Jump to... Basics / Structure / Metabolism / Bacterial Genetics / Viruses / Microbial Ecology
The first microorganisms – organisms measured in microns – were observed in the 17th century by cloth merchant van Leeuwenhoek. French chemist Pasteur disproved the theory spontaneous generation with swan neck flasks and helped invent pasteurization, and German microbiologist Koch established four postulates that helped prove that pathogens cause disease:
All microorganisms are living systems that can metabolize, reproduce, differentiate, move, communicate, and evolve. Prokaryotes, which are actually more diverse than eukaryotes, include archaea and the domain that split from them, bacteria. They have no nucleus (with a nucleoid and one chromosome of circular, haploid DNA instead) and lack certain membrane-bound organelles. They reproduce through fission. Eukaryotes are usually larger and have a nucleus with multiple chromosomes of linear DNA. They split from archaea after bacteria did.
Bacteria may be Gram-positive, Gram-negative, or Gram-variable This is determined by the structure of the cell envelope. A Gram-negative bacterium will have a periplasmic space in their cell wall. Most bacteria are Gram-negative and will stain purple in a Gram stain. Gram-positive bacteria will stain pink and appear "smooth".
Microorganisms can also be categorized based on their sources of carbon and energy. Heterotrophs must derive their carbon from organic sources, and autotrophs get it from inorganic sources. Chemoorganotrophs and chemolithotrophs will get their energy from organic carbon and inorganic chemicals, respectively, and phototrophs get their energy from light.
Most of a bacterium's weight is water mass – as much as 70%, just like humans and the surface of earth! This dry weight is compose of various macromolecules and polymers, and at least half of it is proteins.
Proteins are made up of amino acids, their monomers. Amino acids in biology are typically left-handed, and there are 21 that occur commonly in nature (which can be categorized as ionizable-acidic, ionizable-basic, nonionizable-polar, and nonpolar). These will typically have an amino/imino functional group, an organic acid functional group, and an R group. Together, they are joined by peptide linkage.
Carbohydrates/polysaccharides are chains of monosaccharides (that is, sugars). In contrast to proteins, carbohydrates are right-handed, or dextral. Structurally, they are made up of C:H:O in a 1:2:1 ratio. The most relevant of these are usually 4-7 carbons long. Their linkage comes in two types: α-glycosidic bonds are used to store energy in bacteria and eukaryotes, and β-glycosidic bonds are seen in structural cell components like cellulose.
Lipids are formed by fatty acids that bind to glycerol; that is, they have two monomeric units. There are polar and used to form membranes.
Nucleic acids are made up of nucleotides. They are the genetic information in a cell. Purines (adenine and guanine) bind to pyrimidines (thymine and cytosine), the former of which have two rings instead of one. A useful mneumonic is "purinA doG food"!
Bacterial structure is categorized into six different forms: coccus (ball), rod, spirillum (wigglier rod), spirochete (springy), hypha and stalk, and filamentous (very long).
The cell wall of most bacteria is made up of peptidoglycan, chains of polysaccharies and proteins. This is thinner in Gram-negative bacteria. Archaea instead have a alternating pseudocrystalline S-layers made up of pseudomurein, which structurally resembles peptidoglycan. In eukaryotes, the membrane is strengthened by sterols, a form of lipids (despite being technically alcohols), while bacteria use hopanoids, also lipids. Within the membrane ae transport proteins. Uniporter proteins only allow a single substance to enter the cell. Antiporters may allow some kinds in and others out, while symporters will transport multiple kinds of substances in. Almost invariably, the inside of a cell has a negative charge, creating a gradient that helps these transport proteins function.
Photosynthesis is the process by which phototrophs get their carbon. Most of these are also autotrophs. Photoautotrophs use carbon fixation, while photoheterotrophs get theirs directly from the environment using energy from photosynthesis. This process requires light-sensitive pigments known as chlorophyll.
This process has two separate reactions going on. The light reaction occurs when light energy is trapped by a chlorophyll or a carotenoid that will funnel it towards chlorophyll, where it will be used as an energy source in ATP synthesis by reducing NADP+, whic will later power the dark reaction. This latter resembles the glycolytic pathway and synthesizes glucose from CO₂.
Overall, the classic photosynthetic reaction is...
6CO₂ + 6H₂O -> C₆H₁₂O₆ + 6O₂
TKTK
DNA, RNA, and protein are considered "informational molecules" due to the biological information in their sequences. As established in basic genetics, genes are a unit of heredity and contain the coded sequence needed to form proteins. DNA is replicated and can be transcribed into RNA, which in turn may be translated into proteins. Nucleotides are always added to the 3' end of what is being synthesized. Cytosine binds to guanine with three hydrogen bonds and adenine to thymine with two, pyrimidine to purine. These form anti-parallel strands.
RNA has four functions: carrying genetic information (mRNA), structure/function in ribosomes (rRNA), transporting amino acids (tRNA), and regulation (sRNA). It uses uracil instead of thymine. tRNA tends to come in a "t"-shaped structure of stem-loops, the tips of which are anticodons (which bind to codons on mRNA). Operons are sections of DNA with promoter operator sequences that contain genes which encode either mRNA or rRNA. These operator sequences are upstream of origination and regulate transcription. The alpha subunit of an RNA polymerase complex attaches itself to the DNA, the beta subunit binds to the section, the beta prime subunit elongates the RNA, and the sigma subunit detects promoters.
Plasmids are usually-circular genetic elements that replicate independently of the host chromosome. They are double-stranded and supercoiled with no extracellular form. Plasmids usually code for enzymes involved in timing cellular replication and apportionment of replicated plasmids between daughter cells; usually, these are specialized, non-essential functions. The amount of a plasmid in a cell is its copy number. In Gram-negative bacteria, plasmids will replication bidirectionally like the bacterial chromosome does. Gram-positive plasmids go through rolling circle replication. There are also incompatibility groups that may prevent the replication of certain other plasmids within the same group. If a plasmid is removed, the cell is considered to be "cured", and if it is integrated into the host chromosome, it is known as an episome.
To remain supercoiled (by DNA topoisomerase II/gyrase), prokaryotic DNA is kept pinioned in a circular configuration and further supercoiled by folding part of the DNA over itself, making a double-stranded cut, and then resealing it on the other side. DNA topoisomerase I will relax it again, forming a circle, for replication later.
DNA also has secondary structures. Bent DNA is a run of 5-6 adenines interrupted by 4-5 other bases, and inverted repeats are stretches of DNA where the code is complementarily on the same strand. These may pair with each other to form a stem-loop structure, and may also be called a hairpin structure if there is no visible loop. If this self-pairing happens at the end of a linear molecule, it's known as a sticky end. DNA may also be methylated (have an attached methyl group) at its recognition site to prevent it from being cut by restriction enzymes.
DNA as we tend to recognize it is usually in the form of right-handed B-DNA. Z-DNA is a left-handed form that is thought to fascilitate transcription; A-DNA is either dsRNA or a combination of RNA and DNA. The average nucleotide weighs 330 Daltons, so if the average gene coding for one protein is 1,000 base pairs, the average gene has a molecular weight of about 1000 × 2 × 330 = 660,000 Da, and 1,000 genes – the bare minimum for independent life – are about 660,000,000 Da. Since each amino acid comes from a codon of three bases, this also means the average protein is 333.3 amino acids long.
E. coli, as one of the best-studied organisms, has a well-documented chromosome about 100 "minutes" long, but we generously estimate that we can only make assumptions about maybe 61.9% of its genes' functions (meaning that 38.1% of it is still of unknown function to us). Of those, only 80% seem to be necessary for normal growth. Maybe about 21% of its total genome is dedicated to metabolism; other uses include transport, regulation, and structure.
When an organism inherits a change in its genetic code that makes it differ from the wild-type, it is a mutant. However, there is also genetic recombination (when genetic material from two separate individuals is combined into a single unit) and horizontal gene transfer (when genetic information is transferred by means other than reproduction). A wild-type organism describes an organism as isolated from its natural habitat, the archetypal organism. This does not necessarily make it more fit for survival than a mutant, or even more common. Auxotrophs are a specific type of mutant that require an additional nutrient that the wild type prototroph does not.
Spontaneous mutations occur throughout an organisms life "naturally", but can also be induced through chemicals, radiation, and infection. Point mutations only affect a single base pair. Transition mutations swap a purine for a purine and pyrimidine for a pyrimidine, while transversion mutations swap a purine for a pyrimidine and vice versa.
Point mutations have many types. A silent mutation occurs when a base pair change does not change what amino acid is being called for by the codon, but a nonsense mutation will change it into a stop codon and result in an incomplete protein. Missense mutations will change what amino acid is called for and result in a faulty protein. More extreme examples may result in the loss of a stop codon (readthrough mutations), a shift by one base pair (microinsertion/microdeletion) that totally jumbles what each codon downstream of it encodes (frameshift mutations), or the insertion/deletion of a codon altogether (nonframeshift indel). If DNA is too damaged, or replication stalls, it activates RecA, and the SOS DNA repair regulon will be activated to repair the DNA.
Mutagens are agents responsible for mutation induction. Chemical mutagens include base analogs, chemicals that react with DNA, intercalating agents, and ionizing radiation. We can use the Ames Test to detect the presence of mutagenic agent. A suspected mutagen is placed on a filter in the middle of an agar plate lacking a particular nutrient so that it diffuses into the agar. Plated bacteria is unable to grow if it is auxotrophic, but may revert in response to the mutagen. The more bacteria revert, the more potent the mutagen.
A lot of people don't realize genetics nomenclature can be very specific. A gene's name is three lowercase letters (representing the protein encoded) and a capital (representing order of discovery), all in italics. Mutations are defined by a number at the end of the name. The product of the gene have a capitalized first letter and a lack of italics. algD is a gene that contains the code for the protein AlgD.
Gene expression can be regulated in a lot of ways, primarily by focusing on enzyme activity/synthesis. Enzyme activity can be inhibited via feedback inhibition, where the end product interferes with the activity of the beginning of the pathway. Allosteric inhibition changes the shape of an enzyme entirely, and isozymes (isofunctional enzymes) are enzymes that catalyze the same reaction, but have binding sites for multiple different inhibitors.
After translation, an enzyme may be modified with methyl groups, ADP, or other additions that change its conformation and reduce its activity, or it may be cleaved at a leader peptide to increase its activity. These latter types are usually used for protein trafficking. Intein splices may also occur, in which the intein is spliced from a synthesized protein to create two active separate peptides.
DNA can also be transferred between cells, as shown by Griffith's experiments with rats. Transformation occurs when bare DNA is transferred into a recipient cell without a donor/virus intermediate by taking up free-floating fragments of lysed chromosomes/cells. A cell capable of doing so is called a competent cell. Transduction occurs as a result of viral infection. Phages may sometimes package DNA from a bacterium errantly. They will be unable to carry out lysis of the new cell because they have lost a lot of their original genome, and the transduced cell will recomdbine to include this new genome. Generalized transduction packages up random sites of a donor, and it doesn't happen frequently. Specialized transduction will package a specific site and is more likely, but can only be done by temperate phages and will always occur at a site adjacent to that of prophage integration. Conjugation is a transfer of DNA via cell-to-cell contact. Bacteria with an F plasmid can produce an F pilus that will attach to recipient bacteria and transfer upon contraction. The DNA will be replicated as this happens. If this F plasmid is actually integrated into the chromosome, this is Hfr (high-frequency recombination), but recipients will usually not become Hfr as a result.
A lot of modern genetic engineering efforts rely on electroporation to move genetic information between cells, where cells are exposed to a powerful electric pulse that makes them swell and contract, releasing or uptaking free DNA. Other genetic engineering forms include molecular cloning, where source DNA is isolated and fragmented by restriction enzymes, then integrated with DNA in a host. Plasmids are the easiest vector through which to manipulate DNA due to size, shape, and structure, but lambda and M13 bacteriopages are also useful, with the former having the ability to integrate into the genome and the latter being able to exit without killing its host to turn hosts into "factories".
[TKTK] Orthologs are genes that are similar between organisms, but differ due to speciation. Paralogs, by contrast, are similar due to the duplication of a gene within a chromosome.
All viruses have a protein coat (capsid) surrounding a nucleic acid genome, the combination of which is known as a nucleocapsid, but otherwise come in many neat, regular geometric forms. They are considered particles, not cells, and are very small, smaller than host cells, with tiny genomes. Virsues cannot replicate without hijacking the metabolic machinery of a host, a cell. The introduction of a viral particle into a cell is called infection. The only cells considered immune to viral infection must lack a proper genome and metabolic activity – such as red blood cells.
Viruses usually have very specialized receptors and have trouble infecting new types of host cells, even if they belong to the same multicellular organism. Most viruses are classified based on their preferred host. In an extracellular environment, they are referred to as virions.
The majority of microbiologists don't consider viruses to be living things. This page will assume they aren't, because that's the approach my course takes, but the status of viruses remains contentious and weird, as many things about viruses tend to be.
It might be tempting think viruses predate cellular life, but evidence shows it is most likely the other way around. Viruses need a host cell to reproduce, As long as there are cells with metabolic processes, there is always the potential for a novel virus to emerge.
Virions can come in rods (helical) or spheres (icosaherdral) forms. Complex viruses are unique, with a head, tail, and tail fibers, recognizable in bacteriophages. Enveloped viruses have an additional membranous material coating the capsid for additional strealth and are derived from host cell lipids. However, viral receptors must inevitably stick out of this envelope to latch onto a host cell, so this is not a perfect mode of stealth.
While viruses have no metabolic activity of their own, they may still sometimes have viral enzymes: lysozymes that aid in penetration and the release of virions, for example, or forms of nucleic acid polymerization initiators. One can cultivate viruses in a lab with tissue cultures, and they can be quantified by spreading viral particle dilution over a petri dish lawn. As a cell dies, it leaves behind a hole (plaque). Viral concentration is called titer.
Viruses reproduce in seven steps: attachment/adsorption, penetration/injection, alteration of host cell machinery, genome replication, protein synthesis, assembly/packing, and release. During attachment, proteins along the outside of a virion interact with the receptors of a host cell, so attachment can be prevented by blocking or removing them. The virion will otherwise inject its nucleic acids into a cell, or enter the entire cell if it lacks a cell wall, or even fuse with the membrane. Some viruses, however, can enter without a receptor, such as through phagocytosis. Once inside a cell, it will direct it to first make early proteins necessary for replication, and middle proteins that modify host metabolism. Late proteins come after, include virus coat proteins, and are made in huge numbers. This process can be timed very accurately, and assembly occurs as the components are synthesized. To ensure this goes off right, they may also instruct the cell to make a new kind of Sigma factor that also calls for the destruction of the cell's own Sigma factor. Once the cell is expended, the virus tells the cell to self-destruct and release hundreds, if not thousands, of new virions.
All viral proteins come from viral-specific mRNA. If the RNA is translated into protein, it's RNA+, and RNA or DNA complementary to it is RNA-/DNA-; an RNA+ virus has the advantage of not needing to carry around an RNA polymerase since its mRNA contains the instructions needed to synthesize it. The formation of new virions often includes switching from one type of nucleic acid to another. Reverse transcription refers to the formation of DNA from RNA, and retroviruses utilize this process by going through a DNA intermediate.
Viruses can be classed with the Baltimore system:
Bacterial viruses include the infamous T-speries phages. T-even phages have longer tails than their T-odd counterparts. Most bacteriophages are ssRNA. ΦX174 is an ssDNA virus that is being studied as a means of genetic engineering. It converts ssDNA to dsDNA (to Replicative Form) and then makes new ssDNA using rolling circle replication. Lambda, another notable virus, is a temperate phage that may not always kill its host. Usually, after viruses are assembled, they direct the synthesis of lysozyme to make the cell self-destruct and release the virions. A temperate phage may enter a state of lysogeny in which the viral genome becomes integrated with the host genome without producing viral progeny. These viruses are then called prophages, maintained by a repressor molecule, but if this repressor fails, viral reproduction will initiate and the host cell will be lysed. If a virus never exits this stage, however, it becomes cryptic and permanently part of the bacterial genome.
Animal cells go through viral infection in many ways. There may be lysis, as in bacteria, but they may also deal with latent or persistent infection, where the cell continues to live while infected; in the former case, they release viral particles constantly, and in the latter, the virus is present without replicating... for now. A viral infection may even cause malignant tumor cells to form by deactivating tumor suppressor genes or turn proto-oncogenes into oncogenes, which deprives surrounding cells of nutrients and can kill the individual. To protect themselves, bacteria will have restriction endonucleases that cut up invasive viral DNA (though viruses, in turn, will try to prevent this with a glucose). These are very specific and often palindromic. There are five types:
Viroids are RNA with no capsid or proteins, and a very shot genome. None are known to affect animals. Prions are, conversely, solely made of protein. Prions cause other proteins to misfold, but may replicate through other means we currently do not understand. These then accumulate and cause harm, particularly in brain tissues.
The progeny of a single cell is known as a population, while guilds are metabolically-related populations, and communities are sets of guilds in turn.
Click here to return to the main page.