Chapter 2 Book Notes
Microbial Cell Structure and Function
2.1 Light Microscopy
Light microscopes are used to examine cells at relatively low magnifications. Electron microscopes are used to examine cells and cells structures at very high magnification.
Resolution: the ability to distinguish two adjacent objects as distinct and separate Resolution is determined by the wavelength of light (shorter is better) and the numerical aperture (higher is better).
The total magnification of light microscope is the product of the magnification of the objective and ocular lenses.
∙ The highest resolution in a light microscope is about 0.2 um. This means that anything smaller than 0.2 um cannot be seen as distinct and separate. ∙ The highest resolution in a electron microcope is 0.2 nm.
Many dyes used in microbiology are positively charged and are called basic dyes. ∙ Ex) Methylene blue, Crystal violet, Safranin We also discuss several other topics like What are the bone stem cells?
These bind strongly to negatively charged cell components
Gram staining: Bacteria can be divided into:
∙ Gram positive- These appear purple-violet after being stained with crystal violet. These do not get decolorized with ethanol.
∙ Gram negative- These are counterstained after being decolorized with ethanol with Safranin. They appear pink. If you want to learn more check out What happened in nat turner’s rebellion?
DNA is linear and found in a nucleus Contains membrane-enclosed organelles Typically 2 copies of each chromosome Nucleus divides by mitosis (cell division) Genome is halved by meiosis (sexual reproduction)
DNA is a single circular chromosome It aggregates in the nucleoid region No membrane bound organells My have chromosomal plasmids
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2.5 Cell Morphology (Bacteria and Archaea)
Morphology means cell shape. Major shapes include:
∙ Spherical shaped– Coccus
∙ Cylinder shaped – Rod
∙ Spiral shaped rods – Spirilla
o Tightly coiled bacteria – Spirochetes
o Have tubes or stalks – Appendaged bacteria
o Filamentous bacteria – forms long chains
Morphology is not used to predict or show physiology, phylogeny or pathogenic potential.
Why are some organisms shaped the way they are?
∙ Optimization for nutrient uptake- small cells have a larger surface to volume ratio which makes it easier to intake nutrients
∙ Swimming motility- spiral shaped cells swim easier in viscous environments ∙ Gliding motility- filamentous bacteria are more suited for gliding
2.6 Membranes (Bacteria and Eukarya)
The cytoplasmic membrane surrounds the cytoplasm and separates it from the environment and has selective permeability.
∙ Composition If you want to learn more check out What is the scientific study of interactions between organics and their environment?
o Phospholipid bilayer (Fatty acids and glycerol-phosphate components) o Ester linkages bond hydrophobic side chain to glycerol o Fatty acids point inwards away from the cytoplasm (hydrophobic)
∙ The membrane has many proteins. Hydrophobic parts of the protein spans the membrane while the other sides interact with the environment and the cytoplasm.
The outer surface of the membrane interacts with the
extracellular fluid (environment). The inner surface
interacts with the cytoplasm.
Types of membrane proteins:
o Integral- firmly embedded in the membrane
o Peripheral- does not go through the membrane, but
is associated with the surface of it
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o Ether bonds hydrophobic side chains to glycerol
o Archaeal membranes thus lack fatty acids
o Hydrophobic side chains are not fatty acids, they are isoprenes
The membrane can be composed of diglycerol diethers which have 20 carbon side chains (called phytanyl group). Or diglycerols tetraethers which have 40 carbon side chains. The phytanyl groups that stick out from the glycerol are covalently linked. This formas a lipid monolayer. We also discuss several other topics like How do you factor extra credit into a grade?
Monolayers are extremely resistant to heat and are found most in extremist Archaea.
Some archael lipids contain rings within the hydrocarbon side chain. ∙ Example) Crenarchaeol is a lipid that has 5 rings.
2.8 Membrane function (All domains)
The membrane has 3 major functions:
1. Permeability – prevents the leakage of solutes into or out of the cell 2. Protein anchor – some of these proteins are enzymes for energy conservation and others are for transport of solutes into and out of the cell
3. Energy conservation – it can exist in an energetically charged form, separating ions for the purpose of energy
The hydrophobic portion of the membrane is a tight barrier to diffusion of things located inside of the cytoplasm; especially molecules that are polar and charged. These molecules must be transported.
∙ Can H+ diffuse across the membrane? NO! It is charged
∙ Can water diffuse across the membrane? YES! Water is essential to the cell and is somewhat polar but is small enough to diffuse. Other examples are O2 and CO2
Because of the selective permeability, transport proteins are essential. Transport reactions move nutrients from low concentration to high concentration. This takes energy to do.
∙ Transport reactions are much faster than simple diffusion but they do have a saturation effect. This means that no matter if there is a lot of substrate outside of the cell, if all of the proteins are being used up (already transporting substrate inside of the cell) then the rate cannot go any faster.
Active – this type requires energy. It transports solutes against concentration gradient. (From low concentration to high)
Passive – this type does not require energy. There is transport along the concentration gradient. (From high to low)
∙ Pores (simple channels) in the membranes
∙ Carrier proteins that undergo conformational changes to put substrate across membrane.
Transport Types in Prokaryotes
Simple transport: uses only a membrane spanning transport protein Group translocation: uses a series of proteins in the transport event ABC transport system- uses 3 components:
1. Substrate binding protein
2. Membrane-integrated transporter
3. ATP hydrolyzing protein
2.10 Cell Walls (Bacteria and Archaea)
Bacteria can be divided into gram-positive and gram-negative. The cell walls of bacteria have a rigid layer added for strength called peptidoglycan. It is composed of:
1. N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)
2. D-alanine and D-glutamic acid
3. Lysine or DAP
4. And cross linkages that make it stronger. These differ in gram positive and gram negative bacteria
Gram-positive cell walls are composed of 90% peptidoglycan. There are usually several sheets of it stacked upon each other. Their cell walls also contain techoic acids that are embedded within the wall. Lipotechoic acids are ones that covalently bound to the membrane lipids.
Gram negative cell walls only contain a small amount (10%) of peptidoglycan. Most of their cell wall is composed of the outer membrane or Lipopolysaccharide layer (LPS). LPS is composed:
1. Lipid A
2. O-specific polysaccharide
3. Core polysaccharide
The Lipid A is known to be very toxic to animals (endotoxin). Examples of this is salmonella and certain pathogenic strains of E. coli.
Gram negative cell walls also have a space between the outer membrane and the cell membrane called the periplasmic space. In this space is where you would find proteins that are embedded within the cell membrane.
During gram staining, you use crystal violet, iodine, alcohol, and Safranin. When using the crystal violet, it stains all cells (gram negative and positive) purple. When you use alcohol, it dehydrates gram positive cells, causing the purple stain to be trapped inside of the cell. (Making them stay purple.) In gram-negative cells, alcohol penetrates the lipid-rich outer membrane and extracts the crystal violet, allowing them to be stained by the Safranin.
2.12 Archaeal Cell Walls
Archaeal cell walls do NOT contain peptidoglycan. It also does not have an outer membrane.
Instead, some of the cell wall consists of a polysaccharide called Pseudomurein. It is composed of
2. N-acetyltalosaminuronic acid
The most common type of cell wall in Archea is the S-layer. It is also found in some bacteria. It is composed of interlocking proteins or glycoproteins.
2.13 Cell surface structures
Many prokaryotes secrete sticky or slimy materials on their cells surface. These are called either capsules or slime layers.
Traditionally, if the layer is organized into a tight matrix, it is called a capsule. It is easily defined under an electron microscope. If it is more difficult to see and more easily deformed, it is called a slime layer.
Capsules usually stick to the cell wall, some even covalently linked to peptidoglycan.
Uses of capsule and slime layers include:
1. Helps in the attachment of microorganisms to solid surfaces. 2. Acts as virulence factors in certain disease, preventing the cell from suffereing dehydration
3. Protect against phagocytosis
Other structures on the cell surface include fimbriae and pili. Fimbriae allow for cells to stick to surfaces. Pili allow for genetic exchange between cells (conjugation) and helps in the adhesion of pathogen to specific host tissues.
Type IV pili assist cells in twitching motility.
Flagella is a structure that assists in swimming. These are helical in shape and have different arrangements: peritrichous, polar, and lophotricous.
2.14 Cell Inclusion
Inclusions function as energy reserves.
One of the most common bodies to includsion in prokaryotes is poly-B hydroxybutyric acid (PHB).
Glycogen, which is the polymer of glucose, is used as storage for carbon and energy
The cell accumulates inorganic phosphate. This is useful for a source of phosphate for nucleic acid and phospholipid biosynthesis.
Cells also store sulfur (elemental), carbonate materials such as barium, strontium and magnesium. Last, they also store magnetosomes, sometimes with particles of iron oxide.
Certain bacterias produce endospores. They are highly differentiated cells that are resistant to heat, harsh chemicals and radiation. They can be thought to be a dormant stage of bacterial life cycle. They are present only in gram positive bacteria.
They can be found at the end of the cell
Near the end of the cell, (subterminal). Or
In polar flagellation, the flagella are attached at one or both ends of a cell. This allows for the cells to move very rapidly and typically spin around. In peritricous flagellation, flagella are inserted at many locations around the cell surface.
Prokaryotes often encounter gradients of physical or chemical agents in nature and they respond by moving toward or away from the agent.
Chemotaxis – responding to chemicals
Phototaxis- responding to light
In the absence of a gradient, cells move in a random fashion that is described as “runs”. When it stops and changes direction, it is known as tumbling.
Runs- Flagella rotates CCW
Tumble- Flagella rotates CW, forward motions stops and change directions