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Spring_2021_Bis2A_Singer_Lecture_11 - Biology

Spring_2021_Bis2A_Singer_Lecture_11 - Biology


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Cellular structure of bacteria and archaea

In this section, we will discuss the basic structural features of both bacteria and archaea. Both bacteria and archaea lack a membrane-bound nucleus and membrane-bound organelles, which are hallmarks of eukaryotes.

While bacteria andarchaeaare separate domains, morphologically they sharea number ofstructural 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 relatedto cell size.

Although bacteria and archaea come in a variety of shapes, the most common three shapes areas follows: cocci (spherical), bacilli (rod-shaped), andspirilli(spiral-shaped) (figure below). Both bacteria and archaea aregenerallysmall compared to typical eukaryotes. For example, most bacteriatend to beon the order of 0.2 to 1.0µm(micrometers) in diameter and 1-10µmin length. However, there are exceptions. Epulopisciumfishelsoni is a bacillus-shaped bacterium that is typically 80µmin diameter and 200-600µmlong. Thiomargaritanamibiensis is a spherical bacterium between 100 and 750µmin diameter and is visible to the naked eye. For comparison, a typical human neutrophil is approximately 50µmin 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).


Possible NB Discussion Point: Why are bacteria and archaea so tiny anyway?

Why are bacteria and archaea typically so small? What are the constraints that are keeping them microscopic in size (i.e., what is preventing from getting bigger?)? How then exactly does the relatively giant Thiomargarita namibiensis (which has a cell volume that is three million times the volume of an average bacteria and is visible to the naked eye) and other larger bacteria overcome these constraints? Think ofpossibleexplanations 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.

Introduction to bacterial and archaeal diversity

Perhaps bacteria may tentativelybe regardedas 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 innaturaleconomy 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 composedof 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, theynevertheless,represent evolutionarily distinct domains of life. The figure below shows a simple phylogenetic tree with the three main domains of life: Bacteria, Archaea, andEukarya. This means that we should not use the use of the term prokaryote intending to group the bacteria and archaea based on 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 probably do so. When you hear or use the term "prokaryote", therefore, make surethatit is not being used to or implying that the bacteria and archaea are part of the same phylogenetic group. Rather, makesure that the use of the term "prokaryote" is limitedto describing the common physical characteristics of these two microbial groups.

Figure 1. Although bacteria and archaea are both described as prokaryotes,they have been placedin separate domains of life.An ancestor of modernarchaeais believedto have given rise toEukarya, the third domain of life.Archaealand 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 many 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. Bacteria and archaea comprise most living things in all ecosystems. Certain bacterial and archaeal species can thrive in environments 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 thoughtto be about 4.54 billion years old.This estimate is basedon 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 andwas subjectedto 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 evolution adapted these first organisms to very high temperatures.Early Earth was also bombardedwith mutagenic radiation from the sun. The first organisms, therefore, needed 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, wedohavea number ofhypotheses based on various biological and geological data that we briefly describe below.

The ancient atmosphere

Evidenceindicatesthat 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—could live. Autotrophic organisms that convert solar energy into chemical energyare calledphototrophs, and theyappearedwithin 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-utilizingcatabolic pathways. It also opened up the land to increased colonization, becausesome O2is convertedinto O3 (ozone), and ozone 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? Unlikewithanimals, 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 inthe field ofcomparative 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 dataindicatesthat 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 thattend to behighly resistant to ionizing radiation. Cyanobacteria arephotosynthesizers, 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.Eukaryadiverged off the Archaean line later. There were bacteria able to grow in the anoxic environment that existed prior tothe advent ofcyanobacteria (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 proposedthat 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 (largebiofilms) maybe representative ofthe 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 ofbacteriabut 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 matare heldtogether 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 identifiedthat 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 releasesgeothermallyheated 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 shown by the arrow, allow gases to escape. (b) In this micrograph, bacteria within a matare visualizedusing fluorescence microscopy. (credit a: modification of work by Dr. Bob Embley, NOAA PMEL, Chief Scientist; creditb: modification of work by Ricardo Murga, Rodney Donlan, CDC; scale-bar data from Matt Russell)

Stromatolites

A stromatolite is a sedimentary structure formed when minerals precipitate out of waterdue tothe 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,growingstromatoliteshave been foundin the Anza-Borrego Desert State Park in San Diego County, California.

Figure 3. (a)These livingstromatolitesare locatedin Shark Bay, Australia. (b) These fossilized stromatolites, found in Glacier National Park, Montana, are nearly 1.5 billion years old. (credit a: Robert Young; creditb: 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 othersare able tothrive and grow under conditions that would kill a plant or an animal. Almost all bacteria and archaea havesome form ofa cell wall, a protective structure that allows them to survive in both hyper- and hypo-osmotic conditions. Some soil bacteriaare able toform endospores that resist heat and drought,therebyallowing 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 archaeaare adaptedto grow under extreme conditions andare calledextremophiles, meaning “lovers of extremes.”Extremophileshave been foundin all kinds of environments, such as in the depths of the oceans and the earth; in hot springs, theArtic, and the Antarctic; invery dryplaces; 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 aremany differentgroups ofextremophiles.They are categorizedbased 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 alkaliphilesand 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.


Possible NB Discussion Point: How do extremophiles do it?

You just read that soil bacteria are able to survive through heat and droughts by forming dormant heat- and drought-resistant endospores. However, not all extremophiles form endospores as a means to survive their own harsh environmental conditions. Can you think of other strategies that other extremophiles might have developed? Choose a row in Table 1 (below) and try to brainstorm some creative survival mechanisms specific for that extremophile type!


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

Figure4.Deinococcusradiodurans, 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 ifit has been brokeninto hundreds of pieces by radiation or heat. (credit: modification of work by Michael Daly; scale-bar data from Matt Russell)

Footnotes

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.

Eukaryotes

Living things fall into three large groups:Archaea, Bacteria, and Eukarya. The first two groups include non-nucleated cells, and the third contains all eukaryotes. A relatively sparse fossil record is available to help us discern what the first members of each of these lineages looked like, so it is possible that all the events that led up to the last common ancestor of extant eukaryotes will remain unknown. However, comparative biology of extant organisms and the limited fossil record provide some insights into the history of Eukarya.

The earliest fossils found appear to be bacteria, most likely cyanobacteria. They are about 3.5 billion years old and are recognizable because of their relatively complex structure and, for bacteria, relatively large cells. Most other bacteria and archaea have small cells, 1 or 2µmin size, and would be difficult to pick out as fossils. Most living eukaryotes have cells measuring 10µmor greater. Structures this size, which might be fossils, appear in the geological record about 2.1 billion years ago.

Characteristics of eukaryotes

Data from these fossils have led biologists to the conclusion that living eukaryotes are all descendants of a single common ancestor. Mapping the characteristics found in all major groups of eukaryotes reveals that the following characteristics must have been present in the last common ancestor, because these characteristics are present in at leastsome of themembers of each major lineage.

  1. Cells with nuclei surrounded by a nuclear envelope with nuclear pores. This is the single characteristic that is both necessary and sufficient to define an organism asaeukaryote. All extant eukaryotes have cells with nuclei.
  2. Mitochondria. Some extant eukaryotes have very reduced remnants of mitochondria in their cells, whereas other members of their lineages have “typical” mitochondria.
  3. A cytoskeleton containing the structural and motility components calledactinmicrofilaments and microtubules. All extant eukaryotes have these cytoskeletal elements.
  4. Flagella and cilia, organelles associated with cell motility. Some extant eukaryotes lack flagella and/or cilia, butthey are descendedfrom ancestors that possessed them.
  5. Chromosomes, eachconsisting ofa linear DNA molecule coiled around basic (alkaline) proteins called histones. The few eukaryotes with chromosomes lacking histonesclearlyevolved from ancestors that had them.
  6. Mitosis, a process of nuclear division wherein replicated chromosomesare dividedand separated using elements of the cytoskeleton. Mitosis is universally present in eukaryotes.
  7. Sex, a process of genetic recombination unique to eukaryotes in which diploid nuclei at one stage of the life cycle undergo meiosis to yield haploid nuclei and subsequent karyogamy, a stage where two haploid nuclei fusetogetherto create a diploid zygote nucleus.
  8. Members of all major lineages have cell walls, and it might be reasonable to conclude that the last common ancestor could make cell walls during some stage of its life cycle. However, not enoughis knownabout eukaryotes’ cell walls and their development to know how much homology exists among them. If the last common ancestor could make cell walls,it is clear thatthis ability must have been lostin many groups.

Endosymbiosis and the evolution of eukaryotes

In order tounderstand eukaryotic organisms fully, it is necessary to understand that all extant eukaryotes are descendants of a chimeric organism that was a composite of a host cell and the cell(s) of an alpha-proteobacteriumthat “took up residence” inside it.This major theme in the origin ofeukaryotesis knownas endosymbiosis, one cell engulfing another such that the engulfed cell survives and both cells benefit. Over many generations, a symbiotic relationship canresult intwo organisms that depend on each other so completely that neither could survive on its own.Endosymbioticevents likely contributed to the origin of the last common ancestor of today’s eukaryotes and to later diversification in certain lineages of eukaryotes. Before explaining this further, it is necessary to consider metabolism in bacteria and archaea.

Bacterial and archaeal metabolism

Many important metabolic processes arose in bacteria and archaea, and some of these, such as nitrogen fixation,are never foundin eukaryotes. The process of aerobic respirationis foundin all major lineages of eukaryotes, andit is localizedin the mitochondria.Aerobic respiration is also foundin many lineages of bacteria and archaea, but it is not present in all of them, and many forms of evidence suggest that such anaerobic microbes never carried out aerobic respiration nor did their ancestors.

While today’s atmosphere is about one-fifth molecular oxygen (O2), geological evidence shows that it originally lacked O2. Without oxygen, aerobic respiration would notbe expected, and living things would have relied on fermentation instead. Around 3.5 billion years ago, some bacteria and archaea began using energy from sunlight to power anabolic processes that reduce carbon dioxide to form organic compounds. They evolved the ability to photosynthesize. Hydrogen, derived from various sources,was capturedusing light-powered reactions to reduce fixed carbon dioxide in the Calvin cycle. The group of Gram-negative bacteria that gave rise to cyanobacteria used water as the hydrogen source and released O2 as a waste product.

Eventually, the amount of photosynthetic oxygen built up in some environments to levels that posed a risk to living organisms, since it can damage many organic compounds. Various metabolic processes evolved that protected organisms from oxygen; one of which, aerobic respiration, also generated high levels of ATP. It became widely present among microbes, including in a group we now call alpha-proteobacteria. Organisms that did not gain aerobic respiration had to remain in oxygen-free environments. Originally, oxygen-rich environments were likely localized around places where cyanobacteria were active, but by about 2 billion years ago, geological evidence shows that oxygen was building up to higher concentrations in the atmosphere. Oxygen levels similar to today’s levels only arose within the last 700 million years.

Recall that the first fossils that we believe to be eukaryotes are about 2 billion years old, so they appeared as oxygen levels were increasing. Also, recall that all extant eukaryotes descended from an ancestor with mitochondria. These organelles were first observed by light microscopists in the late 1800s, where they appeared to be worm-shaped structures that seemed to move around in the cell. Some early observers suggested that they might be bacteria living inside host cells, but these hypotheses remained unknown or rejected in most scientific communities.

Endosymbiotictheory

As cell biology developed in the twentieth century,it became clear thatmitochondria were the organelles responsible for producing ATP using aerobic respiration. In the 1960s, American biologist Lynn Margulis developed endosymbiotictheory, which states that eukaryotes may have been a product of one cell engulfing another (one living within another) and evolving until the separate cells were no longer recognizableas such. In 1967, Margulis introduced new work on the theory and substantiated her findings through microbiological evidence. Although Margulis’ work initiallywas metwith resistance, this once-revolutionary hypothesis is now widely (but not completely) accepted, with work progressing on uncovering the steps involved in this evolutionary process and the key players involved. Much remains tobe discoveredabout the origins of the cells that now make up the cells in all living eukaryotes.

Broadly, it has become clear that many of our nuclear genes and the molecular machinery responsible for replication and expression appear closely related to those inArchaea.On the other hand, themetabolic organelles and genes responsible formany energy-harvesting processes had their origins in bacteria. Much remains tobe clarifiedabout how this relationship occurred; this continues to be an exciting field of discovery in biology. For instance, itis not knownwhether the endosymbiotic event that led to mitochondria occurred before or after the host cell had a nucleus. Such organisms would be among the extinct precursors of the last common ancestor of eukaryotes.

Mitochondria

One of the major features distinguishing bacteria and archaea from eukaryotes is mitochondria. Eukaryotic cells may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of energy consumption. Each mitochondrion measures 1 to 10 or greater micrometersin lengthand exists in the cell as an organelle that can be ovoid, worm-shaped, or intricately branched. Mitochondria arise from the division of existing mitochondria; they may fuse; andthey may be movedaround inside the cell by interactions with the cytoskeleton. However, mitochondria cannot survive outside the cell. As the atmospherewas oxygenatedby photosynthesis, and as successful aerobic microbes evolved, evidence suggests that an ancestral cell with some membrane compartmentalization engulfed a free-living aerobic bacterium, specifically an alpha-proteobacterium,therebygiving the host cell the ability to use oxygen to release energy stored in nutrients. Alpha-proteobacteriaare a large group of bacteria that includes species symbiotic with plants, disease organisms that can infect humans via ticks, and many free-living species that use light for energy. Several lines of evidence support that mitochondriaare derivedfrom this endosymbiotic event. Most mitochondriaare shapedlike alpha-proteobacteriaandare surroundedby two membranes, which would result when one membrane-bound organismis engulfedinto a vacuole by another membrane-bound organism. The mitochondrial inner membrane is extensive and involves substantialinfoldingscalled cristae that resemble the textured, outer surface of alpha-proteobacteria. The matrix and inner membrane are rich with the enzymes necessary for aerobic respiration.

Evolution and Natural Selection

Brief overview

Evolution and natural selection are core concepts in biology that are typically invoked to help explain the diversity of and relationships between life on Earth, both extant and extinct. Fortunately, in BIS2A, you need to understand and use only a few core ideas related to evolution and natural selection. We describe these below. You will expand your understanding and add details to these core concepts in BIS2B and BIS2C.

The first idea you need to grasp is that evolution can be simply defined as the development/change of something over time. In the automotive industry, the shapes and features of cars can be said to evolve (change in time). In fashion, it can be said that style evolves. In biology, life and, in particular, reproducing populations of organisms with different traits evolve.

The second thing to understand is that natural selection is a process by which nature filters organisms in a population. What is the filter? Here it becomes a little more complicated (but only a little). The simplest explanation is that the selective filter is just a combination of all living and nonliving factors in an environment, which influence how successfully an organism can reproduce. The factors that influence the ability of an organism to reproduce are known as selective pressures. A small but important complication is that these factors are not the same everywhere; they change in time and by location. Thus, the selective pressures that create the filter are constantly changing (sometimes rapidly, sometimes slowly), and organisms in the same reproducing population could experience different pressures at different times and in different locations.

The theory of evolution by natural selection puts these two ideas together; it stipulates that change in biology happens over time and that the variation in a population is constantly subjected to selection based on how differences in traits influence reproduction. But what are these characteristics or traits? What traits/features/functions can be subject to selection? The short answer is: just about anything associated with an organism for which variation exists in a population and for which this variation leads to a differential likelihood of generating offspring will probably be subject to filtering by natural selection. We also call these traits heritable phenotypes. Organisms in a population that have phenotypes, which enable them to pass the selective filter more efficiently than others, are said to have a selective advantage and/or greater fitness.

It is important to reiterate that while the phenotypes carried by individual organisms may be subject to selection, the process of evolution by natural selection both requires and acts on phenotypic variation within populations. If neither variation nor populations in which that variation can reside exist, there is no opportunity or need for selection. Everything is and stays the same.

Common misconceptions and a course specific note

Finally, we draw your attention to a critical point and common misconception among beginning students in biology. This misconception can arise when, for the sake of discussion, we decide to anthropomorphize nature by giving it an intellect. For example, we may try to build an example for evolution by natural selection by proposing that a surplus of a particular food exists in an environment and there is an organism close by that is starving. It would be correct to reason that if the organism could eat that food that this might give it a selective advantage over other organisms that cannot. If later we find an example of organisms that have the capability to eat that surplus food, it might be tempting to say that nature evolved to solve the problem the surplus food. The process of evolution by natural selection, however, happens randomly and without direction. That is, nature does NOT identify “problems” that are limiting fitness. Nature does NOT identify features that would make an organism more successful and then start creating diverse solutions that meet this need. The generation of variation is not guided. Variation happens and natural selection filters what works best. The observation that an organism exists that can eat the surplus food is not a reflection of nature actively solving a problem, but rather, a reflection of whatever processes that led to phenotypic variation in an ancestral population that created—among many other variants—a phenotype that increased fitness (possibly because the ancestral organisms were able to eat the surplus food).

This point of the preceding paragraph is particularly important to understand in the context of BIS2A because of the way we will be utilizing the Design Challenge to understand biology (more on this later in the reading). While the Design Challenge is intended to help focus our attention on functions under selection and their relationship to determining fitness, it can be easy—if we aren’t attentive—to lapse into language that would suggest that nature purposefully designs solutions to solve specific problems. Always remember that we are looking retrospectively at what nature has selected and that we are attempting to understand why a specific phenotype may have been selected over many other possibilities. In doing so, we will be inferring or hypothesizing to the best of our ability (which is sometimes wrong) a sensible reason to explain why a phenotype might have provided a selective advantage. We are NOT saying that the phenotype evolved TO provide a specific selective advantage. The distinction between these two ideas may be subtle, but it is critical!


Possible NB Discussion Point

Examine the following statement: "Natural selection acts for the good of the species." Discuss what you think about this statement - perhaps invoking some of the reading above.




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