S2019_Lecture_08_Reading - Biology

S2019_Lecture_08_Reading - Biology

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An important chemical compound is adenosine triphospate (ATP). The main cellular role of ATP is as a "short-term" energy transfer device for the cell. The hydrolysis reactions that liberate one or more of ATP's phosphates are exergonic and many, many cellular proteins have evolved to interact with ATP in ways that help facilitate the transfer of energy from hydrolysis to myriad other cellular functions. We will see many examples of ATP "at work" in the cell, so be looking for them. As you see them, try to think of them as functional examples of Nature's uses for ATP that you could be expected to see in another reaction or context.

ATP structure and function

At the heart of ATP is the nucleotide called adenosine monophosphate (AMP). Like the other nucleotides, AMP is composed of a nitrogenous base (an adenine molecule) bonded to a ribose molecule and a single phosphate group. The addition of a second phosphate group to this core molecule results in the formation of adenosine diphosphate (ADP); the addition of a third phosphate group forms adenosine triphosphate (ATP).

Figure 1. ATP (adenosine triphosphate) has three phosphate groups that can be removed by hydrolysis to form ADP (adenosine diphosphate) or AMP (adenosine monophosphate).

The phosphorylation (or condensation of phosphate groups onto AMP) is an endergonic process. By contrast, the hydrolysis of one or two phosphate groups from ATP, a process called dephosphorylation, is exergonic. Why? Let's recall that the terms endergonic and exergonic refer to the sign on the difference in free energy of a reaction between the products and reactants, ΔG. In this case we are explicitly assigning direction to the reaction, either in the direction of phosphorylation or dephosphorylation of the nucleotide. In the phosphorylation reaction the reactants are the nucleotide and an inorganic phosphate while the products are a phosphorylated nucleotide and WATER. In the dephosphorylation/hydrolysis reaction, the reactants are the phosphorylated nucleotide and WATER while the products are inorganic phosphate and the nucleotide minus one phosphate.

Since Gibbs free energy is a state function, it doesn't matter how the reaction happens; you just consider the beginning and ending states. As an example, let's examine the hydrolysis of ATP. The reactants ATP and water are characterized by their atomic makeup and the kinds of bonds between the constituent atoms. Some free energy can be associated with each of the bonds and their possible configurations—likewise for the products. If we examine the reaction from the standpoint of the products and reactants and ask "how can we recombine atoms and bonds in the reactants to get the products?," we find that a phosphoanhydride bond between an oxygen and a phosphorus must be broken in the ATP, a bond between an oxygen and hydrogen must be broken in the water, a bond must be made between the OH (that came from the splitting of water) and the phosphorus (from the freed PO3-2), and a bond must be formed between the H (derived from the splitting of water) and the terminal oxygen on the phosphorylated nucleotide. It is the sum of energies associated with all of those bond rearrangements (including those directly associated with water) that makes this reaction exergonic. A similar analysis could be made with the reverse reaction.

Possible Exercise

Use the figure of ATP above and your knowledge of what a water molecule looks like to draw a figure of the reaction steps described above: breaking of the phosphoanhydride bond, breaking of the water, and formation of new bonds to form ADP and inorganic phosphate. Track the atoms in different colors if that helps.

Is there something special about the specific bonds involved in these molecules? Much is made in various texts about the types of bonds between the phosphates of ATP. Certainly, the properties of the bonds in ATP help define the molecule's free energy and reactivity. However, while it is appropriate to apply concepts like charge density and availability of resonance structures to this discussion, trotting these terms out as an "explanation" without a thorough understanding of how these factors influence the free energy of the reactants is a special kind of hand-waving that we shouldn't engage in. Most BIS2A students have not had any college chemistry and those who have are not likely to have discussed those terms in any meaningful way. So, explaining the process using the ideas above only gives a false sense of understanding, assigns some mystical quality to ATP and its "special" bonds that don't exist, and distracts from the real point: the hydrolysis reaction is exergonic because of the properties of ATP and ALSO because of the chemical properties of water and those of the reaction products. For this class, it is sufficient to know that dedicated physical chemists are still studying the process of ATP hydrolysis in solution and in the context of proteins and that they are still trying to account for the key enthalpic and entropic components of the component free energies. We'll just need to accept a certain degree of mechanistic chemical ignorance and be content with a description of gross thermodynamic properties. The latter is perfectly sufficient to have deep discussions about the relevant biology.

"High-Energy" bonds

What about the term "high-energy bonds" that we so often hear associated with ATP? If there is nothing "special" about the bonds in ATP, why do we always hear the term "high-energy bonds" associated with the molecule? The answer is deceptively simple. In biology the term "high-energy bond" is used to describe an exergonic reaction involving the hydrolysis of the bond in question that results in a "large," negative change in free energy. Remember that this change in free energy does not only have to do with the bond in question but rather the sum of all bond rearrangements in the reaction. What constitutes a large change? It is a rather arbitrary assignment usually associated with an amount of energy associated with the types of anabolic reactions we typically observe in biology. If there is something special about the bonds in ATP, it is not uniquely tied to the free energy of hydrolysis, as there are plenty of other bonds whose hydrolysis results in greater negative differences in free energy.

Figure 2. The free energy of hydrolysis of different types of bonds can be compared to that of the hydrolysis of ATP. Source:

Table 1. Table of common cellular phosphorylated molecules and their respective free energies of hydrolysis.

The cycling of ATP pools

Estimates for the number of ATP molecules in a typical human cell range from ~3x107 (~5x10-17 moles ATP/cell) in a white blood cell to 5x109 (~9x10-15 moles ATP/cell) in an active cancer cell. While these numbers might seem large, and already amazing, consider that it is estimated that this pool of ATP turns over (becomes ADP and then back to ATP) 1.5 x per minute. Extending this analysis yields the estimate that this daily turnover amounts to roughly the equivalent of one body weight of ATP getting turned over per day. That is, if no turnover/recycling of ATP happened, it would take one body weight worth of ATP for the human body to function, hence our previous characterization of ATP as a "short-term" energy transfer device for the cell.

While the pool of ATP/ADP may be recycled, some of the energy that is transferred in the many conversions between ATP, ADP, and other biomolecules is also transferred to the environment. In order to maintain cellular energy pools, energy must transfer in from the environment as well. Where does this energy come from? The answer depends a lot on where energy is available and what mechanisms Nature has evolved to transfer energy from the environment to molecular carriers like ATP. In nearly all cases, however, the mechanism of transfer has evolved to include some form of redox chemistry.

In this and the sections that follow we are concerned with learning some critical examples of energy transfer from the environment, key types of chemistry and biological reactions involved in this process, and key biological reactions and cellular components associated with energy flow between different parts of the living system. We focus first on reactions involved in the (re)generation of ATP in the cell (not those involved in the creation of the nucleotide per se but rather those associated with the transfer of phosphates onto AMP and ADP).

Video link

For another perspective - including places you'll see ATP in Bis2a, take a look at this video (10 minutes) by clicking here.

How do cells generate ATP?

A variety of mechanisms have emerged over the 3.25 billion years of evolution to create ATP from ADP and AMP. The majority of these mechanisms are modifications on two themes: direct synthesis of ATP or indirect synthesis of ATP with two basic mechanisms known respectively as substrate level phosphorylation (SLP) and oxidative phosphorylation. Both mechanisms rely on biochemical reactions that transfer energy from some energy source to ADP or AMP to synthesize ATP. These topics are substantive, so they will be discussed in detail in the next few modules.

Introduction to bacterial and archaeal diversity

Perhaps bacteria may tentatively be regarded as biochemical experiments; owing to their relatively small size and rapid growth, variations must arise much more frequently than in more differentiated forms of life, and they can in addition afford to occupy more precarious positions in natural economy than larger organisms with more exacting requirements. - Marjory Stephenson, in Bacterial Metabolism, (1930)

Prokaryotes are single-celled organisms with neither a membrane-bound nucleus nor other lipid membrane-bound organelles. They are composed of two phylogenetically distinct groups of organisms: Bacteria and Archaea. In recent years, the term prokaryote has fallen out of favor for many microbiologists. The reason is that while bacteria and archaea share many morphological characteristics, they nevertheless, represent evolutionarily distinct domains of life. The figure below shows a simple phylogenetic tree with the three main domains of life: Bacteria, Archaea, and Eukarya. This means that the use of the term prokaryote should not be used with the intention to group the bacteria and archaea on the basis of shared evolutionary history. It is, however, convenient to use the term "prokaryote" when describing the groups of organisms that share the common morphological characteristics (i.e. no nucleus) and some of your instructors will likely do so. When you hear or use the term "prokaryote", therefore, make sure that it is not being used to or implying that the bacteria and archaea are part of the same phylogenetic group. Rather make sure that the use of the term "prokaryote" is limited to describing the common physical characteristics of these two microbial groups.

Figure 1. Although bacteria and archaea are both described as prokaryotes, they have been placed in separate domains of life. An ancestor of modern archaea is believed to have given rise to Eukarya, the third domain of life. Archaeal and bacterial phyla are shown; the exact evolutionary relationship between these phyla is still open to debate.

Although bacteria and archaea share many morphological, structural, and metabolic attributes, there are numerous differences between the organisms in these two clades. The most notable differences are in the chemical structure and compositions of membrane lipids, the chemical composition of the cell wall, and the makeup of the information processing machinery (e.g., replication, DNA repair, and transcription).

Bacterial and archaeal diversity

Bacteria and archaea were on Earth long before multicellular life appeared. They are ubiquitous and have highly diverse metabolic activities. This diversity allows different species within clades to inhabit every imaginable surface where there is sufficient moisture. For example, some estimates suggest that in the typical human body, bacterial cells outnumber human body cells by about ten to one. Indeed, bacteria and archaea comprise the majority of living things in all ecosystems. Certain bacterial and archaeal species can thrive in environments that are inhospitable for most other life. Bacteria and archaea, along with microbial eukaryotes, are also critical for recycling the nutrients essential for creating new biomolecules. They also drive the evolution of new ecosystems (natural or man-made).

The first inhabitants of Earth

The Earth and its moon are thought to be about 4.54 billion years old. This estimate is based on evidence from radiometric dating of meteorite material, together with other substrate material from Earth and the moon. Early Earth had a very different atmosphere (contained less molecular oxygen) than it does today and was subjected to strong radiation; thus, the first organisms would have flourished in areas where they were more protected, such as in ocean depths or beneath the Earth's surface. During this time period, strong volcanic activity was common on Earth, so it is likely that these first organisms were adapted to very high temperatures. Early Earth was also bombarded with mutagenic radiation from the sun. The first organisms, therefore, needed to be able to withstand all these harsh conditions.

So, when and where did life begin? What were the conditions on Earth when life began? What did LUCA (the Last Universal Common Ancestor), the predecessor to bacteria and archaea look like? While we don't know exactly when and how life arose and what it looked like when it did, we do have a number of hypotheses based on various biological and geological data that we briefly describe below.

The ancient atmosphere

Evidence indicates that during the first two billion years of Earth’s existence, the atmosphere was anoxic, meaning that there was no molecular oxygen. Therefore, only those organisms that can grow without oxygen—anaerobic organisms—were able to live. Autotrophic organisms that convert solar energy into chemical energy are called phototrophs, and they appeared within one billion years of the Earth's formation. Then, cyanobacteria, also known as blue-green algae, evolved from these simple phototrophs one billion years later. Cyanobacteria began oxygenating the atmosphere. Increased atmospheric oxygen allowed the development of more efficient O2-utilizing catabolic pathways. It also opened up the land to increased colonization, because some O2 is converted into O3 (ozone), and ozone effectively absorbs the ultraviolet light that would otherwise cause lethal mutations in DNA. Ultimately, the increase in O2 concentrations allowed the evolution of other life forms.

Note: The evolution of bacteria and archaea

How do scientists answer questions about the evolution of bacteria and archaea? Unlike with animals, artifacts in the fossil record of bacteria and archaea offer very little information. Fossils of ancient bacteria and archaea look like tiny bubbles in rock. Some scientists turn to comparative genetics which, as its name suggests, is a domain of biology that makes quantitative comparisons of the genetic information between two or more species. A core assumption in the field of comparative genetics is that the more recently two species have diverged, the more similar their genetic information will be. Conversely, species that diverged long ago will have more genes that are dissimilar. Therefore, by comparing genetic sequences between organisms can shed light on their evolutionary relationships and allow scientists to create models of what the genetic makeup of the ancestors of the organisms being compared might have looked like.

Scientists at the NASA Astrobiology Institute and at the European Molecular Biology Laboratory collaborated to analyze the molecular evolution of 32 specific proteins common to 72 species of bacteria. The model they derived from their data indicates that three important groups of bacteria—Actinobacteria, Deinococcus, and Cyanobacteria (which the authors call Terrabacteria)—were likely the first to colonize land. Organisms in the genus Deinococcus are bacteria that tend to be highly resistant to ionizing radiation. Cyanobacteria are photosynthesizers, while Actinobacteria are a group of very common bacteria that include species important in decomposition of organic wastes.

The timelines of species divergence suggest that bacteria (members of the domain Bacteria) diverged from common ancestral species between 2.5 and 3.2 billion years ago, whereas archaea diverged earlier: between 3.1 and 4.1 billion years ago. Eukarya diverged off the Archaean line later. Furthermore, there were bacteria able to grow in the anoxic environment that existed prior to the advent of cyanobacteria (about 2.6 billion years ago). These bacteria needed to be resistance to drying and to possess compounds that protect the organism from radiation. It has been proposed that the emergence of cyanobacteria with its ability to conduct photosynthesis and produce oxygen was a key event in the evolution of life on Earth.

Microbial mats

Microbial mats (large biofilms) may be representative of the earliest visible structure formed by life on Earth; there is fossil evidence of their presence starting about 3.5 billion years ago. A microbial mat is a multi-layered sheet of microbes composed mostly of bacteria but that may also include archaea. Microbial mats are a few centimeters thick, and they typically grow at the interface between two materials, mostly on moist surfaces. Organisms in a microbial mat are held together by a glue-like, sticky substance that they secrete, forming an extracellular matrix. The species within the mat carry out different metabolic activities depending on their environment. As a result, microbial mats have been identified that have different textures and colors reflecting the mat composition and the metabolic activities conducted by the microorganisms that make up the mat.

The first microbial mats likely harvested energy through redox reactions (discussed elsewhere) from chemicals found near hydrothermal vents. A hydrothermal vent is a breakage or fissure in the Earth’s surface that releases geothermally heated water. With the evolution of photosynthesis about 3 billion years ago, some organisms in microbial mats came to use a more widely available energy source—sunlight—whereas others depended on chemicals from hydrothermal vents for energy and food.

Figure 2. (a) This microbial mat, about one meter in diameter, grows over a hydrothermal vent in the Pacific Ocean in a region known as the “Pacific Ring of Fire.” Chimneys, such as the one indicated by the arrow, allow gases to escape. (b) In this micrograph, bacteria within a mat are visualized using fluorescence microscopy. (credit a: modification of work by Dr. Bob Embley, NOAA PMEL, Chief Scientist; credit b: modification of work by Ricardo Murga, Rodney Donlan, CDC; scale-bar data from Matt Russell)


A stromatolite is a sedimentary structure formed when minerals precipitate out of water due to the metabolic activity of organisms in a microbial mat. Stromatolites form layered rocks made of carbonate or silicate. Although most stromatolites are artifacts from the past, there are places on Earth where stromatolites are still forming. For example, growing stromatolites have been found in the Anza-Borrego Desert State Park in San Diego County, California.

Figure 3. (a) These living stromatolites are located in Shark Bay, Australia. (b) These fossilized stromatolites, found in Glacier National Park, Montana, are nearly 1.5 billion years old. (credit a: Robert Young; credit b: P. Carrara, NPS).

Bacteria and archaea are adaptable: life in moderate and extreme environments

Some organisms have developed strategies that allow them to survive harsh conditions. Bacteria and archaea thrive in a vast array of environments: some grow in conditions that would seem very normal to us, whereas others are able to thrive and grow under conditions that would kill a plant or an animal. Almost all bacteria and archaea have some form of a cell wall, a protective structure that allows them to survive in both hyper- and hypo-osmotic conditions. Some soil bacteria are able to form endospores that resist heat and drought, thereby allowing the organism to survive until more favorable conditions recur. These adaptations, along with others, allow bacteria to be the most abundant life forms in all terrestrial and aquatic ecosystems.

Some bacteria and archaea are adapted to grow under extreme conditions and are called extremophiles, meaning “lovers of extremes.” Extremophiles have been found in all kinds of environments, such as in the depths of the oceans and the earth; in hot springs, the Artic, and the Antarctic; in very dry places; in harsh chemical environments; and in high-radiation environments, just to mention a few. These organisms help to give us a better understanding of the diversity of life and open up the possibility of finding microbial species that may lead to the discovery of new therapeutic drugs or have industrial applications. Because they have specialized adaptations that allow them to live in extreme conditions, many extremophiles cannot survive in moderate environments. There are many different groups of extremophiles. They are categorized based on the conditions in which they grow best, and several habitats are extreme in multiple ways. For example, a soda lake is both salty and alkaline, so organisms that live in a soda lake must be both alkaliphiles and halophiles. Other extremophiles, like radioresistant organisms, do not prefer an extreme environment (in this case, one with high levels of radiation) but have adapted to survive in it.

Table 1. This table lists some extremophiles and their preferred conditions.
Extremophile TypeConditions for Optimal Growth
AcidophilespH 3 or below
AlkaliphilespH 9 or above
ThermophilesTemperature of 60–80 °C (140–176 °F)
HyperthermophilesTemperature of 80–122 °C (176–250 °F)
PsychrophilesTemperature of -15 °C (5 °F) or lower
HalophilesSalt concentration of at least 0.2 M
OsmophilesHigh sugar concentration

Figure 4. Deinococcus radiodurans, visualized in this false-color transmission electron micrograph, is a bacterium that can tolerate very high doses of ionizing radiation. It has developed DNA repair mechanisms that allow it to reconstruct its chromosome even if it has been broken into hundreds of pieces by radiation or heat. (credit: modification of work by Michael Daly; scale-bar data from Matt Russell)


1. Battistuzzi, FU, Feijao, A, and Hedges, SB. A genomic timescale of prokaryote evolution: Insights into the origin of methanogenesis, phototrophy, and the colonization of land. BioMed Central: Evolutionary Biology 4 (2004): 44, doi:10.1186/1471-2148-4-44.

Cellular structure of bacteria and archaea

In this section, we will discuss the basic structural features of both bacteria and archaea. There are many structural, morphological, and physiological similarities between bacteria and archaea. As discussed in the previous section, these microbes inhabit many ecological niches and carry out a great diversity of biochemical and metabolic processes. Both bacteria and archaea lack a membrane-bound nucleus and membrane-bound organelles, which are hallmarks of eukaryotes.

While Bacteria and Archaea are separate domains, morphologically they share a number of structural features. As a result, they face similar problems, such as the transport of nutrients into the cell, the removal of waste material from the cell, and the need to respond to rapid local environmental changes. In this section, we will focus on how their common cell structure allows them to thrive in various environments and simultaneously puts constraints on them. One of the biggest constraints is related to cell size.

Although bacteria and archaea come in a variety of shapes, the most common three shapes are as follows: cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped) (figure below). Both bacteria and archaea are generally small compared to typical eukaryotes. For example, most bacteria tend to be on the order of 0.2 to 1.0 µm (micrometers) in diameter and 1-10 µm in length. However, there are exceptions. Epulopiscium fishelsoni is a bacillus-shaped bacterium that is typically 80 µm in diameter and 200-600 µm long. Thiomargarita namibiensis is a spherical bacterium between 100 and 750 µm in diameter and is visible to the naked eye. For comparison, a typical human neutrophil is approximately 50 µm in diameter.

Figure 1. This figure shows the three most common shapes of bacteria and archaea: (a) cocci (spherical), (b) bacilli (rod-shaped), and (c) spirilli (spiral-shaped).

A thought question:

One question that comes to mind is why are bacteria and archaea typically so small? What are the constraints that keep them microscopic? How could bacteria such as Epulopiscium fishelsoni and Thiomargarita namibiensis overcome these constraints? Think of possible explanations or hypotheses that might answer these questions. We'll explore and develop an understanding of these questions in more detail below and in class.

The bacterial and archaeal cell: common structures

Introduction to the basic cell structure

Bacteria and archaea are unicellular organisms, which lack internal membrane-bound structures that are disconnected from the plasma membrane, a phospholipid membrane that defines the boundary between the inside and outside of the cell. In bacteria and archaea, the cytoplasmic membrane also contains all membrane-bound reactions, including those related to the electron transport chain, ATP synthase, and photosynthesis. By definition, these cells lack a nucleus. Instead, their genetic material is located in a self-defined area of the cell called the nucleoid. The bacterial and archaeal chromosome is often a single covalently closed circular double-stranded DNA molecule. However, some bacteria have linear chromosomes, and some bacteria and archaea have more than one chromosome or small non-essential circular replicating elements of DNA called plasmids. Besides the nucleoid, the next common feature is the cytoplasm (or cytosol), the "aqueous," jelly-like region encompassing the internal portion of the cell. The cytoplasm is where the soluble (non-membrane-associated) reactions occur and contains the ribosomes, the protein-RNA complex where proteins are synthesized. Finally, many bacteria and archaea also have cell walls, the rigid structural feature surrounding the plasma membrane that helps provide protection and constrain the cell shape. You should learn to create a simple sketch of a general bacterial or archaeal cell from memory.

Figure 2. The features of a typical prokaryotic cell are shown.

Constraints on the bacterial and archaeal cell

One common, almost universal, feature of bacteria and archaea is that they are small, microscopic to be exact. Even the two examples given as exceptions, Epulopiscium fishelsoni and Thiomargarita namibiensis, still face the basic constraints all bacteria and archaea face; they simply found unique strategies around the problem. So what is the largest constraint when it comes to dealing with the size of bacteria and archaea? Think about what the cell must do to survive.

Some basic requirements

So what do cells have to do to survive? They need to transform energy into a usable form. This involves making ATP, maintaining an energized membrane, and maintaining productive NAD+/NADH2 ratios. Cells also need to be able to synthesize the appropriate macromolecules (proteins, lipids, polysaccharides, etc.) and other cellular structural components. To do this, they need to be able to either make the core, key precursors for more complex molecules or get them from the environment.

Diffusion and its importance to bacteria and archaea

Movement by diffusion is passive and proceeds down the concentration gradient. For compounds to move from the outside to the inside of the cell, the compound must be able to cross the phospholipid bilayer. If the concentration of a substance is lower inside the cell than outside and it has chemical properties that allow it to move across the cell membrane, that compound will energetically tend to move into the cell. While the "real" story is a bit more complex and will be discussed in more detail later, diffusion is one of the mechanisms bacteria and archaea use to aid in the transport of metabolites.

Diffusion can also be used to get rid of some waste materials. As waste products accumulate inside the cell, their concentration rises compared to that of the outside environment, and the waste product can leave the cell. Movement within the cell works the same way: compounds will move down their concentration gradient, away from where they are synthesized to places where their concentration is low and therefore may be needed. Diffusion is a random process—the ability of two different compounds or reactants for chemical reactions to interact becomes a meeting of chance. Therefore, in small, confined spaces, random interactions or collisions can occur more frequently than they can in large spaces.

The ability of a compound to diffuse depends on the viscosity of the solvent. For example, it is a lot easier for you to move around in air than in water (think about moving around underwater in a pool). Likewise, it is easier for you to swim in a pool of water than in a pool filled with peanut butter. If you put a drop of food coloring into a glass of water, it quickly diffuses until the entire glass has changed color. Now what do you think would happen if you put that same drop of food coloring into a glass of corn syrup (very viscous and sticky)? It will take a lot longer for the glass of corn syrup to change color.

The relevance of these examples is to note that the cytoplasm tends to be very viscous. It contains many proteins, metabolites, small molecules, etc. and has a viscosity more like corn syrup than water. So, diffusion in cells is slower and more limited than you might have originally expected. Therefore, if cells rely solely on diffusion to move compounds around, what do you think happens to the efficiency of these processes as cells increase in size and their internal volumes get bigger? Is there a potential problem to getting big that is related to the process of diffusion?

So how do cells get bigger?

As you've likely concluded from the discussion above, with cells that rely on diffusion to move things around the cell—like bacteria and archaea—size does matter. So how do you suppose Epulopiscium fishelsoni and Thiomargarita namibiensis got so big? Take a look at these links, and see what these bacteria look like morphologically and structurally: Epulopiscium fishelsoni and Thiomargarita namibiensis.

Based on what we have just discussed, in order for cells to get bigger, that is, for their volume to increase, intracellular transport must somehow become independent of diffusion. One of the great evolutionary leaps was the ability of cells (eukaryotic cells) to transport compounds and materials intracellularly, independent of diffusion. Compartmentalization also provided a way to localize processes to smaller organelles, which overcame another problem caused by the large size. Compartmentalization and the complex intracellular transport systems have allowed eukaryotic cells to become very large in comparison to the diffusion-limited bacterial and archaeal cells. We'll discuss specific solutions to these challenges in the following sections.

The Discovery: Evidence for a Genetic Origin of Cancer

00:00:0109 When I began my career in cancer research,
00:00:0427 really nothing was known about how the disease arises.
00:00:1015 And now we know exactly why cancer occurs.
00:00:1419 We don't know all the causes, which is a problem.
00:00:1717 But we do know that once those causes have done their job,
00:00:2315 all cancer arises from the malfunction of genes.
00:00:3107 When I arrived to take up my position
00:00:3411 at the University of California, San Francisco,
00:00:3710 I met Warren Levinson,
00:00:4002 who was another newly recruited young scientist,
00:00:4324 who had been trained to study Rous sarcoma virus.
00:00:4922 Now, Rous sarcoma virus
00:00:5313 was discovered by Peyton Rous at the turn of the 20th century.
00:00:5716 And it was the first tumor virus ever described to any credible level.
00:01:0421 It was a historic discovery.
00:01:0713 And it was utterly neglected for over 50 years.
00:01:1112 This was a chicken virus.
00:01:1301 This virus was discovered in chickens originally.
00:01:1500 And did it bother me that it was a chicken virus?
00:01:1626 Not at all.
00:01:1718 I was a great believer in what we call the universality of nature,
00:01:2017 and if I could find out anything about cancer in a chicken,
00:01:2414 I knew it would apply to humans,
00:01:2618 and boy was I right.
00:01:3016 The biological effects were dramatic.
00:01:3204 You could take normal chick.
00:01:3424 chicken fibroblasts in a petri dish,
00:01:3622 put Rous sarcoma virus on them, on those cells,
00:01:3920 and within 24 hours they.
00:01:4300 their whole phenotype changed.
00:01:4512 Their appearance changed.
00:01:4627 Their replicative behavior changed to be more aggressive.
00:01:5003 They started crawling over each other in a.
00:01:5421 in a chaotic manner, like cancer cells can do.
00:01:5724 And of course, if you put the virus into a chicken
00:01:5926 you would also get a tumor.
00:02:0214 That's what Rous had originally done.
00:02:0421 That's how he discovered the virus.
00:02:0802 He took a tumor, lysed the cells,
00:02:1202 put it through a filter to take out any living cells,
00:02:1605 put that lysate, or filtrate as we called it,
00:02:1928 into. into chickens,
00:02:2401 and they would get the same tumor.
00:02:2601 And then he could make extracts from that tumor, filter it,
00:02:3103 put it in another chicken, and get a tumor again.
00:02:3407 Hence, Rous sarcoma virus.
00:02:3610 Another very important discovery was made that
00:02:4008 was overshadowed to an unfortunate extent
00:02:4225 by the discovery of reverse transcriptase.
00:02:4511 And that was a discovery made by Steven Morton,
00:02:4815 at the University of California, Berkeley,
00:02:5106 that Rous sarcoma virus had at least one gene
00:02:5602 -- and it turned out to be only one gene --
00:02:5818 that was responsible for the tumorigenic capacity
00:03:0200 of the virus.
00:03:0326 And that brings me to Harold Varmus,
00:03:0606 who joined me as a colleague in 1970,
00:03:0920 the year that reverse transcriptase was discovered,
00:03:1215 and two years after I started my work at UCSF.
00:03:1617 Harold joined me in an extremely informal process.
00:03:2319 He had been a postdoctoral fellow
00:03:2716 at National Institutes of Health,
00:03:3028 and had taken a course in tumor viruses.
00:03:3604 He was. he was working at the time with phage and bacteria.
00:03:3924 And I think about five minutes into the conversation,
00:03:4218 I decided. we gotta this guy in the lab,
00:03:4513 because he was obviously very smart.
00:03:4720 And we were on the same wavelength scientifically:
00:03:4929 we wanted to do molecular biology of the virus.
00:03:5229 And we shared other interests, cultural interests,
00:03:5600 particularly literary interests.
00:03:5920 We decided that we ought to look for src in normal cells.
00:04:0327 Now, this was well before recombinant DNA.
00:04:0529 If we'd had recombinant DNA,
00:04:0719 we could have done the subsequent experiments in a few months.
00:04:1017 As it was, it took four years.
00:04:1314 And here we were helped, again, by genetics.
00:04:1626 Peter Vogt, a long-standing collaborator of ours.
00:04:2114 Peter Vogt was a master of the biology of these viruses
00:04:2501 and the genetics,
00:04:2706 and he had isolated mutants in Rous sarcoma virus
00:04:3119 that were deletions of src.
00:04:3602 So, we had available to us the deletion mutant,
00:04:4001 which had no src, or a very little piece of src in it.
00:04:4526 And of course we have the full Rous sarcoma virus genome
00:04:4924 with src in it.
00:04:5125 So, the idea was that we would copy.
00:04:5419 use reverse transcriptase to copy the genome of Rous sarcoma virus
00:04:5801 into radioactive DNA.
00:05:0013 And then we would use the deletion mutant to fish.
00:05:0329 to pull out, by molecular hybridization.
00:05:0927 we would use the deletion mutant to pull out all of the nucleotide sequences
00:05:1320 of the replicative genes
00:05:1705 and leave the src nucleotides in the.
00:05:2112 in the residue, if you will.
00:05:2408 It worked like a charm.
00:05:2623 It was hard work.
00:05:2904 The first hints that it would work came from
00:05:3314 a postdoctoral fellow named Ramareddy Guntaka,
00:05:3618 but he had a full-blown project well underway.
00:05:3909 And once he had shown that we could probably make a probe this way,
00:05:4300 we recruited another postdoctoral fellow, Dominique Stehelin,
00:05:4700 to run with it.
00:05:4918 And he did, in spades.
00:05:5207 We began to make this src-specific probe.
00:05:5521 We were. we were able to demonstrate its specificity
00:05:5826 in a variety of ways.
00:06:0027 He was able to make this probe consistently,
00:06:0505 and to use it,
00:06:0819 and soon found that the probe
00:06:1302 would react with normal chicken DNA.
00:06:1426 If you want to use the probe to
00:06:1917 assess the presence of the sequences in the probe in DNA,
00:06:2410 you first have to take the DNA apart,
00:06:2622 denature it as they say.
00:06:2908 The strands separate.
00:06:3026 And then you put the radioactive probe in there,
00:06:3315 and you allow the seq.
00:06:3602 the strands to reassociate.
00:06:3814 And the radioactive probe gets taken up in the mix.
00:06:4202 And so, although the bulk of the DNA
00:06:4504 will reassociate with its unlabeled original complement,
00:06:5007 some of it will reanneal with the radioactive probe.
00:06:5315 There was something in the DNA of normal avian cells
00:06:5704 that was homologous to the oncogene,
00:07:0003 the cancer gene,
00:07:0129 of Rous sarcoma virus.
00:07:0314 And we called it "cell src",
00:07:0502 for the sake of the argument.
00:07:0621 If you fiddled with the reaction conditions,
00:07:0820 the probe would react with DNA from any avian species we tested,
00:07:1117 including the most primitive species,
00:07:1412 such as ostrich or the ratite.
00:07:1702 the so-called ratites: the ostrich, the emu, the rhea.
00:07:2026 Incidentally, it was not easy to come by the DNA for these creatures,
00:07:2405 but we managed one way or another.
00:07:2714 I vividly remember the morning that Dominique
00:07:3117 brought us the first positive results.
00:07:3410 They'd come in late Saturday evening,
00:07:3814 when Harold and I,
00:07:4021 who were in a partnership at the time,
00:07:4302 that lasted for 15 years,
00:07:4513 first saw the data.
00:07:4813 I. I was dumbfounded.
00:07:5322 I recognized that this was a heretical discovery,
00:07:5825 and that we were gonna have to.
00:08:0027 we were gonna have to construct an airtight argument.
00:08:0407 So, I think I was a little less enthusiastic
00:08:0708 than Dominique would have liked,
00:08:0826 because he was beside himself with excitement.
00:08:1208 But Harold and I both understood from the get-go
00:08:1529 that if this was real we were looking.
00:08:2102 we were looking at a possible entree
00:08:2503 to the very fundamental underpinning of cancer.
00:08:3417 By the time I gave my Nobel lecture,
00:08:3901 I had a slide with something like 30 retroviral oncogenes,
00:08:4414 each of which had a demonstrable proto-oncogene progenitor,
00:08:5007 if you will, in normal cells.
00:08:5227 And as they. as the number mounted,
00:08:5424 it became clear that here was.
00:08:5710 here was the makings of a fun.
00:09:0023 of a. a unifying theory of cancer.
00:09:0601 And we were cautious about how we stated that publicly, at first.
00:09:1222 But by the early '80s,
00:09:1510 I was using that term,
00:09:1714 a unifying theory of how all cancers come about.
00:09:2201 It was a gradually building thrill
00:09:2612 to realize that we had the cancer cell by the neck,
00:09:3015 in terms of understanding it.
00:09:3213 Not in terms of throttling it,
00:09:3505 but in terms of understanding it.

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  1. Arashir

    In my opinion it has already been discussed

  2. Dan

    the Justa phrase

  3. Maclane

    This is the simply excellent idea

  4. Windham

    I think you are wrong. I can defend my position.

  5. Bodwyn

    And yet it seems to me that you need to think carefully about the answer ... Such questions cannot be resolved in a rush!

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