1. Nucleus
   Protons and neutrons
2. Energy levels and electrons
   Arranged in concentric spheres around the nucleus. Negatively charged, move at speeds approaching the speed of light.

1. Autotrophy
   Autotrophs ("self-feeders") can take non-living sources of matter and energy and transform them into biological, chemical energy (green plants--photosynthesis). Photoautotrophs are able to convert light energy into chemical energy (ATP). Chemoautotrophs are able to extract energy from chemicals in the environment (non-living).
2. Heterotrophy
   We are heterotrophs require matter and energy from living sources. (We can stand in the sun all day and never photosynthesize one iota of our own energy.) Examples: Osprey eating fish; dung beetles eating dung; Dr. St. Clair's dad eating a hogi.

6 CO₂ + 12 H₂O ----> C₆H₁₂O₆ + 6 O₂ + 6 H₂O
Photosynthesizers take CO₂ from the atmosphere, hydrogen from water, light energy (usually from the sun), and a light-capturing molecule (chlorophyll) and are able. through the photosynthetic pathway, to convert the carbon, the oxygen, and the hydrogen from the water into the energy-rich molecule glucose: a simple sugar. And as a biproduct the plant will kick off some free oxygen into the atmosphere and also generate some metabolic water:** Light energy drives the process, (which involves the controlled manipulation of electrons using oxidation-reduction reactions).

1. Prokaryotic cells
   Remember the slide of the cyanobacterium? A heterocyst is a specialized cell that photosynthesizes. (Don't worry about it.) Photosynthesis in prokaryotes occurs in the cell membrane, which can infold to provide more surface area for photosynthesis to take place.
2. Eukaryotic cells
   Looking at a cross-section of a geranium leaf we can see the layers: upper epidermis (like a skin), palisade layer (major photosynthetic area: packed with chlorophyll), spongy layer (accomodates gas exchange: CO₂ from atmosphere, O₂ into atmosphere), lower epidermal layer, and then a vascular bundle (conductive tissue: able to move water and minerals into the leaf, and photosynthetic products (glucose) away from the leaf to the non-photosynthetic parts of the plant: the stem, roots.) Looking at one of the palisade cells we can see it has a nucleus, several chloroplasts, and a rather large vacuole in the center. Looking at a single chloroplast we see the double membrane system, the inner membrane folding into stacks of membranes, where photosynthesis takes place.

Photosynthesis: light reaction
8.1 Light Reaction
Overview information: Photosynthesis is divided into the light and dark reactions. The light reaction is where light energy is converted into intermediate forms of chemical energy; the dark reaction is where the intermediate forms of energy (from the light reaction) are transformed into the final energy product of photosynthesis: glucose. (Note that photosynthesis is more complex than what we will cover here, but that what follows covers the basics.)

1. Chlorophyll absorbs light energy
   Chlorophyll is a light-absorbing pigment that allows photosynthesis to happen. There are other light-absorning, photosynthetic (yellow, red) pigments in plants, but chlorophyll is the most important. Chlorophyll appears green: you're seeing the waves of light that are being reflected. The chlorophyll absorbs all but the green in the visible light spectrum. (In the fall, the chlorophyll pigments are the first to break down, revealing the other (red, yellow, orange) pigments that were always there, but masked by the larger quantity of chlorophyll.)
   Extracted chlorophyll absorbs light energy, (energizes electrons); when separated from the rest of the chloroplast, the excited electrons (in the chlorophyll) have no place to go so they collapse back down into the chlorophyll molecule, releasing their energy, which causes a red flourescence.
2. Light energy splits H20:
   Usually from the sun.
1. Oxygen released to atmosphere
   (We breathe this biproduct.)
2. Electrons are transferred from hydrogen atoms to chlorophyll
   
3. Hydrogen ions are shunted (to dark reaction for incorporation into glucose).
   Will be combined with carbon and oxygen to form glucose and will also be reunited with electrons, which will be energized electrons when they get them back.
3. Light energy (absorbed by chlorophyll) energizes electrons (oxidation reaction).
   When energized (pushed to a higher energy level), the high-energy electrons are stabilized by the electron acceptor:
4. Energized electrons are transfered to an electron acceptor (chlorophyll-oxidation reaction, compound Q-reduction reaction).
   
5. Energized electrons are processed using a series of electron acceptors between photosystem II and photosystem I.
   It is necessary to release the energy in the energized electrons in small, manageable amounts. This is through a series of oxidation-reduction reactions between electon-acceptors (which are proteins).
6. Thus, energy is released in small manageable amounts by manipulating electrons through a series of oxidation / reduction reactions.
   With each reaction, a small amount of energy is released, until the electrons reach photosystem I. The released energy is used to combine ADP and phosphate into ATP: the first intermediate form of energy from the light reaction.
7. Energy released in this fashion is used to form ATP by bonding a third phosphate to a molecule of ADP and by transferring energized electrons to the nucleotide NADP_ox to form NADP_red.
   In photosystem I (contains a slightly different chlorophyll molecule than photosystem II) electrons are energized again by the chlorophyll and pushed up to another receptor molecule. From there, the energized electrons are passed to another nucloetide, NADP_oxidized which, undergoing a reduction reaction, becomes the energy-rich NADP_reduced. NADP_red is the second intermediate form of energy from the light reaction.
   The ADP, phosphate (P_i, and NADP_ox move back and forth between the light and dark reactions.
   (ATP is the universal energy-carrying molecule of any living cell: the energy currency of life.)

Photosynthesis: dark reaction (a true cycle)
8.2 Dark Reaction
A true cycle begins and ends with the same material.
The dark reaction (not that it happens in the dark, but that it's light-independent) uses the ATP and NADP_red from the light reaction. As shown in figure 8.2, a five-carbon sugar (RUBP) is the beginning and end material of the dark reaction. (Just as we did with the light reaction, we are simplifying a very complex process here.)

1. Carbon, oxygen (from CO₂) and hydrogen (from water) are covalently bonded to from glucose (C₆H₁₂O₆).
   Carbon and oxygen from carbon dioxide (from the atmosphere) and hydrogen (from water) are covalently bonded to form glucose (C₆H₁₂O₆), which is the end product of the dark reaction.
2. This bonding requires energy from the light reaction (in the form of ATP and NADP_red)
   The intermediate forms of energy produced in the light reaction (ATP and NADP_red) are used to bond the carbon, oxygen, and hydrogen to build a glucose molecule.
3. Six turns of the cycle (1 carbon / turn) are required to form a single glucose molecule.
   One glucose molecule has six carbon atoms, each one gained from a single cycle of the dark reaction (figure 8.2). Each turn requires new energy (another ATP & NADP_red from the light reaction). What happens to the ADP and P_i, as well as the NADP_ox that remain after releasing their energy in the dark reaction? They cycled back to the light reaction (figure 8.1). It's beautiful, I tell you, beautiful.

1. Light reaction
   
1. Water is split, releasing oxygen gas (O2), hydrogen ions (H+), as well as a continuous supply of electrons (from hydrogen atoms).
   The hydrogen is ultimately combined with the carbon and oxygen to form the glucose. The supplied electrons make a one-way trip through the light reaction phase, eventully ending up as a part of the glucose molecule (from the dark reaction).
2. Light energy is transformed into chemical energy (ATP and NADPred) by manipulating energized electrons.
   (. . . using a series of oxidation-reduction reactions.)
2. Dark reaction
   
1. Energy is released from the bonds of ATP and NADPred (formed in light reaction) and then recaptured to bond carbon, hydrogen, and oxygen to form glucose.
   Where does the energy come from? The bonds. When the energy is released, the remaining ADP and phosphate (from the used ATP) and the oxidized NADP (NADP_ox) recycle to the light reaction where they are reformed into ATP and NADP reduced (NADP_red).

1. Incorporation of carbon into living tissue
   ALL the carbon in your body comes from atmospheric CO₂ through photosynthesis into plant material, and then to us through eating the plant material itself, or animal material that has eaten the plant material.
2. Release of free oxygen into the atmosphere
   Ever since the Doctor spanked your little behind, you've been breathing the stuff, and you will continue to do so, until you're done.

We're finding out more and more that our (human) activities impact the earth's life support system: photosynthesis. Have/ could we damage that system?
Your generation (you) will need to make important decisions about how we consume resources, in order to maintain healthy planet.

Remember: matter cycles, energy flows through the system, downhill.

1. Prokaryotic cells
   In bacteria and cyanobacteria (prokaryotes) glycolysis occurs in the cytoplasm, and cellular respiration occurs in the only available prokaryotic membrane system: the cell membrane, which will often infold to provide more surface area.
2. Eukaryotic cells
   In plants and animals, glycolysis occurs in the cytoplasm, and cellular respiration takes place in the inner-folded membrane of the mitochondrion: the powerhouse of the cell. (Much of metabolism, though not all, requires membrane surfaces, with folding providing more surface area.)

Note this ADP ---> ATP Diagram, (it's not in the syllabus). To bond the third phosphate onto ADP, it takes a certain amount of energy, (say, 100 units). The energy available from that bond will be 40-50% of what it took to form the bond, as some will be lost as heat. (Remember the 2nd law of thermodynamics: entropy.) 40-50% is actually quite efficient, an efficiency due to the use of enzymes; (internal combustion engines are 16-20% efficient).

1. Glycolysis
   Figure 8.3
   Glycolysis is a cytoplasmic pathway (occurs in the cytoplasm, NOT in the mitochodrion). It consists of 10 chemical reactions, but we will only be looking at the basics. Glycolysis begins with glucose (plants get it through autotrophy (photosynthesis), animals (like us) through heterotrophy--food). The glucose molecule is processed into 2 pyruvic acid molecules. Each glucose consists of 6 carbons; each pyruvic acid consists of 3 carbons. (Basically, the glucose is broken in half.) In the process of this conversion, energy is involved: first, 2 ATP are used (invested). Since the purpose of these energy transformations is to produce ATP, this seems counterproductive, but it is necessary to get things going. (Analogy: To use the potential energy in the carbohydrate-cellulose-glucose-news-paper (Daily Universe) we need to add a little energy (light a match). The added energy destabilizes the newspaper molecules and: burn-baby-burn, the energy is released. Note: in biological systems the energy release is controlled, not like burning paper.)
   So those first 2 ATP (in glycolysis) are an "energy investment."
   Next, as we process glucose into pyruvic acid (glycolysis) energized electrons are released from the splitting glucose. These energized electrons are vacuumed up into 2 NAD_ox molecules forming 2 NAD_red. There is also enough energy in the process to form 4 ATP molecules (from 4 ADPs and 4 phosphates). Both of these are energy returns: the 4 ATP, and the NAD_red (an indirect source of ATP as it will be processed to form more ATP. (See "electron transport chain" below.)) So, the results of glycolysis are: 2 ATP are spent, 2 NAD_red, 4 ATP, and 2 pyruvic acid are produced. With the 2 pyruvic acid molcules, we are ready for the big time: cellular respiration.

Cellular Respiration: three basic steps ending in the conversion of the energy from the 2 pyruvic acid molecules into the life-energy: ATP.


2. Oxidation of pyruvic acid to acetyl-COA
   (Oxidation: losing electrons.) In step 1 of cellular respiration, the pyruvic acids (3 carbons each--from the split 6-carbon glucose (glycolysis)), are broken down into two acetyl groups (2 carbons each) and 2 molecules of CO₂. (This is carbon dioxide we exhale.) So only 4 carbons from the original glucose molecule remain in the process (2 go into the atmosphere). As the carbons are ripped from the pyruvic acids to form the acetyl groups, some energized electrons are released, to be stabilized in the formation of 2 NAD_red: an energy gain (NAD_red is an indirect energy gain, as it will be processed to form ATP.)

To continue the process of cellular respiration (move into step 2: the Krebs cycle), the 2 acetyl groups need a co-enzyme: CoA. (A coenzyme is a molecule that works together (co-) with an enzyme.) The acetyl groups combined with the coenzymess form acetyl CoA, which brings us to the Krebs cycle. Figure 8.3


3. Krebs cycle
   The Krebs cycle is a true cycle: the beginning and ending material being 2 Oxaloacetic acid, which react with the 2 Acetyl CoA to form 2 Citric acid. Note that the 2 CoA (coenzymes) are kicked out, to be re-used by the next 2 needy acetyl groups. Every time we cycle the 2 citric acids through the Krebs cycle we end up with the 2 Oxaloacetic acids needed to do it again. There are actually 8 steps in the Krebs cycle, but for our purposes we'll leave it at that: we begin with 2 citric acids, end with 2 oxoaloalacetic acids, and here are the energy transformations that occur in the process: 2 ATP are formed, 6 NAD_ox pick up energized electrons (reduction) to form 6 NAD_red, and 2 FAD_ox also pick up electrons to form FAD_red. (NAD_red and FAD_red are indirect sources of energy.) Also, the 4 remaining carbons from the original glucose molecule are kicked off as carbon dioxide.
4. Electron transport chain
   8.4 Electron Transport Chain
   The 3rd phase of cellular respiration. The NAD_red and FAD_red are indirect sources of energy. They must go through electron transport chain to form ATP. This process releases the energy in electrons in small, manageable amounts, combining an ADP and a phosphate to form ATP as the electrons move down a step in the stairway-like chain of electron acceptors. (Each step involves an oxidation-reduction reaction from one electron acceptor to another.) The NAD_red generates 3 ATP through the electron transport chain, while the FAD_red, beginning a step lower on the chain, yields 2 ATP molecules.

Glycolysis and cellular respiration: results
8.5 Summary table
Hpw many ATP (gross/net) do we get per molecule of glucose? At each stage of processing the glucose? How many ATP do we get out of a NAD_red molecule through the electon transport chain? FAD_red? (Look at the table.) Glycolysis and cellular respiration are 40-50%, which is quite good. (Enzymes play a key role in efficiency.)
Remember: Matter cycles; Energy flows.

1. The energy stored in glucose bonds is released and recaptured in ATP bonds.
   ATP does the work of life.
2. CO₂ and H₂O are by-products of cellular respiration.
   

1. ATP is the energy currency of life.
   ATP is the UNIVERSAL energy currency of life. All living things make use of some form of glycolysis and cellular respiration to gain energy.
2. CO₂ and H₂O are obviously significant to life.
   Good little molecules to have around, especially on a rainy day, or when you just feel like you would like to keep on living.

The relationship between cellular respiration and photosynthesis:
Note from the diagram: Matter cycles; Energy flows.