Microbiology Flashcards
Capsid
Viruses are tiny infectious agents, much smaller than bacteria. In its most basic form, a virus consists of a protein coat, called a capsid, and from one to several hundred genes in the form of DNA or RNA inside the capsid (and potentially some enzymes). No virus contains both DNA and RNA.
Most animal viruses do not leave capsids outside the cell, but enter the cell through receptor-mediated endocytosis.
Virus envelope
Most animal viruses, some plant viruses, and very few bacterial viruses surround themselves with a lipid-rich envelope either borrowed from the membrane of their host cell or synthesized in the host cell cytoplasm. The envelope typically contains some virus-specific proteins. A mature virus outside the host cell is called a virion.
Viral host
A viral infection begins when a virus adheres to a specific chemical receptor site on the host (the cell that is being infected).
Receptor
A specific glycoprotein on the host cell membrane. The virus cannot infect the cell if the specific receptor is not available.
Bacteriophage
A virus that infects bacteria, in which the nucleic acid is injected through the tail after viral enzymes have digested a hole in the cell wall.
Endocytotic process
Most viruses that infect eukaryotes are engulfed in an endocytotic process. Once inside the cell, there are two possible paths: lysogenic or lytic infection.
Lytic infection
Virus commandeers the cell’s reproductive machinery and begins reproducing new viruses. Thereis a brief period before the first fully formed virion appears, called the eclipse period.
The cell may fill with new viruses until it lyses (bursts), or it may release the new viruses one at a time in a reverse endocytotic process.
The period from infection to lysis is called the latent period, which also includes the eclipse period. A virus following a lytic cycle is called a virulent virus.
Cycle: virus adheres to cell wall –> viral nucleic acid injected into cell –> replication of active virus –> assembly of new viruses –> lysis of cell –> creation of virons
Virulent virus
A virus following a lytic cycle
Lysogenic infection
A lysogenic cell is a cell that harbors an inactive cirus in its genome.
The viral DNA is incorporated into the host genome, or, if the virus is an RNA virus and it possesses the enzyme reverse transciptase, DNA is actually reverse-transcribed from RNA and THEN incorporated into the host cell genome. When the host cell replicates its DNA, the viral DNA is replicated as well.
A virus in a lysogenic cycle is called a temperate virus.
While the viral DNA remains incorporated in the host DNA, the virus is said to be dormant/latent, and is called a provirus (or prophage, if the host cell is a bacterium). the dormant virus may become active when the host cell is under some kind of stress, or upon exposure to UV light or carcinogens. When the virus becomes active, it becomes virulent.
Cycle: Virus adheres to cell wall –> viral nucleic acid injected into cell –> reduction to provirus –> viral DNA integrated into chromosome –> reproduction of lysogenic bacteria –> induction of provirus to active virus –> replication of active virus –> assembly of new viruses –> lysis of cell –> creation of virons
Reverse transcriptase
The viral DNA is incorporated into the host genome, or, if the virus is an RNA virus and it possesses the enzyme reverse transcriptase, DNA is actually reverse-transcribed from RNA and THEN incorporated into the host cell genome.
Temperate virus
A virus in a lysogenic cycle is called a temperate virus. A host cell infected with a temperate virus may show no symptoms of infection.
Plus-strand RNA
There are many types of viruses. One strategy of classifying them is by the type of nucleic acid they possess.
A virus with unenveloped plus-strand RNA is responsible for the common cold. The “plus strand” indicates that proteins can be directly translated from the RNA. Enveloped plus-strand RNA viruses include retroviruses such as the virus that causes AIDS.
Minus-strand RNA
Viruses include measles, rabies, and the flu. Minus-strand RNA is the complement to mRNA and must be transcribed to plus-RNA before being translated.
Single- and double-stranded DNA viruses
Viruses classified by the type of nucleic acids they possess.
Double-stranded DNA viruses:
chicken pox and shingles (pathogen varicella-zoster virus), Hep B (pathogen hepadnavirus), herpes (pathogen herpes simplex), mono (pathogen epstein-barr virus), smallpox (pathogen flavivirus)
Double-stranded RNA viruses
Viruses classified by the type of nucleic acids they possess.
Include:
AIDS (pathogen HIV), ebola (pathogen filovirus), influenza (pathogen same name), measles (pathogen paramyxovirus), polio (pathogen enterovirus), rabies (pathogen rhabdovirus), SARS (pathogen coronavirus), yellow fever (flavivirus)
Vaccine
The human body fights viral infections with antibodies, which bind to a viral protein, and with cytotoxic T cells, which destroy infected cells. A vaccine can be either an injection of antibodies or an injection of a nonpathogenic virus with the same capsid or envelope. The latter allows the host immune system to create its own antibodies. Vaccines against rapidly mutating viruses are generally not very effective.
Carrier population
Another difficulty of fighting viral infections. If one animal acts as a carrier populations– even if all viral infections of a certain type was eliminated in humans– the virus may continue to thrive in another animal, thus maintaining the ability to reinfect the human population.
Virus structure and size
Capsid, nucleic acid, and lipid-rich protein envelope for some viruses, and tail, base plate, and tail fibers for most bacteriophages.
Viruses are very small. Remember that a bacterium is the size of a mitochondrion, and hundreds of viruses may fit within a bacterium.
Retrovirus
Carries enzyme reverse transcriptase in order to create DNA from its RNA. The DNA is then incorporated into the genome of the host cell. One important retrovirus is HIV, the pathogen that causes AIDS.
Virion
A mature virus outside the host cell. May contain all of the following: capsid, envelope made of phospholipid bilayer, either RNA or DNA. The capsid of a virion might contain: double-stranded RNA, ribosomes, reverse transcriptase
Prokaryotes
Do not have a membrane-bound nucleus. They are split into 2 domains: bacteria and archaea.
Archaea
One type of prokaryotes that have as much in common with eukaryotes as they do with bacteria. Part of the kingdom Monera obsolete. Typically found in extreme environments, such as salty lakes or boiling hot springs. Unlike bacteria, the cell walls of archaea are not made from peptidoglycan.
Bacteria
The other type of prokaryote (other than archaea). Part of the kingdom Monera obsolete.
Fixing CO2
In order to grow, all organisms require the ability to acquire carbon, energy, and electrons (usually from hydrogen).
A carbon source can be organic or inorganic. Most carbon sources also contribute oxygen and hydrogen. Carbon dioxide is a unique inorganic carbon source because it has no hydrogens. To some degree, all microorganisms are capable of fixing CO2– reducin it and using the carbon to create organic molecules, usually via the Calvin cycle). However, the reduction of CO2 is energy expensive, and most microorganisms cannot use it exclusively as their carbon source.
Autotrophs
Organisms that are capable of using CO2 as their sole source of carbon
Heterotrophs
Use preformed organic molecules as their source of carbon. Typically these organic molecules come from other organisms both living and dead, but it is believed that at the dawn of life they formed spontaneously in the environment of primitive Earth.
Phototrophs
All organisms acquire energy from one of two sources. Organisms that use light as their energy source are called phototrophs.
Only prokaryotes can acquire energy from an inorganic source other than light.
Chemotrophs
All organisms acquire energy from one of two sources. Organisms that use the oxidation of organic or inorganic matter are called chemotrophs.
(Note that electrons or hydrogens can be acquired from inorganic matter by lithotrophs, or from organic matter by organotrophs.)
Nucleoid
Prokaryotes don’t have a nucleus. Instead, they have a single, circular, double-stranded molecule of DNA. This molecule is twisted into supercoils, and associated with histones in Archaea and different proteins (not histones) in Bacteria.
The DNA, RNA, and protein complex in prokaryotes forms a structure visible under the light microscope called a nucleoid (aka chromatin body, nuclear region, or nuclear body).
The nucleoid is not enclosed by a membrane.
Cocci
One of the two major shapes of bacteria (round).
Bacilli
One of the two major shapes of bacteria (rod shaped)
Spirilla
Besides cocci and bacilli, some bacteria are helically shaped. If a helically shaped bacteria is rigid, it’s called spirilla.
Spirochetes
Besides cocci and bacilli, some bacteria are helically shaped. If a helically shaped bacteria is non-rigid, it’s called a spirochete. Certain species of spirochete may have given rise to eukaryotic flagella through a symbiotic relationship.
Ribosomes
Prokaryotes have no complex, membrane-bound organelles and no nucleus. All living organisms contain both DNA and RNA. Prokaryotes have RNA. Since they translate proteins, they also have ribosomes, which are smaller than eukaryotic ribosomes.
Prokaryotic ribosomes are made from a 50S and a 30S subunit to form a 70S ribosome.
Mesosome
Invaginations of the plasma membrane in some prokaryotes. Can be shaped as tubules, lamellae, or vesicles. May be involved in cell wall formation during cellular division.
Inclusion bodies
Found in prokaryotes. Granules of organic or inorganic matter that may or may not be bound by a single layer membrane.
Plasma membrane
The cytosol of nearly all prokaryotes is surrounded by a phospholipid bilayer called the plasma membrane. THe phospholipid is composed of a phosphate group, two fatty acid chains, and a glycerol backbone.
The phospholipid is often drawn as a balloon with two strings: balloon is the phosphate group, and strings ar ethe fatty acid chains. The phosphate group is polar, while the fatty acid chains are nonpolar, making the molecule amphipathic.
Amphipathic molecules
When placed in aqueous solution, amphipathic molecules spontaneously aggregate, turning their polar ends toward the solution, and their nonpolar ends towatd each other. The resulting spherical structure is a micelle.
Micelle
Micelles form spontaneously whereas membranes must be actively assembled. If you dump some phospholipids into an aqueous solution, a micelle will most likely form because it is the most thermodynamically stable conformation.
Integral/intrinsic proteins
Amphipathic proteins that traverse the membrane from the inside of the cell to the outside.
Both integral and peripheral proteins may contain carbohydrate chains making them glycoproteins.
Peripheral/extrinsic proteins
Situated entirely on the surface of the membrane. Ionically bonded to integral proteins or the polar group of a lipid.
Both integral and peripheral proteins may contain carbohydrate chains making them glycoproteins.
Fluid mosaic model
Since the forces holding the entire membrane together are intermolecular, the membrane is fluid, its parts can move laterally but cannot separate. The mosaic aspect of the membrane is reflected in the asymmetrical layout of its proteins. In eukaryotic membranes, cholesterol moderates the membrane’s fluidity. In the prokaryotic plasma membrane, hopanoids probably reduce the fluidity of the membrane.
(Remember that prokaryote and eukaryote membranes differ only slightly.)
Diffusion
If two compounds, X and Y, are placed on opposite sides of the same container, the net movement of X will be toward Y. This is called diffusion.
For molecules without an electric charge, diffusion occurs int he direction of lower concentration.
For molecules with a charge, there is also an electrical gradient pointing in the direction that a positively charged particle will tend to move.
Chemcial concentration gradient
A gradual change in concentration of a compound over a distance. A series of vectors pointing in the direction of lower concentration.
Electrical gradient
For molecules with a charge, electrical gradient points int he direction that a positively charged particle will tend to move.
Electrochemical gradient
Chemical concentration gradient (points in direction of lower concentration) + electical gradient (points in direction that a positively charged particle will tend to move).]\
The EC gradient for compound X points int he direction that particle X will tend to move.
Semipermeable membrane
If the molecules of X can wiggle their way across the membrane, then diffusion is slowed. Since the membrane slows the diffusion of X, but does not stop it, it is considered semipermeable.
Two factors of a compound affecting semipermeability are size and polarity.
Size and permeability
The larger the molecule, the less permeable the membrane is to that molecule. A natural membrane is generally imperable to polar molecules with a molecular weight greater than 100 without some type of assistance.
Polarity and permeability
The greater the polarity of a molecule (or if the molecule has a charge), the less permeable the membrane to that molecule.
Very large lipid soluble (nonpolar) molecules like steroid hormones can move right through the membrane.
Passive diffusion
Most of the diffusion of polar or charged molecules across a natural membrane takes place through incidental holes (sometimes called leakage channels) created by the irregular shapes of integral proteins. This is not meant to aid in diffusion– it is merely an incidental contribution.
This is an example of passive diffusion. Passive diffusion depends on lipid solubility (Are you nonpolar enough to slide right through the phospholipid bilayer?) and size (Can you fit through the cracks around the integral proteins?).
Transport/carrier proteins
Some molecules are too large or too charged to passively diffuse, yet they are needed for the survival of the cell. To assist these molecules in moving across the membrane, specific proteins are embedded in the membrane, which are designed to facilitate the diffusion of specific molecules across the membrane.
Transport proteins aid in facilitated diffusion, which occurs down the electrochemical gradient of all species involved. Most human cells rely on facilitated diffusion for their glucose supply. Facilitated diffusion is said to make the membrane selectively permeable because it is able to select between molecules of similar size and charge.
Active transport
Movement of a compound against its electrochemical gradient. Requires expenditure of energy. Can be accomplished:
- By the direct expenditure of ATP to acquire or expel a molecule against its EC gradient
- Indirectly, using ATP to create an EC gradient, and then using the energy of the EC gradient to acquire or expel a molecule (secondary active transport).
Bacterial envelope
The bacterial plasma membrane and everything inside is called the protoplast. Surrounding the protoplast is the bacterial envelope. The component of the envelope adjacent to the plasma membrane is the cell wall.
Hypertonic
Most bacteria are hypertonic to their environment. This means that the aqueous solution of their cytosol contains more particles than the aqueous solution surrounding them. (Swollen.)
Isotonic
Cytosol contains the same amount of particles as the aqueous solution around it.
Hypotonic
Cytosol contains less particles than the aqueous solution around it (shriveled).
Hydrostatic pressure
Builds as the cell fills with water
Osmotic pressure
When there are more particles on one side of a barrier than the other, the particles want to move down their concentration gradient to the other side of the barrier. IF the particles are prevented from crossing the barrier, water will try to cross in the opposite direction. The cell wall is strong and able to withstand high pressure. As the cell fills with water and the hydrostatic pressure builds, it eventually equals the osmotic pressure and the filling stops. Water continues to move in/out of the cell, but an equilibrium is reached.
Peptidoglycan
Also called murein, what the cell wall is made of. Please note that archaea do not have peptidoglycan cell walls. Peptidoglycan is a series of disaccharide polymer chains with amino acids. These chains are connected by their amino acids, or crosslinked by an interbridge of more amino acids– and are continuous, forming a single molecular sac around the bacterium.
Peptidoglycan is more elastic than cellulose, the main component of plant cell walls.
It is also porous, and allows large molecules to pass through.
Gram staining
A method of classifying bacteria. Staining technique used to prepare bacteria for viewing under the light microscope which stains 2 major cell walls differently.
Gram-positive bacteria
Thick peptidoglycan cell wall prevents the gram stain from leaking out. These cells show up as purple when stained with this process. Gram-positive bacteria have a cell wall approx. 4x thicker than the plasma membrane. The space between the plasma membrane and the cell wall contains many proteins that help the bacteria acquire nutrition.
Gram-negative bacteria
Appear pink when gram stained. Their thin peptidoglycan cell wall allows most of the gram stain to be washed off (it’s slightly different from that of gram-positive). Outside the cell wall, gram-negative bacteria have a phospholipid bilayer. This second membrane is more permeable than the first, allows large molecules to pass.
The polysaccharide is a long chain of carbs that protrude outward from the cell: form a long protective barrier from antibodies and antibiotic.s
A lipoprotein in the outer membrane points inward to ward the cell wall and bonds covalently to the peptidoglycan.
Here, the space between the two membranes is the periplasmic space.
Bacterial flagella
Long, hollow, rigid, helical. Made of a globular protein called flagellin. (Don’t confuse them with eukaryotic flagella, which are made of microtubules!)
They rotate counterclockwide to propel the bacterium in a single direction.
If rotated clockwise, the bacteria tumbles; tumbling changes the orientation of the bacterium, allowing it to move in a new direction.
Flagellum is propelled using energy from a proton gradient (not ATP).
Genetic recombination in bacteria
Bacteria do not undergo mitosis or meiosis, and cannot reproduce sexually. They have 3 alternative forms of genetic recombination: conjugation, transformation, and transduction.
Binary fission
How bacteria divide their cells asexually. The circular DNA is replicated in a process similar to replication in eukaryotes. 2 DNA polymerases begin at the same point on the circle (origin of replication) and move in opposite directions, making complementary single strands that combine with their template strands to form 2 complete DNA double-stranded circles. The cell then divides, leaving 1 circular chromosome in each daughter cells.
DNA replication –> Cell elongation –> Septum formation –> Cell seperation
Binary fission results in 2 genetically identical daughter cells.
Conjugation
A type of genetic recombination. Requires that one of the bacterium have a plasmid with a gene coding for the sex pilus. Note that not all bacteria with plasmids can conjugate– it must have a conjugative plasmid specifically. Conjugative plasmids possess the gene for the sex pilis, which allows DNA passage from the cell containing the conjugative plasmid to the cell that doesn’t. One strand is nicked, and one end begins to seperate from its complement as its replacement is replicated. The loose strand is replicated and fed through the pilus.
Plasmid
Small circles of DNA that exist and replcate independently of the bacterial chromosome.
Sex pilus
A hollow protein tube that connects 2 bacteria to allow the passage of DNA
Fertility factor/F factor
AKA the F plasmid. The first plasmid to be described. A bacterium with the F factor is called F+ (without? F-.) The F plasmid can be in the form of an episome, and if the pilus is made while the F factor is integrated into the chromosome, some or all of the rest of the chromosome may be replicated and transferred.
R plasmid
Donates resistance to certain antibiotics. A conjugative plasmid. Prescribing multiple antibiotics at once promotes conjugation of different R plasmids, providing different resistances to antibiotics and producing a super-bacterium that contains many antibiotics resistances on 1+ R plasmids.
Transformation
The process by which bacteria may incorporate DNA from their external environment into their genome.
- When bacterium dies, DNA fragments released.
- A live bacterium takes up the DNA fragment
- Through homologous recombination, DNA is incorporated into the genome of the live bacterium
The living bacteria receive the genes of the heat-killed bacteria through transformation, and become virulent.
Transduction
Occurs when the capsid of a bacteriophage mistakenly encapsulates a DNA fragment of the host cell. If this virion infects a new bacterium, it injects harmless bacterial DNA fragments instead of virulent viral DNA fragments. This can be mediated artificially in the lab.
Vector
The virus that mediates transduction.
Fungi
Represent a distinct kingdom of organisms with tremendous diversity.
Has 3 divisions (seperated into divisions, not phyla):
- Zygomycota
- Ascomycota
- Basidomycota
Eukaryotic heterotrophs: obtain food by absorption > ingestion, secrete digestive enzymes outside bodies and then absorb the products of digestion.
Saphrophytes.
Many possess cell walls, called septa, made of the polysaccharide chitin.
Other than yeasts, fungi are multicellular. May contain 1+ nuclei. Fungi have no centrioles, and mitosis in fungi takes place in the nucleus. THe nuclear envelope never breaks down.
In growth state, fungi are mycelium of hyphae.
Fungi spend most of their lives in the haploid state, and can reproduce sexually or asexually.
Saprophytic
To live off dead matter (eg, most fungi).
Septa
Cell walls of fungi
Chitin
Polysaccharide which makes up fungi cell walls. More resistant to microbial attack than cellulose. Same substance of which the exoskeleton of arthropods is made.
Mycelium
In growth state, fungi are a tangled mass– called a mycelium, made of hyphae
Hyphae
Multiply-branched threadlike structures which make up mycelium
Haploid stage of fungal reproduction
Fungi alternate between haploid and diploid stages in their life cycle. THe haploid stage predominates, and is their growth stage. Hyphae are haploid. Hyphae may form structures which release haploid spores, which give rise to new mycelia in asexual reproduction.
Spores
Can be formed asexually or sexually; borne by air currents, water, or animals to locations suitable for new mycelial growth. Hyphae (fungi) release haploid spores that give rise to new mycelia in asexual reproduction.
Budding
AKA cell fission: smaller cell pinches off from single parent cell
