Cell Biology

A. Step 1: The Light Dependent Reaction

AGAIN, the purpose of the light-dependent reaction is to convert radiant energy to chemical energy. Obviously, light must be present; so this reaction "depends" on sunlight.  There is one group of Archaeans that performs photosynthesis (Halobacteria), but their process of harvesting light energy seems quite different from the process in eubacteria and chloroplasts in eukarya and probably evolved independently. Within the eubacteria, there are also a wide variety of photosynthetic processes. We will focus on a couple major types and make reference to others as we go.

1. PRIMITIVE SYSTEMS:

a. cyclic phosphorylation in "purple non-sulphur" and "green non-sulpher" bacteria:Like all bacteria, they have a double membrane (two bilayers). Proteins nested within the inner membrane form "reaction centers (also called "photosystems") and "electron transport chains" (ETC's) used in photosynthesis. This inner membrane is often highly convoluted, increasing the surface area and the number of reaction centers and ETC's that can be imbedded. Each reaction center contains proteins arrayed around molecules of bacteriochlorophyll, which contain atoms of Magnesium. In the presence of light, the photons transfer energy to these electrons. The electrons are raised to a higher energy state, lost from the atom, and transferred to an 'electron acceptor molecule' in the inner membrane of the bacterium, which transfers the electron the the electron transport chain. When a high-energy electron is transferred down the chain, protons (H+) follow ('electrostatically') and are pumped across the inner membrane into the intramembrane space. This build-up of H+ ions in the intermembrane space creates an electrostatic charge differential across the membrane. There are closed protein channels that, when opened, allow the H+ to flood through in response to the charge gradient. This electric discharge energy is used by the enzyme ATP-synthetase to add a phosphate group to ADP, making ATP. This is called 'chemiosmotic synthesis' or 'chemiosmosis'. So, what has happened is that the passage of an electron -excited by light energy - has been used to 'pump protons' into the intermembrane space, establishing an H+ ion charge gradient. The flow of H+ ions through protein channels transforms this electric energy to chemical bond energy in the form of a bond between ADP and P--> ATP. The high-energy electron is then passed down the electron transport chain. and ATP is produced. The electron, having lost its energy, can be recycled back to the Mg atom. This cyclic production of ATP, powered by sunlight, is called cyclic phosphorylation. As discussed below, these odd bacteria do not perform the light independent pathways. In other words, they do not use the energy in ATP to make glucose. This has two interesting consequences. First, it means they can't rely on photosynthesis, alone, for energy harvest, because ATP isn't stable enough to last over the course of an evening. So, they must also 'eat' - they are heterotrophs, and can harvest energy from the food they ingest. The other consequence is discussed below.

b. "green sulphur" and "purple sulphur" bacteria that use sulphides as the electron donors:

When the excited electron is recieved by the 'electron acceptor',something else can happen. Instead of the Electron Acceptor giving the electron to the ETC, it can give the electron to NADP... another 'energy transport molecule' like ADP. When this happens, the NADP gains energy and a negative charge and is NADP-. It reacts with free H+ ions that are always present in aqueous solutions (you should know why...), to make the high energy transport molecule, NADPH. In this case, the electron isn't returned to the Magnesium.... photosynthesis would stop, unless the photosystem can strip electrons from other molecules in solution. There are several groups of primitive eubacteria ("green sulphur bacteria" and "purple sulphur bacteria") that use sulfides (like hydrogen sulfide - H₂S) as the electron donor.

Sulphur bacteria have photosystems that strip electrons from Hydrogen Sulphide (H₂S). This releases 2H+ ions and S as a waste product. So, sulphur bacteria that are still present today photosynthesize in sulphur springs and do not produce oxygen as a waste product. This explains an interesting geological pattern: The oldest fossil life on record are photosynthetic bacteria that date to 3.8 billion years old. However, the first evidence of oxygen in the Earth's atmosphere occurs at about 2 billion years ago. So, how can you now explain how there were photosynthetic bacteria present for 1.8 billion years, without any oxygen being produced? Sulphur bacteria. And they have another interesting characteristic - they are anaerobic organisms poisoned by oxygen gas. So, not only don't they produce oxygen, but they can only survive in its absence. All these factors suggest that they may be similar to the first photosynthetic life forms that thrive in the anaerobic environment of the early earth. There is a problem for them, however. These bacteria can only survive in places where H₂S is abundant - like sulphur springs. These places are rare. If something evolved a system that could strip electrons from a more abundant source, like water (H₂O), then these new organisms could exploit almost the whole planet - as 75% of the planet is covered by H₂O.

2. ADVANCED SYSTEM: most other photosynthetic bacteria (cyanobacteria), and photosynthetic eukaryotes.

       - In photosynthetic Eukaryotes(photosynthetic protists and plants), these reactions occur on the inner membrane of the Chloroplast - a specific membrane-bound organelle very much like a bacterium within the larger eukaryotic cell. Indeed, as described above, eukaryotic chloroplasts are probably the deescendants of free-living cyanobacteria - with whom they share basic membrane structure and DNA similarity.
       - In cyanobacteria and chloroplasts, there are two types of reaction centers called "photosystems". The second photosystem (PSII) has a lower electronegativity than the first, so it can exert a 'stronger' pull and can strip electrons from WATER (which holds the electrons more strongly than H₂S does.) The splitting of water releases oxygen gas as a waste product, so this type of photosynthesis is also called "oxygenic photosynthesis".
        - Here's how it works: Light strikes the phosystems nested in the inner membrane (called the 'thylakoid' membrane in chloroplasts). An electron in each photosystem is excited and lost from the Mg in the chlorophyll molecule. The electrons are accepted by partcular electron acceptor molecules. The electron lost from PS I is ultimately passed to NADP, which accepts a H+ to balance the charge, making the high energy molecule, NADPH. The electron lost from PSII is passed to an electron acceptor, and then to molecules in the electron transport chain. As the electron is passed down the chain, ATP is produced by chemiosmosis (as described above). When this electron has lost it's energy, it replaces the electron lost from PS I. So, PS I is all set, and need not strip electrons from an electron donor. However, PS II has lost an electron, and must replace this electron for photosynthesis to continue. PSII strips electrons from H₂O. Water is split into oxygen, 2 H+, and 2 electrons. The electrons are passed to the cholorophyll in PS II, excited by light, and energized. The oxygen reacts with another oxygen atom to produce oxygen gas, which is released as a waste product. The propose of photosynthesis is not "to produce oxygen". The purpose of the light reaction of photosynthesis is to transform radiant energy into chemcial energy, and produce ATP and NADPH. The two molecules, ATP and NADPH, are the useful products. Again, oxygen gas is produced as a waste product when electrons are stripped from water. The presence of oxygen in the oceans 2.5-2 billion years ago, indicated by the presence of sedimentary deposits with oxidized iron (banded iron formations), indicates the evolution of this more advanced type of photosynthesis that evolved in ancient photosynthetic bacteria. Almost all of the oxygen gas present in the earth's atmosphere is produced by photosynthetic organisms. Before modern oxygenic photosynthesis evolved, there was no free oxygen gas in the atmosphere.

3. SUMMARY OF LIGHT REACTIONS:

• Radiant energy excites electrons, which are passed down an electron transport chain and ATP is made.
• The first organisms to evolve this process probably used H₂S as the donor of these electrons. These sulphur bacteria do not produce oxygen as a waste product; they produce sulphur.
• The evolution of PSII was very important, because photosynthetic organisms could use H₂O as the electron donor and were no loner limited to living in places where H₂S was abundant. These organisms that use water as the electron donor produce oxygen as a waste product, and the geologic record suggests that this process evolved about 2.3-2.0 bya.
• Ultimately, the electrons are passed to NADP, making NADPH.
• Water + ADP + NADP --> in the presence of light --> ATP + NADPH + O₂ (waste)

B. Step 2: The Light Independent Reactions:

The purpose of the "Light Independent Reactions" is to convert the chemical energy in fragile ATP and NADPH molecules into a more stable energy form by building covalent bonds between carbon atoms to make glucose. In prokaryotes, these reactions occur in the cytoplasm of the cell; in eukaryotes, these reactions occur in the stroma - or cytoplasm - of the chloroplasts. It is important to appreciate that organisms using both primitive and advanced light reactions perform the light independent reactions.

The primary reaction is called the Calvin-Benson Cycle, and it works like this:
        - 6 CO₂ molecules bind to 6 C₅ molecules of Ribulose Biphosphate (RuBP), making 6 C₆ molecules.  (ATP is broken and the energy that is released is used to link CO₂ to RUBP).
        - These energized C₆ molecules are unstable; the split into 12 C₃ molecules. So, since the first stable product is a C3 molecule, this type of reaction is called the C3 pathway.
        - 2 C₃ molecules are used to form 1 glucose (C₆) molecule. More ATP is used, and NADPH is used, too, and H is transferred to put the 'hydrogen' in 'carbohydrate'.
        - the 10 remaining C₃ molecules (30 C total) are rearranged, using ATP and NADPH, and 6 C₅ molecules are generated (30 C total).

The reaction can be summarized like this: Six CO₂ molecules are used to make one molecule of glucose. Six RuBP molecules are involved, and are recycled through the process. The ATP and NADPH formed in the light reaction are used to power this reaction; the energy in these molecules is used top make bonds between the CO₂, and the H from NADPH is used to reduce the CO₂ to form glucose (C₆H₁₂O₆). As such, the radiant energy initially trapped in chemical bonds in ATP and NADPH is transferred to form bonds between carbon atoms in glucose. The energy intially trapped in fragile molecules has been stored in a more stable form.

When cells build glucose from CO2, they have not only stored energy in a stable form - they have also harvested carbon from the environment and transformed it into a usable organic molecule. Since all biologically important molecules (except water) are carbon-based organic molecules, all life forms needs a source of carbon to build amino acids, nucleotides, sugars, and lipids. "Heterotrophs" get organic carbon in the 'food' they eat. "Autotrophs" get their carbon through the light independent reaction, which also stores energy.   The first group of bacteria discussed above - the green non-sulphur bacteria and purple non-sulphur bacteria - perform the Light Dependent Reaction and make ATP using sunlight, but they do not perform the light indepedent reactions. So, they do not absorb CO2 to make their organic molecules. Instead, they must consume organic molecules to acquire their carbon. These organisms are "photoheterotrophs". They may represent the first step in the evolution of photosynthesis: the evolution of light-trapping reactions by heterotrophic cells. They use cyclic phosphorylation to make ATP in the presence of light, but they use organic molecules as electron donors.

C. A History of Photosynthesis

The history of photosynthesis is closely tied, as one would imagine, to the history of life, itself. The oldest fossils date to 3.8 by (3.8 billion years ago). These are microfossils (that look very much like living photosynthetic bacteria), and stromatolites -- which are layers of bacteria.   The first evidence of oxygen gas in the atmosphere (and dissolved in water), however, dates to only 2.3 by. This evidence is the first existence of "oxidized" metals (like oxidized -or rusted - red iron) in sediments that date to that age. Previous to 2.3 bya, the iron that settled out in sediments was not ixidized - it was in its grey and reduced state. So, it might seem curious that photosynthetic organisms were alive for 1.6 by but apparently did not pruduce oxygen gas. Well, it shouldn't be confusing to you! You now know that the two most primitive types of photosynthesis, cyclic phosphorylation and sulphur photosynthesis, do NOT produce oxygen gas as a waste product. So, apparently, the evolution of modern photosynthetic pathways occurred about 2.3 bya, and began to produce the oxygen gas that oxidized the iron precipitating out of the water in the sediments of that age.

In addition, the balance between photosynthesis and respiration affects the composition of the atmosphere. About 350 mya (350 million years ago), most continents were ringed by very extensive coastal swamps. Plants had evolved on land about 400 mya, and by 350 there were very large tree-like plants present, forming extensive forests. When these trees died and fell into the swamps, they were covered by sediment and protected against decomposition. Under progressively deeper layers of sediment, pressure and heat build up and converted the long chains of cellulose (which are carbohydrate hydrocarbons) in coal and natural gas... our "fossil fuels" are truly fossils. Now think about: as a consequence of photosynthesis, the plants were extracting carbon dioxide from the atmosphere and adding oxygen gas. Then, all that carbon was sequestered below sediments, protected from decomposing bacteria and fungi. Typically, the decomposers would break the bonds between the carbons through CELLULAR RESPIRATION to harvest the energy... and they would release the single carbon atoms as carbon dioxide to the atmosphere. To do this, these bacteria and fungi would USE oxygen as the final electron acceptor in their electron transport chains during aerobic respiration. So typically, plants take CO2 from the air and add oxygen, and animals take oxygen from the air and add CO2. When this cycle in disrupted by sequestering the plants under sediment, CO2 in the atmosphere delcines (and is not replenished) and oxygen accumulates (and is not used by decomposers because they have nothing to decompose). During this time 400 mya, oxygen concentration in the atmosphere rose to nearly 35% (they are 21% now).

What happened to all that carbon stored as fossil fuel? Well, we are burning it NOW, breaking the carbon bonds and harvesting the energy to power our coal-burning electrical power plants.... and we are adding that carbon to the atmosphere as carbon dioxide.

IV. Protein Synthesis

As we've already mentioned, protein synthesis is fundamental to nearly everything a cell does. Protein channels are used to transport large molecules across the membrane. Almost all chemical reactions occuring in cells are catalyzed by protenaceous enzymes, including those involved in energy harvest, DNA replication, and cell division. Proteins perform important structural functions within cells and multicellular organisms, too; such as the histone proteins in chromosomes, the proteins in ribosomes, the collagen and elastin fibers that hold skin cells together, the collagen on which calcium and phosphate is deposited in bone, the protein myofibrils of actin and myosin in muscle cells, the neurotransmitters used for cell-cell communication between neurons, and the enzymes that digest food in the stomach and intestine of animals. So, proteins are fundamental to what cells and organisms ARE, structurally, and what they DO functionally. As you know, the genetic information determines the types of proteins a cell can make. The subset of proteins a cell actually DOES make, and the timing of WHEN they are made, is determined by what genes are "on" and what genes are "off" at a given time. This regulation of gene activity is ALSO co-ordinated by proteins - called transcription factors - that bind to DNA and promote or inhibit gene activity. So, proteins also regulate protein synthesis. Hopefully you see just how important proteins are to cells and organisms. So, the process of making these proteins is important, too.

A. Overview

The sequence of nitrogenous bases in a region of DNA is 'read' by a complex of enzymes that build a complementary strand of RNA. This process of reading DNA and making RNA is called 'transcription'. This is a great word for the process, as the message written in the language of nucleic acids is copied in essentially the same language - the language of nucleic acids. This RNA may be a recipe for a protein (m-RNA), or it may be an RNA that will act on its own as t-RNA, mi-RNA, si-RNA, or be complexed with proteins in the ribosome (r-RNA). Obviously, in "protein synthesis", only the m-RNA is read to make a protein. However, the other molecules all play a role. The sequence of nitrogenous bases in the m-RNA is then 'read' by a ribosome, which links a specific sequence of amino acids together into a protein based on that sequence of nitrogenous bases in the m-RNA. This process is called 'translation'. This is a great choice of a word, too. Here the sequence of information written in the language of nucleic acids is rewritten in a new language (hence, translation) - the language of amino acids.

Many of the initial RNA products have specific regions (introns) cut out of their sequence before they become functional. This step is known as "RNA processing" or "RNA splicing". Introns are present in nearly all eukaryotic RNA's, and are also in the DNA genes that encode them. Up until a few years ago, the only introns in prokaryotes had been found in t-RNA molecules of archaeans. More recently, however, introns have been found in m-RNA and r-RNA molecules of a few eubacteria and a few more archaeans. So, although they are rare in prokaryotes, we will describe a generic, simplified process of protein synthesis that includes introns and RNA processing.

In addition to splicing the RNA product of transcription, the initial protein product of translation may also be spliced and modified before it becomes functional. In eukaryotes, this protein processing often occurs in the Golgi apparatus.

The description presented here is a simple model of protein synthesis. You will learn more complex aspects of this process in Genetics.

B. The Process of Protein Synthesis

1. Transcription:

a. The message is on one strand of the double helix - the sense strand: The DNA double helix is composed of two anti-parallel complementary strands of DNA. Only one strand in a coding region ("gene") is read; this strand carries a meaningful recipe that "makes sense". This is called the "sense" strand. The other strand, limited by complementarity, is not a meaningful message - it is the "non-sense" (or "anti-sense") strand. Think about it this way. Given a meaningful message of "C-A-T" (a small furry mammal), the complementary strand is limited to the meaningless sequence of "G-T-A" (????...). As the meaningful sequence gets longer, it is even LESS likely that, just by chance, the complementary strand would be meaningful, too. Again, in all eukaryotic genes and in some rare prokaryotic ones, there will be non-functional "introns" interspersed throughout the meaningful message. The meaningful parts are called "exons". The process of transcription is continuous, so introns and exons get transcribed and these regions - if present in the DNA - will also be present in the RNA product.

b. The cell 'reads' the correct strand based on the location of the promoter, the anti-parallel nature of the double helix, and the chemical limitations of the 'reading' enzyme, RNA Polymerase. RNA Polymerase binds to the DNA at a specific sequence next to the gene, called the 'promoter'. It binds in a specific way, so it is pointed towards the gene. RNA polymerase can only create a strand of RNA in the 5' to 3' direction, adding a new base to the free -OH group of the preceeding nucleotide on the chain. So, from its position at the promoter, looking down the two strands in the gene, the RNA Polymerase can only 'read' one strand - the DNA strand that is 3'-5'. It must create a strand that is anti-parallel to the DNA' template', and it can only bind nucleotides in 5'-3' direction. So, only the 3'-5' DNA strand is read in this region, and only one RNA strand, 5'-3' is made. It is important to appreciate that this relationship is 'local'. In another region of the DNA, the promoter may be on the other side of the gene, and the other strand may be read.

c. Transcription ends at a sequence called the 'terminator'. These regions have specific sequences that destabilize the attachment of the RNA Polymerase to the DNA... it detaches and transcription stops. VIDEO
So, the process of transcription can be summarized like this: RNA Polymerase binds at the promoter and reads the sense strand of DNA. The ploymerase links together RNA nucleotides 5--> 3, in a sequence complementary to the DNA sense strand. This process is continuous, so all DNA bases are 'read', including exon and intron sequnces. This process continues until a terminator region is reached. Reading this region destabilizes the RNA polymerase. It detaches from the DNA, and transcription stops. All types of RNA (m-RNA, r-RNA, t-RNA) are made through this process.

2. Transcript Processing:

At this point in the process, the cell has read the gene and synthesized a complementary copy of strand of RNA. In all eukaryote sequences and many prokaryotic ones, this RNA molecule will have non-functional introns that need to be 'cut-out'. Enzymes cut the introns out and splice the ends together. In some cases, the introns catalyze their own excision - they are RNA molecules with enzymatic activity. These are one class of "ribozymes" - a very interesting class of molecules. There are other ribozymes that cleave other RNA molecules (not themselves) and others that catalyze other chemical reactions unrelated to RNA splicing.

In eukaryotes, the m-RNA, t-RNA and r-RNA is shunted through the nuclear membrane to the cytoplasm. In prokaryotes, there is no nucleus so the RNA is already in the cytoplasm. In all organisms, the r-RNA is complexed with proteins to form functional ribosomes. The t-RNA's bind specific amino acids.

VIDEO

3. Translation:

In this process, amino acids are linked together into a protein. The particular sequence of amino acids that are linked together is determined by the sequence of nitrogenous bases in m-RNA. This process occurs at the ribosome.

a. m-RNA attaches to the ribosome at the 5' end. The ribosome has two reactive sites. The RNA moves through the ribosome until a specific sequence of nucleotides, AUG, is positioned in the first site. Three base sequence in the m-RNA are called 'codons'. This specific codon AUG, which starts the process of translation, is called the 'start codon'. All proteins made by all life forms initially begin with methionine, and use the codon AUG..

b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence, binds to the m-RNA/ribosome complex. This t-RNA always carries the amino acid methionine. The genetic code describes the relationship between 3-base codons in m-RNA and the amino acids they code for. BE SURE TO LOOK AT THIS CODE. SEE HOW 'AUG' CODES FOR METHIONINE? SEE HOW 'UGA' IS CALLED A 'STOP' CODON? All life uses this same genetic code.

c. Binding of the t-RNA to the first site opens a second site that reads the second 3-base codon (GCC in picture at right). Another t-RNA binds here - one with the specific anti-codon sequence (CGG). This t-RNA, with this anti-codon, always binds with the amino acid alanine.

d. Now a complex series of reactions occurs. Methionine is cleaved from its t-RNA and bound to alanine (this peptide bond between amino acids forms via dehydration synthesis). The t-RNA in position 1 vacates the site, and the t-RNA in site 2 moves to site 1. This is called a 'translocation reaction'. The next 3-base codon is positioned in the second site - ready to accept the next t-RNA/ammino acid complex (for tryptophan in the picture to the right).

e. Polymerization proceeds. This process continues down the m-RNA strand, reading the message one codon (3-base "word") at a time. For each codon, a specific amino acid is added to the chain. Thus, the nucleotide sequence in the m-RNA - copied from the nucleotide sequence in the DNA gene - determines the sequence of amino acids in the protein.

f. Termination. There are some codons that have no corresponding t-RNA molecule. When these codons enter the second site, no t-RNA/amino acid is added. When the ribosome translocates, no new amino acid is added and the chain is terminated. These particular codons that stop translation are called "stop codons".

VIDEO

4. Protein Processing:

The initial protein product usually needs to be modified to become functional. These modifications are termed "post-translational modifications". First of all, the methionine is usually cut off - this relieves an important constraint on the structure of functional proteins... functional proteins DON'T all start with methionine! Then, the protein may be spliced, or it may be bound with a sugar group (glycoprotein), lipid (lipoprotein), nucleic acid (nucleoprotein), or another protein (quaternary protein). In eukaryotes, much of this processing occurs in the Golgi apparatus.

C. Regulation of Protein Synthesis

Aside from somatic mutations, all the cells in a multicellular organism are genetically identical. So, the cells in your retina, bone, muscle, and stomach lining all contain the same genes. These cells perform different functions because they are reading different genes and making different proteins. Your muscle has the gene for rhodopsin (a photoreceptive pigment produced in the retina), but that gene is not transcribed in muscle cells. In contrast, retinal cells have the genes for the muscle proteins actin and myosin, but these genes are not transcribed. So, cell specialization and the developmental process by which cells specialize from the fertilized egg occurs by regulating this process of protein synthesis.

D. The Universal Code

One of the most striking thing about life is that all living things - from humans to bacteria to oak trees - uses DNA as the recipe for proteins and the process of making proteins occurs in the same way. In fact, even the way translation occurs is the same... such that when CCC occurs in any organism, the amino acid 'proline' is placed in position.... regardless of where the organism is a cat, tree, or germ. This is why the genetic code is called "universal". And, it has allowed humans to manipulate genes - taking them out of one organism and putting it into another. This is called "recombinant DNA technology" Here are two examples:

1) Humulin: Diabetics need to inject the protein 'insulin' to regulate the level of sugar in their blood. Prior to the 1980's, insulin had to be purified from horses and pigs. Sometimes, humans would reject this insulin, causing blood clots and sometimes death. In the 1980's, the gene for insulin was found in the human genome (chromosomes). It was cut out, and put in bacteria that reproduce very rapidly. These bacteria now read this recipe for human insulin, and made that protein just like they made their own bacteria proteins. There is nothing "special" in the structure of human DNA - the recipes for human proteins can be read by other organisms, too. Now, the pharmaceutical company Eli Lilly manufactures human insulin using these genetically engineered bacteria that make human insulin... this insulin - because it is fully "human"... does not cause rejection in anyone and is much easier to make than bleeding horses and pigs and isolating their insulin.

2) Bt-crops: There is a bacterium that lives in the soil called Bacillus thurigiensis. It produces a protein that happens to inhibit the growth of caterpillar larvae and eventually causes them to die. This isn't how the bacterium uses the protein (caterpillars don't eat soil), but the protein has that effect on caterpillars none the less. So, Monsanto cut the gene out of the bacterial genome and spliced it into the genes in corn. Now, the corn is a "GMO - genetically modified organism" - that reads this gene and makes this toxic protein. Caterpillars that eat the corn die, but it does not affect other insects or mammals, like us. Farmers used to have to spray their corn field with insecticide - in fact, the same toxin produced by this bacterium! Now, they grow corn with the toxin already present - saving money and time that use to be used on buying and spraying the insecticide.

STUDY QUESTIONS:

1. Draw what happens in the primitive light reaction of sulphur bacteria, and explain the events that occur.

2. What is the electron donor for sulphur bacteria? What type of limitation does this impose on where these organisms can live?

3. Draw and explain what happens in the more advanced light dependent reaction. Why can we call this an 'adaptation'? (Why is this an improvement over the the more primitive system, considering the habitats available on Earth?)

4. Describe the correlations between these observations:

- the oldest fossils are 3.8 billion years old and look like photosynthetic organisms

- eukaryotic photosynthetic organisms about 2 billion years ago

- 'red beds', the oldest sedimentary deposits that include oxidized minerals, date to about 2 billion years

- previous to these red beds, minerals in sedimentary deposits are in their reduced state, suggesting that they were not exposed to an oxidizing atmosphere during their erosion and deposition, suggesting that the atmosphere contained no oxygen gas.

5. Draw the Light Indepedent reaction and describe the events that occur.

6. What 'cues' determine where transcription will start and stop?

7. Describe the translocation reaction.

8. What are introns and exons, and how is protein synthesis modified to accomodate this structural change?

9. The process of protein synthesis and the universal genetic code provides one of the dramatic pieces of evidence of a common ancestry to all life. Explain why.

10. Describe an example where we exploit the universality of the code to get an organism to make another organism's protein.