarily stored in ATP and NADPH molecules, the cell has the fuel needed to build carbohydrate molecules for long-term energy storage. The products of the light-dependent reactions, ATP and NADPH, have lifespans in the range of millionths of seconds, whereas the products of the light- independent reactions (carbohydrates and other forms of reduced carbon) can survive for hundreds of millions of years. The carbohydrate molecules made will have a backbone of carbon atoms. Where does the carbon come from? It comes from carbon dioxide, the gas that is a waste product of respiration in microbes, fungi, plants, and animals.

The Calvin Cycle
In plants, carbon dioxide (CO2) enters the leaves through stomata, where it diffuses over short distances through intercellular spaces until it reaches the mesophyll cells. Once in the mesophyll cells, CO2  diffuses into the stroma of the chloroplast—the site of light-independent reactions of photosynthesis. These reactions actually have several names associated with them. Another term, the Calvin cycle, is named for the man who discovered it, and because these reactions function as a cycle. Others call it the Calvin-Benson cycle to include the name of another scientist involved in its discovery. The most outdated name is dark reactions, because light is not directly required (Figure 1.9). However, the term dark reaction can be misleading because it implies incorrectly that the reaction only occurs at night or is independent of light, which is why most scientists and instructors no longer use it.
 Figure 1.9 Light reactions harness energy from the sun to produce chemical bonds, ATP, and NADPH. These energy- carrying molecules are made in the stroma where  carbon fixation takes place.

The light-independent reactions of the Calvin cycle can be organized into three basic stages: fixation, reduction, and regeneration.
Stage 1: Fixation

In the stroma, in addition to CO2, two other components are present to initiate the light-independent reactions: an enzyme called ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), and three molecules of ribulose bisphosphate (RuBP), as shown in Figure 1.10. RuBP has five atoms of carbon, flanked by two phosphates.

Figure 1.10 The Calvin cycle has  three  stages. In stage 1, the enzyme RuBisCO  incorporates carbon dioxide into an organic  molecule, 3-PGA. In stage 2, the organic  molecule is reduced using  electrons supplied by NADPH. In stage 3, RuBP,  the molecule that starts the cycle, is regenerated so that the cycle can  continue. Only one carbon dioxide molecule is incorporated at a time, so the cycle must be completed three  times to produce a single three- carbon GA3P molecule, and six times to produce a six-carbon glucose molecule.

Which of the following statements is true?
a.   In photosynthesis, oxygen,   carbon dioxide,  ATP,  and  NADPH  are  reactants. GA3P  and  water  are products.
b.   In  photosynthesis,  chlorophyll,   water and   carbon  dioxide  are   reactants. GA3P  and   oxygen   are products.
c.   In photosynthesis, water,  carbon dioxide,  ATP,  and  NADPH  are  reactants. RuBP  and  oxygen  are products.
d. In photosynthesis, water and carbon dioxide are reactants. GA3P and oxygen  are products.
d. In photosynthesis, water and carbon dioxide are reactants. GA3P and oxygen  are products.
RuBisCO catalyzes a reaction between CO2 and RuBP. For each CO2 molecule that reacts with one RuBP, two molecules of another compound (3-PGA) form. PGA has three carbons and one phosphate. Each turn of the cycle involves only one RuBP and one carbon dioxide and forms two molecules of 3-PGA. The number of carbon atoms remains the same, as the atoms move to form new bonds during the reactions (3 atoms from 3CO2 + 15 atoms from 3RuBP = 18 atoms in 3 atoms of 3-PGA). This process is called carbon fixation, because CO2 is “fixed” from an inorganic form into organic molecules.

Stage 2: Reduction

ATP and NADPH are used to convert the six molecules of 3-PGA into six molecules of a chemical called glyceraldehyde
3-phosphate (G3P). That is a reduction reaction because it involves the gain of electrons by 3-PGA. Recall that a reduction is the gain of an electron by an atom or molecule. Six molecules of both ATP and NADPH are used. For ATP, energy is released with the loss of the terminal phosphate atom, converting it into ADP; for NADPH, both energy and a hydrogen atom are lost, converting it into NADP+. Both of these molecules return to the nearby light-dependent reactions to be reused and reenergized.
Stage 3: Regeneration

Interestingly, at this point, only one of the G3P molecules leaves the Calvin cycle and is sent to the cytoplasm to contribute to the formation of other compounds needed by the plant. Because the G3P exported from the chloroplast has three carbon atoms, it takes three “turns” of the Calvin cycle to fix enough net carbon to export one G3P. But each turn makes two G3Ps, thus three turns make six G3Ps. One is exported while the remaining five G3P molecules remain in the cycle and are used to regenerate RuBP, which enables the system to prepare for more CO2 to be fixed. Three more molecules of ATP are used in these regeneration reactions.

The Energy  Cycle
Whether the organism is a bacterium, plant, or animal, all living things access energy by breaking down carbohydrate molecules. But if plants make carbohydrate molecules, why would they need to break them down, especially when it has been shown that the gas organisms release as a “waste product” (CO2) acts as a substrate for the formation of more food in photosynthesis? Remember, living things need energy to perform life functions. In addition, an organism can either make its own food or eat another organism—either way, the food still needs to be broken down. Finally, in the process of breaking down food, called cellular respiration, heterotrophs release needed energy and produce “waste” in the form of CO2 gas.
In nature, there is no such thing as waste. Every single atom of matter and energy is conserved, recycling over and over infinitely. Substances change form or move from one type of molecule to another, but their constituent atoms never disappear (Figure 1.11).
CO2 is no more a form of waste than oxygen is wasteful to photosynthesis. Both are byproducts of reactions that move on to other reactions. Photosynthesis absorbs light energy to build carbohydrates in chloroplasts, and aerobic cellular respiration releases energy by using oxygen to metabolize carbohydrates in the cytoplasm and mitochondria. Both processes use electron transport chains to capture the energy necessary to drive other reactions. These two powerhouse processes, photosynthesis and cellular respiration, function in biological, cyclical harmony to allow organisms to access life-sustaining energy that originates millions of miles away in a burning star humans call the sun.
 Figure  1.11  Photosynthesis consumes carbon dioxide  and  produces oxygen.  Aerobic  respiration consumes oxygen and  produces carbon dioxide. These two processes play an important  role in the carbon cycle. (credit: modification of work by Stuart  Bassil)

PHOTOSYNTHESIS

Introduction
The processes in all organisms—from bacteria to humans—require energy. To get this energy, many organisms access stored energy by eating, that is, by ingesting other organisms. But where does the stored energy in food originate? All of this energy can be traced back to photosynthesis.
Overview of Photosynthesis
Photosynthesis is essential to all life on earth; both plants and animals depend on it. It is the only biological process that can capture energy that originates in outer space (sunlight) and convert it into chemical compounds (carbohydrates) that every organism uses to power its metabolism. In brief, the energy of sunlight is captured and used to energize electrons, which are then stored in the covalent bonds of sugar molecules. How long lasting and stable are those covalent bonds? The energy extracted today by the burning of coal and petroleum products represents sunlight energy captured and stored by photosynthesis almost 200 million years ago.
Plants, algae, and a group of bacteria called cyanobacteria are the only organisms capable of performing photosynthesis (Figure 1.1). Because they use light to manufacture their own food, they are called photoautotrophs (literally, “self-feeders using light”). Other organisms, such as animals, fungi, and most other bacteria, are termed heterotrophs (“other feeders”), because they must rely on the sugars produced by photosynthetic organisms for their energy needs. A third very interesting group of bacteria synthesize sugars, not by using sunlights energy, but by extracting energy from inorganic chemical compounds; hence, they are referred to as chemoautotrophs.

Figure  1.1 Photoautotrophs including (a) plants,  (b) algae, and (c) cyanobacteria synthesize their organic  compounds via photosynthesis using  sunlight  as an energy source. Cyanobacteria and  planktonic  algae can  grow over enormous areas in water,  at  times  completely covering  the  surface. In a  (d) deep sea vent,  chemoautotrophs, such  as these (e) thermophilic  bacteria, capture energy from inorganic  compounds to produce organic  compounds. The ecosystem surrounding the  vents   has   a  diverse array  of  animals, such   as tubeworms, crustaceans, and  octopi  that  derive energy from the bacteria. (credit a: modification  of work by Steve Hillebrand,  U.S. Fish and  Wildlife Service; credit b: modification  of work by "eutrophication&hypoxia"/Flickr; credit c: modification  of work by NASA; credit d: University of Washington, NOAA; credit e: modification of work by Mark Amend, West Coast and Polar Regions Undersea Research Center, UAF, NOAA)

The importance of photosynthesis is not just that it can capture sunlights energy. A lizard sunning itself on a cold day can use the suns energy to warm up. Photosynthesis is vital because it evolved as a way to store the energy in solar radiation (the “photo-” part) as high-energy electrons in the carbon-carbon bonds of carbohydrate molecules (the “-synthesis” part). Those carbohydrates are the energy source that heterotrophs use to power the synthesis of ATP via respiration. Therefore, photosynthesis powers 99 percent of Earths ecosystems. When a top predator, such as a wolf, preys on a deer (Figure 1.2), the wolf is at the end of an energy path that went from nuclear reactions on the surface of the sun, to light, to photosynthesis, to vegetation, to deer, and finally to wolf.

Figure  1.2  The  energy stored in carbohydrate molecules from photosynthesis passes  through  the  food  chain.  The predator that eats these deer  receives a portion of the energy that originated in the photosynthetic vegetation that the deer  consumed. (credit: modification of work by Steve VanRiper,  U.S. Fish and Wildlife Service)

Main Structures and Summary of Photosynthesis
Photosynthesis is a multi-step process that requires sunlight, carbon dioxide (which is low in energy), and water as substrates (Figure 1.3). After the process is complete, it releases oxygen and produces glyceraldehyde-3-phosphate (GA3P), simple carbohydrate molecules (which are high in energy) that can subsequently be converted into glucose, sucrose, or any of dozens of other sugar molecules. These sugar molecules contain energy and the energized carbon that all living things need to survive.

Figure  1.3  Photosynthesis uses solar  energy, carbon dioxide,  and  water  to produce energy-storing carbohydrates. Oxygen  is generated as a waste product  of photosynthesis.

The following is the chemical equation for photosynthesis (Figure 1.4):

Figure  1.4  The  basic  equation for photosynthesis is deceptively simple.  In reality,  the  process takes place  in many steps involving intermediate reactants and  products. Glucose, the  primary  energy source in cells,  is made from two three-carbon GA3Ps.

Although the equation looks simple, the many steps that take place during photosynthesis are actually quite complex. Before learning the details of how photoautotrophs turn sunlight into food, it is important to become familiar with the structures involved.
In plants, photosynthesis generally takes place in leaves, which consist of several layers of cells. The process of photosynthesis occurs in a middle layer called the mesophyll. The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called stomata (singular: stoma), which also play roles in the regulation of gas exchange and water balance. The stomata are typically located on the underside of the leaf, which helps to minimize water loss. Each stoma is flanked by guard cells that regulate the opening and closing of the stomata by swelling or shrinking in response to osmotic changes.
In all autotrophic eukaryotes, photosynthesis takes place inside an organelle called a chloroplast. For plants, chloroplast- containing cells exist in the mesophyll. Chloroplasts have a double membrane envelope (composed of an outer membrane and an inner membrane). Within the chloroplast are stacked, disc-shaped structures called thylakoids. Embedded in the thylakoid membrane is chlorophyll, a pigment (molecule that absorbs light) responsible for the initial interaction between light and plant material, and numerous proteins that make up the electron transport chain. The thylakoid membrane encloses an internal space called the thylakoid lumen. As shown in Figure 1.5, a stack of thylakoids is called a granum, and the liquid-filled space surrounding the granum is called stroma or “bed” (not to be confused with stoma or “mouth,” an opening on the leaf epidermis).

  
Figure  1.5 Photosynthesis takes place  in chloroplasts, which have  an outer  membrane and  an inner membrane. Stacks of thylakoids  called grana form a third membrane layer.

On a hot, dry  day, plants close their stomata to conserve water. What impact will this have on photosynthesis?

The Two Parts of Photosynthesis

Photosynthesis takes place in two sequential stages: the light-dependent reactions and the light independent-reactions. In the light-dependent reactions, energy from sunlight is absorbed by chlorophyll and that energy is converted into stored chemical energy. In the light-independent reactions, the chemical energy harvested during the light-dependent reactions drive the assembly of sugar molecules from carbon dioxide. Therefore, although the light-independent reactions do not use light as a reactant, they require the products of the light-dependent reactions to function. In addition, several enzymes of the light-independent reactions are activated by light. The light-dependent reactions utilize certain molecules to temporarily store the energy: These are referred to as energy carriers. The energy carriers that move energy from light-dependent reactions to light-independent reactions can be thought of as “full” because they are rich in energy. After the energy is released, the “empty” energy carriers return to the light-dependent reaction to obtain more energy. Figure 1.6 illustrates the components inside the chloroplast where the light-dependent and light-independent reactions take place.


Figure  1.6 Photosynthesis takes place  in two stages: light dependent reactions and the Calvin cycle. Light-dependent reactions, which take  place  in the thylakoid membrane, use  light energy to make  ATP and  NADPH. The Calvin cycle, which takes place  in the stroma, uses energy derived  from these compounds to make  GA3P from CO2.

Tuesday, September 06, 2016

Natural Sciences

What would you expect to see in a museum of natural sciences? Frogs? Plants? Dinosaur skeletons? Exhibits about how the brain functions? A planetarium? Gems and minerals? Or, maybe all of the above? Science includes such diverse fields as astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics (Figure 1.1). However, those fields of science related to the physical world and its phenomena and processes are considered natural sciences. Thus, a museum of natural sciences might contain any of the items listed above.


Figure  1.1  The  diversity  of scientific  fields  includes astronomy, biology,  computer science, geology,  logic, physics, chemistry, mathematics, and many other  fields. (credit: “Image Editor”/Flickr)

There is no complete agreement when it comes to defining what the natural sciences include, however. For some experts, the natural sciences are astronomy, biology, chemistry, earth science, and physics. Other scholars choose to divide natural sciences into life sciences, which study living things and include biology, and physical sciences, which study nonliving matter and include astronomy, geology, physics, and chemistry. Some disciplines such as biophysics and biochemistry build on both life and physical sciences and are interdisciplinary. Natural sciences are sometimes referred to as “hard science” because they rely on the use of quantitative data; social sciences that study society and human behavior are more likely to use qualitative assessments to drive investigations and findings.
Not surprisingly, the natural science of biology has many branches or subdisciplines. Cell biologists study cell structure and function, while biologists who study anatomy investigate the structure of an entire organism. Those biologists studying physiology, however, focus on the internal functioning of an organism. Some areas of biology focus on only particular types of living things. For example, botanists explore plants, while zoologists specialize in animals.
One thing is common to all forms of science: an ultimate goal “to know.” Curiosity and inquiry are the driving forces for the development of science. Scientists seek to understand the world and the way it operates. To do this, they use two methods of logical thinking: inductive reasoning and deductive reasoning.
Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. This type of reasoning is common in descriptive science. A life scientist such as a biologist makes observations and records them. These data can be qualitative or quantitative, and the raw data can be supplemented with drawings, pictures, photos, or videos. From many observations, the scientist can infer conclusions (inductions) based on evidence. Inductive reasoning involves formulating generalizations inferred from careful observation and the analysis of a large amount of data. Brain studies provide an example. In this type of research, many live brains are observed while people are doing a specific activity, such as viewing images of food. The part of the brain that “lights up” during this activity is then predicted to be the part controlling the response to the selected stimulus, in this case, images of food. The “lighting up” of the various areas of the brain is caused by excess absorption of radioactive sugar derivatives by active areas of the brain. The resultant increase in radioactivity is observed by a scanner. Then, researchers can stimulate that part of the brain to see if similar responses result.
Deductive reasoning or deduction is the type of logic used in hypothesis-based science. In deductive reason, the pattern of thinking moves in the opposite direction as compared to inductive reasoning. Deductive reasoning is a form of logical thinking that uses a general principle or law to forecast specific results. From those general principles, a scientist can extrapolate and predict the specific results that would be valid as long as the general principles are valid. Studies in climate change can illustrate this type of reasoning. For example, scientists may predict that if the climate becomes warmer in a particular region, then the distribution of plants and animals should change. These predictions have been made and tested, and many such changes have been found, such as the modification of arable areas for agriculture, with change based on temperature averages.

Both types of logical thinking are related to the two main pathways of scientific study: descriptive science and hypothesis- based science. Descriptive (or discovery) science, which is usually inductive, aims to observe, explore, and discover, while hypothesis-based science, which is usually deductive, begins with a specific question or problem and a potential answer or solution that can be tested. The boundary between these two forms of study is often blurred, and most scientific endeavors combine both approaches. The fuzzy boundary becomes apparent when thinking about how easily observation can lead to specific questions. For example, a gentleman in the 1940s observed that the burr seeds that stuck to his clothes and his dogs fur had a tiny hook structure. On closer inspection, he discovered that the burrs’ gripping device was more reliable than a zipper. He eventually developed a company and produced the hook-and-loop fastener popularly known today as Velcro. Descriptive science and hypothesis-based science are in continuous dialogue.