Learning Objectives associated with 2020_Spring_Bis2a_Facciotti_Lecture_09
Perhaps bacteria may tentatively
Prokaryotes are single-celled organisms with neither a membrane-bound nucleus nor other lipid membrane-bound organelles.
Figure 1. Although bacteria and archaea are both described as prokaryotes,
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
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
The ancient atmosphere
Note: The evolution of bacteria and archaea
How do scientists answer questions about the evolution of bacteria and archaea? Unlike
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
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. There were bacteria able to grow in the anoxic environment that existed prior to
Microbial mats (large biofilms) may
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 shown by the arrow, allow gases to escape. (b) In this micrograph, bacteria within a mat
A stromatolite is a sedimentary structure formed when minerals precipitate out of water
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
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
Some bacteria and archaea
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!
|Extremophile Type||Conditions for Optimal Growth|
|Acidophiles||pH 3 or below|
|pH 9 or above|
|Thermophiles||Temperature of 60–80 °C (140–176 °F)|
|Temperature of 80–122 °C (176–250 °F)|
|Halophiles||Salt concentration of at least 0.2 M|
|High sugar concentration|
1. Battistuzzi, FU, Feijao, A, and Hedges, SB. A genomic timescale of prokaryote evolution: Insights into the origin of methanogenesis,
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
Although bacteria and archaea come in a variety of shapes, the most common three shapes are
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 of
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,
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
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
Diffusion can also
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
The relevance of these examples is
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
Based on what we have just discussed, in order for cells to get bigger,
Plasma membranes enclose and define the borders between the inside and the outside of cells. They
Various factors influence fluidity, permeability, and various other physical properties of the membrane. These include temperature, the configuration of the fatty acid tails (some
Clink the following link to see an amoebae in action: Amoebae Hunting Video
A subgoal in our "build-a-cell" design challenge is to create a boundary that separates the "inside" of the cell from the environment "outside". This boundary needs to serve multiple functions that include:
- Act as a barrier by blocking some compounds from moving in and out of the cell.
- Be selectively permeable
in orderto transport specific compounds into and out of the cell.
- Receive, sense, and transmit signals from the environment to inside of the cell.
- Project "self" to others by communicating identity to other nearby cells.
Figure 1. The diameter of a typical balloon is 25cm and the thickness of the plastic of the balloon of around 0.25mm. This is a 1000X difference. A typical eukaryotic cell will have a cell diameter of about
The ratio of membrane thickness compared to the size of an average eukaryotic cell is much greater compared to that of a balloon stretched with air. To think
Fluid mosaic model
It is sometimes useful to start our discussion by recalling the size of the cell membrane relative to the size of the entire cell
Figure 2. The fluid mosaic model of the plasma membrane describes the plasma membrane as a fluid combination of phospholipids, cholesterol, and proteins. Carbohydrates attached to lipids (glycolipids) and
The principal components of a plasma membrane are lipids (phospholipids and cholesterol), proteins, and carbohydrates. Carbohydrates are present only on the exterior surface of the plasma membrane and
Phospholipids are major constituents of the cell membrane. Phospholipids are made of a glycerol backbone to which
Make sure to note in Figure 3 below that the phosphate group has an R group linked to one of the oxygen atoms. R is a variable commonly used in these types of diagrams to indicate that some other atom or molecule is bound at that position. That part of the molecule can be different in different phospholipids—and will impart some different chemistry to the whole molecule. At the moment, however, you are responsible for being able to recognize this type of molecule (no matter what the R group is) because of the common core elements—the glycerol backbone, the phosphate group, and the two hydrocarbon tails.
Figure 3. A phospholipid is a molecule with two fatty acids and a
When many phospholipids
Possible NB Discussion Point
Earlier in the course, we discussed the Second Law of Thermodynamics, which states that the overall entropy of the universe is always increasing. Apply this law in the context of the formation of the lipid bilayer membrane. How is it possible that the lipids are able to spontaneously arrange themselves into such an organized structure instead of scatter into a more disordered state? Or in other words -- if the second law holds true, then how exactly does the spontaneous lipid organization lead to increased entropy?
Figure 4. In the presence of water, some phospholipids will spontaneously arrange themselves into a micelle.
Source: Created by Erin Easlon (own work)
Proteins make up the second major component of plasma membranes. Integral membrane proteins, as their name suggests, integrate completely into the membrane structure, and their hydrophobic membrane-spanning regions interact with the hydrophobic region of the phospholipid bilayer.
Some membrane proteins associate with only one half of the bilayer, while others stretch from one side of the membrane to the other, and
are exposed to the environment on either side. Integral membrane proteins may have one or more transmembrane segments typically consisting of 20–25 amino acids. Within the transmembrane segments, hydrophobic amino acid variable groups arrange themselves to form a chemically complementary surface to the hydrophobic tails of the membrane lipids.
Figure 5. Integral membranes proteins may have one or more
Carbohydrates are a third major component of plasma membranes. They
The integral proteins and lipids exist in the membrane as separate molecules and they "float" in the membrane, moving
Different organisms and cell types in multicellular organisms can tune fluidity of their membrane to be more compatible with specialized functions and/or in response to environmental factors. This tuning can
Saturated fatty acids, with straight tails,
Animal cells have cholesterol, an additional membrane constituent that
Thus, cholesterol extends, in both directions, the range of temperature in which the membrane is appropriately fluid and consequently functional. Cholesterol also serves other functions, such as organizing clusters of transmembrane proteins into lipid rafts.
Figure 7. Cholesterol fits between the phospholipid groups within the membrane.
Review of the components of the membrane
While there are certain trends or chemical properties that can
Energetics of transport
All substances that move through the membrane do so by one of two general methods, which
Passive transport does not require the cell to
Diffusion is a passive process of transport. A single substance moves from an area of high concentration to an area of low concentration until the concentration is equal across a space. You are familiar with diffusion of substances through the air. For example, think about someone opening a bottle of ammonia in a room filled with people. The ammonia gas is at its highest concentration in the bottle; its lowest concentration is at the edges of the room. The ammonia vapor will diffuse, or spread away, from the bottle; gradually, more and more people will smell the ammonia as it spreads. Materials move within the cell’s cytosol by diffusion, and certain materials move through the plasma membrane by diffusion.
Factors that affect diffusion
If unconstrained, molecules will move through and explore space randomly at a rate that depends on their size, their shape, their environment, and their thermal energy. This
Factors influencing diffusion include:
- Extent of the concentration gradient: The greater the difference in concentration, the more rapid the diffusion. The closer the distribution of the material gets to equilibrium, the slower the rate of diffusion becomes.
- Shape, size and mass of the molecules diffusing: Large and heavier molecules move more slowly; therefore, they diffuse more slowly. The reverse is typically true for smaller, lighter molecules.
- Temperature: Higher temperatures increase the energy and therefore the movement of the molecules, increasing the rate of diffusion. Lower temperatures decrease the energy of the molecules, thus decreasing the rate of diffusion.
- Solvent density: As the density of a solvent increases, the rate of diffusion decreases. The molecules slow down because they have a more difficult time getting through the denser medium. If the medium is less dense, rates of diffusion increase. Since cells primarily use diffusion to move materials within the cytoplasm, any increase in the cytoplasm’s density will decrease the rate at which materials move in the cytoplasm.
- Solubility: As discussed earlier, nonpolar or lipid-soluble materials pass through plasma membranes more easily than polar materials, allowing a faster rate of diffusion.
- Surface area and thickness of the plasma membrane: Increased surface area increases the rate of diffusion, whereas a thicker membrane reduces it.
- Distance traveled: The greater the distance that a substance must travel, the slower the rate of diffusion. This places an upper limitation on cell size. A large, spherical cell will die because nutrients or waste cannot reach or leave the center of the cell, respectively. Therefore, cells must either be
small in size, as with many prokaryotes, or be flattened, as with many single-celled eukaryotes.
In facilitated transport, also called facilitated diffusion, materials diffuse across the plasma membrane with the help of membrane proteins. A concentration gradient exists that allows these materials to diffuse into or out of the cell without
Different organisms and tissues in multicellular species express different channel proteins in their membranes depending on the environments they live in or specialized function they play in an organism. This provides each type of cell with a unique membrane permeability profile that is evolved to complement its "needs" (note the anthropomorphism). For example, in some tissues, sodium and chloride ions pass freely through open channels, whereas in other tissues a gate must open to allow passage. This occurs in the kidney where both forms of channels are found in different parts of the renal tubules. Cells involved in the transmission of electrical impulses, such as nerve and muscle cells, have gated channels for sodium, potassium, and calcium in their membranes. Opening and closing of these channels changes the relative concentrations on opposing sides of the membrane of these ions, resulting a change in electrical potential across the membrane that lead to message propagation with nerve cells or in muscle contraction with muscle cells.
Another type of protein embedded in the plasma membrane is a carrier protein. This aptly named protein binds a substance and, in doing so, triggers a change of its own shape, moving the bound molecule from the outside of the cell to its interior; depending on the gradient, the material may move in the opposite direction. Carrier proteins are typically specific for a single substance. This selectivity adds to the overall selectivity of the plasma membrane. The molecular-scale mechanism of function for these proteins remains poorly understood.
Carrier protein play an important role in the function of kidneys. Glucose, water, salts, ions, and amino acids needed by the body
Channel and carrier proteins transport material at different rates. Channel proteins transport much more quickly than do carrier proteins. Channel proteins facilitate diffusion at a rate of tens of millions of molecules per second, whereas carrier proteins work at a rate of a thousand to a million molecules per second.
We will explore active transport more in the next reading!