Viruses, The Prokaryotic Cell, Microbial Growth, & Genetic Recombination
General information about viruses
Acellular and NOT living
They’re ultramicroscopic (most are <0.2um); the largest viruses average 500-1,000 nm
They’re ubiquitous, infecting every taxonomic group of organisms including bacteria, eukaryotes, and archaea
Too many
Each species of virus infects a particular group of host species, known as the host range, but generally are very host specific
About 8% of our DNA comes from viruses
Structure of basic virus (genome, capsid, +/- envelope)
A viral genome is composed of either DNA or RNA and it can be double- or single-stranded
The capsid (or protein coat) keeps the viral genome intact outside the host. It comes in many shapes and is made up of capsomers
Icosahedral (which has the min. # of capsomers)
Helical
Amorphous or complex viruses (no symmetrical form)
Some species have their capsid encased by an envelope, often forming out of host membranes with embedded viral envelope proteins
Mostly associated with animal viruses
Some have spike proteins that help them attach to particular cells
+envelope?
-envelope?
Lytic cycle of bacteriophage
During the lytic cycle of virulent phage, the bacteriophage attaches, penetrates, and takes over the cell; it then reproduces new viral components, assembles new phages, and lyses the cell
The lysogenic cycle of bacteriophage (prophage, lysogenic conversion)
In a lysogenic cycle, the phage genome also enters the cell through attachment and penetration. The phage genome integrates into the bacterial chromosome and becomes part of the host. The integrated phage genome is called a prophage. As the bacterium replicates its chromosome, it also replicates the phage’s DNA and passes it on to new daughter cells during reproduction.
Temperate phages tend to be inactive within the cell
Other viruses will not be able to infect a cell that’s already prophaged
When stressed, the prophage DNA is excised from the bacterial chromosome and enters the lytic cycle
Lysogenic conversion: phage genes in the bacterial chromosome can cause the production of toxins or enzymes that cause pathology
May carry the ability to make a bacterium more virulent
The difference in cycles of animal viruses versus bacteriophage (entering and exiting the cell)
(photo)
Acellular agents in addition to viruses
Viroids
A piece of RNA
No capsid
most/all infect plants
27 identified
Is a satellite virus = dependent on other viruses for replication
Prions (Kuru, Varient Crutzfeld Jakob Disease, Bovine Spongiform Encephalopathy)
No nucleic acid
Abnormal form of a protein
Extremely resistant to normal sterilization
Cooking and autoclaving cannot destroy it
Creutzfeldt-Jakob: deterioration of abilities (neurological); holes in the brain; 100% fatal
Variant Creutzfeldt-Jakob (VarCJD): also from organ transplants
Bovine Spongiform Encephalopathy (BSE) (mad cow disease): meat that came from cow(s) that have Jakob
Scrapie: in sheep and transmissible in sheep
Kuru: obtained through cannabilism; funeral ritual
Viral Disease Wiki
Norovirus
Single-stranded RNA non-envelope
Capsid is about 23-40nm
Highly contagious and mainly infecting children due to lack of handwashing
It is transmitted by human-to-human contact, through contaminated food or water, as well as touching contaminated surfaces.
Often misdiagnose this virus to a stomach bug or food poisoning because they all have similar symptoms
900 people die yearly
Ebola
Nucleocapsid which has helical single-stranded RNA enclosed in a spiked outer envelope
A rare disease that causes affects the immune system and often results in death
The virus spreads among humans through human-to-human contact and is spread to people by wild animals
ALL the structures associated with the prokaryotic cell:
Cell membrane = semi-permeable barrier that regulates the passage of substances
Cell wall = single, interlinked molecule that encloses the entire cell and is made up of peptidoglycan (provides structure to the cell) and 2 sugars: N-acetyl muramic acid (NAM) and N-acetyl glucosamine (NAG)
Some have no cell wall
Some are pleomorphic (have different shapes) and thus can pass through filters
Some lose their cells walls making them more susceptible to changes and lyse
L-forms = survive and reproduce despite lack of cell wall
Protoplast = could mean a cell lost some or all of its cell walls but it can also refer to the cell membrane and the contents inside the cell
Spheroplasts = specifically refer to a rod-shaped organism that loses peptidoglycan and starts to form a sphere
S-layer = a self-assembling highly structured layer of proteins that are found in some bacteria, both gram + and -; it gives structure, protects the organism, and allows attachment
Glycocalyx = coating of glycoproteins outside cell wall that help to protect the cell and also help with attachment
Two types:
Capsule - highly organized, tightly attached
Not all bacteria have a capsule
If it’s small or happy, bacteria would not want to make a capsule b/c it wants to conserve energy
Slime layer - loosely organized and attached
On most bacteria
Cytoplasm = fluid inside the cell, acts as a solvent
Nucleoid = DNA containing region of the bacterial cell
Has chromosomes which are single, circular, double-stranded, and tightly coiled DNA that contains all the genetic info required by a cell
Plasmids may become part of the chromosome → episome
Ribosomes = 70s size and site of protein synthesis
Specialized structures
Fimbriae attach cells to surfaces; shorter and more numerous
F (fertility) pili, or sex pili, facilitates the transfer of DNA between cells (conjugation)
Some specialized cells have stalks
Types of flagella
Monotrichous = one end
Amphitrichous = both ends
Peritrichous = all around
Lophotrichous = tuft at one end
Periplasmic flagella = exist in a spirochetes’ periplasmic space
Gram-negative cell wall
Gram-negative = multilayered cell wall, more complex than a gram-positive, single layer of peptidoglycan, enclosed by an outer membrane with a lipopolysaccharide layer (LPS)
LPS layer contains lipid A, an endotoxin that is released when the cell dies and causes endotoxic shock in patients
Gram-positive cell wall
Gram-positive = thick cell wall, multiple layers of peptidoglycan, teichoic acids
Some cells have a periplasmic space between the cell membrane and the cell wall
Drawing of a monotrichous gram positive bacterial cell
(photo)
Gram staining
Separates bacteria into two groups based on differences in their cell wall structure
Plasmids and types of plasmids
Plasmids are free small circular, double-stranded DNA
Nonessential to bacterial growth and metabolism
But can provide significant advantages to the survival of bacteria in adverse environments
Types of plasmids?
5 differences between the bacterial cell and the archaeal cell
Bacterial cell has a lipid bilayer, archaea cell has a monolayer
Bacterial cell walls have peptidoglycan, archaea cell walls do not have peptidoglycan
Capsules and slime layers are rare in archaea
Many archaea (only) have S layers as the structural component
Some archaea have no cell walls
Reasons endospores are particularly resistant
Being dehydrated and metabolically inactive gives it stability
Production of high amounts of dipocolinic acid (DPA) gives protection from the heat
Increase in SASPs (small acid-soluble proteins) helps to condense and protect the DNA
A thick spore coat gives resistance against enzymes and chemicals
The 4 main layers of the endospore (outer to inner)
Exosporium = lipids, carbs, and proteins
Spore coat = thin protein layers
Cortex = peptidoglycan
Core = DNA, RNA, ribosomes, essential enzymes
Biofilms
A mass of bacteria that stick to and multiply on a solid surface
Produces EPS (extracellular polymeric substance)
Protects the cell
The Growth Curve
Represents the number of live cells in a bacterial population over a period of time
Lag phase = bacteria are metabolically active but not dividing
The bacteria are adjusting to their new conditions
Log phase = time of exponential growth
Once cells have accumulated all that they need for growth, they proceed into cell division. Ideal conditions → rapid growth
Stationary phase = growth reaches a plateau as the number of dying cells equals the number of dividing cells
Nutrients become less available and waste products increase
Death phase = exponential decrease in the number of living cells
Conditions have deteriorated to a point where the cells are irreparably harmed
Carbon source/Energy source terms (chemoheterotroph, photoheterotroph, chemoautotroph, photoheterotroph)
Phototroph = sunlight
Chemotroph = chemical breakdown of carbon source
Heterotroph = organic carbon source
Autotroph = inorganic carbon source
Capneic bacteria - capnophiles
Need carbon dioxide; most pathogens grow better in the presence of CO2
Barophiles
pressure-loving
Temperature terms
Psychrophile = 0°C-20°C
Psychrotroph = 0°C-35°C
Mesophile = 15°C-45°C
Thermophile = 45°C-80°C (high temps)
Hyperthermophile = 65°C-113°C
Cardinal Temperatures = the range that a particular bacterium grows in
Osmotic pressure terms
Osmosis = the net movement of water molecules across a semi-permeable membrane, from an area of low solute (high water activity) concentration to higher solute concentration (lower water activity)
Isotonic = equal amount of solute inside and outside the cell
Hypertonic = more solutes outside of the cell, higher osmotic pressure; there will be a net movement of water out of the cell
Plasmolysis = cell shrinkage
Hypotonic = more solutes inside of the cell relative to the solution and the net movement of water will be into the cell, which may result in lysis of the cell.
Halophiles = need a high concentration of salt
Extreme Halophiles = Growth is even more dependent on large amounts of salt
Osmophiles = Adapted to environments with high osmotic pressures (high salt concentrations)
Osmotolerant = The ability to grow in an environment with a high osmotic pressure
pH terms
Acidophile = acidic conditions (pH 0-5.5)
Neutrophile = neutral conditions (pH 5.5-8.0)
Alkaliphile = basic conditions (pH 8.0-11.5)
Oxygen terms
Aerobe = requires oxygen
Anaerobes = cannot survive in the presence of oxygen because they do not have the enzymes to break down toxic by-products and will quickly die in the presence of oxygen
Microaerophiles = prefer a reduced oxygen atmosphere
Facultative Anaerobe = have the necessary enzymes and can grow with or without oxygen
Aerotolerant Anaerobe = can grow in the presence of oxygen but do not use oxygen for growth
Strict/Obligate Anaerobe = tolerate the presence of oxygen and can only grow in the absence of oxygen.
Mutation
A mutation is a change in the DNA sequence and a main source of diversity in bacteria
Random chance
Might produce a good, neutral, or bad effect
If mutation allows for better survival of the mutated bacterium then that mutation may be selected for and increase in the population
Ames Test
The Ames test is a simple, important test to determine the mutagenic activity of chemicals by observing whether they cause mutations in sample bacteria.
You expose bacteria to said chemical and see if the bacterium changes or undergoes a reverse mutation
If they are mutagenic, they may be carcinogenic
The mutagenicity of chemicals is proportional to the number of colonies observed.
If there is a large number of colonies on the test plate in comparison to the control, then such chemical is said to be mutagens.
it can also be used to detect the mutagenicity of environmental samples such as drugs, dyes, reagents, cosmetics, wastewater, pesticides, and other substances
Conjugation
The DNA donor cell produces an F (sex) pilus to bring cells in contact with each other so they can replicate and pass genetic material to another bacteria
Can take a few hours
Usually doesn't happen all the way
Cells that carry the F-factor plasmid are called F1 cells. The conjugation process begins when a specialized pilus on an F1 donor cell contacts a plasmidless recipient cell called the F2 cell. Once attached, the pilus contracts to draw the two cells together. Their membranes fuse, and the F+ cell forms a protein bridge to connect to the F– cell. The F– recipient cell will be converted to a new F+ donor cell.
Cells carrying integrated F factors are called Hfr cells because of the high likelihood (compared with F+cells) that genes from the Hfr cell’s chromosome will be transferred into the recipient and replace homologous (similar) genes in the recipient’s chromosome (Hfr = high-frequency recombination of chromosomal genes).
An F plasmid that contains host DNA is called an F-prime (F9) plasmid or F-prime (F′) factor
Transduction
Improper de-integration can lead to transduction, the transfer of bacterial DNA from one bacterium to another by a virus
Specialized = takes a piece of the cell DNA they were attached to
Generalized = takes a fragment of bacterial DNA
Transformation
Some bacteria may pick up genes from the surrounding environment (from dead bacteria), via “transformation.”
These genes, often on a plasmid, may code for antibiotic resistance mechanisms.
Transposons
Genes that can undergo transposition, where they can jump from one place in a genome to another (or to a plasmid residing in the same cell)
Contributes to antibiotic resistance when genes move from the chromosome onto a plasmid which can then be transferred to other bacteria