Viruses are tiny infectious agents, much smaller than bacteria.

They are
comparable in size to large proteins. 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. No virus contains both DNA and RNA!! 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!!

- The capsid usually accounts for most of the weight of the virus.

A mature virus outside the host cell is called a virion.

Bacteriophage

Viruses are not currently classified as living organisms; they do not belong to any
of the taxonomical kingdoms of organisms. Viruses differ from living organisms
in the following ways. They ALWAYS require the host cell’s reproductive
machinery in order to replicate!! Viruses don’t metabolize organic nutrients.
Instead they use the ATP made available by the host cell. Viruses possess
either RNA or DNA, but never both. Thus, there are viruses with the familiar
double-stranded DNA, with single-stranded DNA, with double-stranded RNA, and
with single-stranded RNA. Also the nucleic acid could be linear or circular.

- Viruses can be crystallized without losing their ability to infect.

A viral infection begins when a virus adsorbs to a specific chemical receptor site
on the host. The host is the cell being infected.

The chemical receptor is usually a specific glycoprotein on the host cell

membrane!!!

- The virus can’t infect the cell if the specific receptor isn’t
available/there!!!

Next, the nucleic acid of the virus penetrates into the cell. In a bacteriophage, a
virus that infects bacteria, the nucleic acid is normally injected through the tail
after viral enzymes have digested a hole in the cell wall.

Most viruses that infect eukaryotes are engulfed by an endocytotic

process!!! They could also be engulfed by a process called membrane
fusion, in which the envelope of the virus is actually incorporated into
the plasma membrane of the host cell releasing the capsid into the
cytoplasm.

Once inside the cell, there are two possible paths:

1) Lytic infection – the virus commandeers the cell’s reproductive

machinery and begins reproducing new viruses. There is a brief period
before the first fully formed virion appears. This period is called the
eclipse period. The cell may fill with viruses until it lyses or burst, or it
may release the new viruses one at a time in a reverse endocytotic
process. The period of infection to the lysis is called the latent
period!! The latent period encompasses the eclipse period. A virus
following the lytic cycle is called a virulent virus!!

2) Lysogenic infection – 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. When a
host 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 cell, the
virus is said to be dormant or latent, and is called a provirus (a
prophage if the host cell is a bacterium)!!
 There are 2 important results from the lysogenic cycle:

1) The cell infected is immune to reinfection by the same

phage!!!

2) The host cell may exhibit new properties, this is known as

phage conversion

The dormant virus may become active when the host cell is
under some type of stress!! Examples of stress include UV light or
carcinogens. When the virus becomes active, it becomes virulent.
Exhibits exponential growth b/c each new cell will create more
viruses. It is a longer cycle than the lytic cycle!!

There are many types of viruses. One way to classify them is by the type of
nucleic acid that they posses.

A virus with unenveloped plus-strand RNA is responsible for the common cold.
The “plus-strand” indicates the proteins can be directly translated from the
RNA!!! Enveloped plus-strand RNA viruses include retroviruses such as the
virus that causes AIDS. A retrovirus carries the enzyme reverse transcriptase in
order to create DNA from its RNA. The DNA is then incorporated into the
genome of the host cell.

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!!

Note: There are even double stranded RNA viruses, and single and
double stranded DNA viruses!!!

Reassortment – is a method with which virus’ can alter their genetic makeup it occurs
If a virus has a segmented genome and if two variants of that virus infect a single cell,
progeny virions can result with some segments from one parent, some from the other

Viroids are a related form of infectious agent. Viroids are small rings of naked
RNA without capsids. Viroids only infect plants!!

There also exist naked proteins called prions that cause infections in animals.
Prions are capable of reproducing themselves apparently without DNA or RNA.

Defense Against Viral Infection

Although the lipid rich envelope is borrowed from the host cell, spike proteins
encoded from the viral nucleic acids protrude from the envelope!! These
proteins bind to receptors on a new host cell causing the virus to be infectious.
However, it is also the spike proteins that human antibodies recognize when
fighting the infection. Since RNA polymerase doesn’t contain a
proofreading mechanism, changes in the spike proteins are common in
RNA viruses!!! When the spike proteins change, the antibodies fail to recognize
them, and the virus may avoid detection until new antibodies are formed.

A vaccine can be either an injection of antibodies or an injection of a

nonpathogenic virus with the same capsid or envelope. The later allows the host
immune system to create its own antibodies. Vaccines against rapidly
mutating viruses are generally not very effective.

Another difficulty of fighting viral infections is that more than one animal may act
as a carrier population. Even if all viral infections of a certain type were
eliminated in humans, the virus may continue to thrive in another
animal, thus maintaining the ability to reinfect the human population.
For instance, ducks carry the flu virus, apparently without any adverse symptoms.
One of the reasons that the fight against smallpox was so successful was because
the virus can only infect humans.

The structure of a virus: capsid, nucleic acid, and lipid-rich protein envelope
for some viruses: tail, base plate, and tail fibers for most bacteriophages.

Prokaryotes

Prokaryotes don’t have a membrane bound nucleus. They are split into two
distinct domains called Bacteria and Archaea.

Archaea have as much in common with eukaryotes as they do with bacteria.

They are typically found in the extreme environments such as salty lakes and
boiling hot springs. Unlike bacteria, the cell walls of archaea are not made
from peptidoglycan!!!

Most known prokaryotes are members of the domain Bacteria. The introduction
of the two domains makes the kingdom Monera obsolete. The kingdom Monera
was the kingdom containing all prokaryotes.
In order to grow; all organisms require the ability to acquire carbon, energy and
electrons (usually from hydrogen). Organisms can be classified according to the
sources from which they gather these commodities.

A carbon source can be organic or inorganic. Most carbon sources also contribute
oxygen and hydrogen. CO2 is a unique inorganic carbon source because it has
no hydrogens. To some degree, all microorganisms are capable of fixing CO2
(reducing it and using the carbon to create organic molecules usually through a
process called the Calvin Cycle).

1) Autotrophs are organisms that are capable of using CO2, as their sole
source of carbon
2) Heterotrophs use preformed, organic molecules as their source of
carbon.

Organisms can be classified as well according to how they get their energy:

1) Phototrophs use light as their energy source.

a) Ex. Cyanobacteria – blue/green algae that uses photosynthesis.
 Note: Only prokaryotes can acquire energy from an
inorganic source other than light!!!

2) Chemotrophs use the oxidation of organic and inorganic matter as their

energy source

Electrons or hydrogens can be acquired from inorganic matter by lithotrophs, or

organic matter by organotrophs.

- You can recall this one because lithium is an inorganic molecule

and lithotrophs get their hydrogens from inorganic molecules

Note: Humans are chemoheterotrophs

All organisms can be classified as one of each of the three types. Bacteria are
found in all classifications.

Some bacteria are capable of fixing nitrogen. Atmospheric nitrogen is abundant,

but in a strongly bound form that is useless to plants. Nitrogen fixation is the
process by which N2 is converted to ammonia!! Most plants are unable to use
ammonia however and must wait for other bacteria to further process the nitrogen
in a process called nitrification.

Nitrification is a two step process that creates NITRATES, which are useful
to plants, from ammonia!!! Nitrification requires two genera (genus’s) of
chemoautotrophic prokaryotes.

Note: Nitrification is the biological oxidation of ammonia with oxygen

into nitrite followed by the oxidation of these nitrites into
nitrates. Degradation of ammonia to nitrite is usually the rate
limiting step of nitrification.

Note: genus – (plural: genera) taxonomic group containing one or more

species

Chemoautotrophy is an inefficient mechanism for acquiring energy, so

chemoautotrophs require large amounts of substrate. All known
chemoautotrophs are prokaryotes!!

Note: Only prokaryotes can acquire energy from an inorganic source

other than light!!!
Structure of Prokaryotes

Prokaryotes have a single, circular double stranded molecule of DNA. This

molecule is twisted into supercoils and is associated with histones in Archaea
and with proteins that are different from histones in bacteria.

The DNA, RNA and protein complex in prokaryotes forms a structure visible
under the light microscope called a nucleoid (also called the chromatin body,
nuclear region, or nuclear body).

Note: The nucleoid is not enclosed by a membrane!!!

There are three major shapes of bacteria:

1) cocci (round)
2) bacilli (rod shaped)
3) spiral

There are other shapes, including helical. Helically shaped bacteria are called
spirilla, if they are rigid. Otherwise they are called spirochetes. Certain species
of spirochetes may have given rise to eukaryotic flagella through a symbiotic
relationship. The name of the bacteria often reveals the shape.

Prokaryotes have no complex, membrane-bound organelles!! The key words

are ‘complex’ and ‘membrane bound’. They have organelles: ribosomes,
nucleoids, and mesosomes etc….; just not complex membrane-bound
organelles like mitochondria, ER, Golgi, etc!!!

Prokaryotic ribosomes are smaller than eukaryotic ribosomes. They are

made from a 30S subunit and a 50S subunit to form a 70S subunit.

A prokaryote may or may not contain a mesosome. Mesosomes are

invaginations of the plasma membrane and can be seen under the light
microscope!! Their exact function is unknown, but may be involved in cell wall
formation during cell division.

Prokaryotes also have inclusion bodies. Inclusion bodies are granules of organic
or inorganic matter that may be visible under a light microscope. Inclusion
bodies may or may not have a membrane!!

Membranes
The cytosol of nearly all prokaryotes is surrounded by a phospholipid bilayer
called the plasma membrane (the membranes of archaea differ in their lipid
structure). It gives the cell its basic structure and serves as a permeability barrier.
The phospholipid is composed of a phosphate group, two fatty acid chains, and a
glycerol backbone. The phospholipid group is polar, while the fatty acid chains
are nonpolar making the molecule amphipathic. When placed in aqueous solution,
amphipathic molecules spontaneously aggregate, turning their polar ends toward
the solution, and their nonpolar ends toward each other. The resulting spherical
structure is called a micelle.

If enough phospholipids exist, and the solution is subjected to ultrasonic

vibrations, liposomes may form. A liposome is a vesicle surrounded and filled
by aqueous solution. It contains a lipid bilayer like that of a plasma membrane.
The inner and outer layers of a membrane are referred to as leaflets.

Note: The level of saturation in the fatty acids of the phospholipids also
determines the membranes fluidity; an increase in the
unsaturation of these fatty acids increases the fluidity of
the membrane.

If we increase the temperature as well the membrane fluidity

increases.

The plasma membrane contains other types of lipids such as glycolipids. Different
lipid types are arranged asymmetrically between the leaflets. For instance,
glycolipids are found on the outer leaflet only!!!

Unlike eukaryotic membranes, prokaryotic membranes usually DON’T

contain steroids such as cholesterol!! Instead, some bacterial membranes
contain steroid like molecules called hopanoids.

Note: Cholesterol tends to stiffen the bilayer, making it more rigid and
less permeable. Hoponoids probably reduce the fluidity of
the membrane in Prokaryotes!!

Note: In eukaryotes nearly all new membrane synthesis occurs in

the ER!!!

Also embedded within the plasma membrane are proteins. Most of the
functional aspects of membranes are due to their proteins. Membrane proteins act
as transporters, receptors, attachment sites, and enzymes.
Two types of proteins are involved with the plasma membrane:

1) Integral proteins - Ampipathic proteins that transverse the membrane

from inside the cell to the outside.

- Are usually ion channels!

2) Peripheral or extrinsic proteins are situated entirely on the surfaces of

the membrane. They are ionically bonded to integral proteins or the
polar group of a lipid.

Note: Both integral and peripheral proteins may contain carbohydrate

chains making them glycoproteins and the carbohydrate
portion always protrudes toward the outside of the cell!!!
Proteoglycans also exist on the membrane. It can thus form a
carbohydrate layer (glycocalyx) which protects the cell
surface from chemical and mechanical damage.

Recall: Proteoglycans are also a mixture of proteins and carbohydrates,

but they generally consist of more than 50% carbohydrates.
Proteoglycans are a major component of
extracellular matrix

Recall: Glycoproteins are proteins with a carbohydrate group attached and

they are a component of cellular plasma membranes. Also
serve as markers for cellular recognition.

Lipoproteins also exist in some plasma membranes with their lipid portions
embedded in the membrane and their protein portions at the surfaces.

Note: Membrane proteins are distributed asymmetrically throughout

the membrane and between the leaflets!! Neither proteins
nor lipids easily flip from one leaflet to the other.

Note: The shape of the cell and the mechanical properties of the plasma
membrane are determined by a meshwork of fibrous proteins,
called the cell cortex, that is attached to the cytosolic surface of the
membrane. It is made up primarily of spectrin.

Since the forces holding the entire membrane are intermolecular, the
membrane is fluid; its parts can move laterally but can’t separate. The model of
the membrane as just described is known as the fluid mosaic model.
Membrane Transport

Concentration of ions inside and outside a cell are very different:

- Na+ is more plentiful outside the cell

- Cl- is more plentiful outside the cell
- Ca+2 and Mg+2 are more plentiful outside the cell
- K+ is more plentiful inside the cell

A couple rules dictate the permeability of solutes and ions:

1) the smaller the molecule the more permeable it is

2) the lower the polarity, the more permeable it is
3) Lipid bilayers are impermeable to all ions and charged
molecules, no matter how small they are!!

Cell membranes allow water and small nonpolar molecules (including steroids) to
permeate by simple diffusion (dictated by the chemical concentration gradient).
For molecules with a charge there is also an electrical gradient pointing in the
direction that a positively charged particle will tend to move. The two gradients
can be added to form a single electrochemical gradient. The electrochemical
gradient for compound X points in the direction that particle X will tend to move.
Heat and pressure also affect the way particles diffuse.

Note: In strict terms, diffusion occurs in the direction of decreasing

free energy and in increasing universal entropy!!

Note: The ion flow changes the voltage across the membrane – the
membrane potential – thus altering the electrochemical
driving forces for the transmembrane movement of all the
other ions.

If compounds X and Y are separated by an impermeable membrane, diffusion is

stopped. However, if the molecules of X can wiggle their way across the
membrane then diffusion is only slowed. Since the membrane slows the diffusion
of X, but doesn’t stop it, the membrane is said to be semipermeable to compound
X. Facilitated diffusion is also said to make the membrane semipermeable!!!
Most of the diffusion of polar and 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 passive diffusion (down its electrochemical gradient)

Membrane transport proteins can be divided into two main classes:

1) Carrier proteins
a) allows passage only to solute molecules that fit into the binding
site on the protein. Bind their solutes with great specificity
much like how enzymes do

2) Channel proteins

a) discriminates mainly on the basis of size and electric charge

b) Most of the channel proteins in the plasma membrane of animal
and plant cells are quite different and have narrow, highly
selective pores. Almost all of these proteins are ion channels.
Concerned exclusively with the transport of inorganic ions,
mainly Na+ , K+, Cl-, and Ca+2

i) there are three types of ion channels:

- voltage gated ion channels: probability of being

open is determined by the membrane
potential.

Note: All living cells have gated sodium-potassium

ATPases and/or other pumps that are
voltage dependent

- ligand gated ion channel: controlled by the

binding of some molecule (the ligand) to the
channel protein

- stress-activated channel: opening is controlled by a

mechanical force applied to the channel. Ex. In
your ear

Note: Ion channels are either fully open or fully

closed!!!
Facilitated diffusion is diffusion in which the molecule cant naturally diffuse
(because of its size, polarity or both) across the membrane so one of these
membrane transport proteins assists it. It is still down the electro-chemical
gradient however.

Note: Most, but not all, human cells rely on facilitated diffusion for their
glucose supply.

Recall: Only certain epithelial cells in the digestive tract and the
proximal tube of the kidney are capable of
absorbing glucose against a concentration gradient

- This is done via a secondary active transport mechanism

down the concentration gradient of sodium!!

Recall: In the absence of insulin, only neural and hepatic cells

are capable of absorbing sufficient amounts of
glucose via the facilitated transport system.

Facilitated diffusion is said to make the membrane selectively permeable because

it is able to select between molecules of similar size and charge.

To move a solute against its concentration gradient, a transport protein must do

work: it has to drive the “uphill” flow by coupling it to some other process that
provides energy (usually via ATP hydrolysis or through coupling it with a
“downhill” movement). This is called active transport.

It can also be accomplished indirectly by using ATP to create an electrochemical

gradient, and then using the energy of the electrochemical gradient to acquire or
expel a molecule. The latter method is called secondary active transport.

- Whenever we are moving against an electrochemical gradient it

MUST be active transport
For coupling transport of two molecules:

- if both solutes move in the same direction its called symport

- if they move in opposite directions its called antiport

If a carrier protein ferries only one type of molecule across the membrane (and is
therefore not a couple transporter) its called a uniport.
Under normal conditions, the interior of most cells is at a negative electrical
potential compared to the exterior, so that positive ions tend to be pulled into
the cell; thus the inward electrochemical driving force for Na+ is large, as it
includes the driving force due to the concentration gradient and a driving force in
the same direction to the voltage gradient.

Therefore to maintain this balance we need a pump which pumps out Na+. This is
achieved through the Na+-K+ pump. It couples the export of Na+ to the import
of K+ and hydrolyzes ATP to do so. The Na+-K+ pump helps to maintain
osmotic balance of pressure in a cell so it wont flood with H2O and burst!!
Bacterial Envelope

The bacterial plasma membrane and everything inside of it is called the

protoplast!!! A protoplast isn’t a complete bacterium.

Protoplast - Plant, bacterial or fungal cell with the cell wall removed using
either mechanical or enzymatic means

Surrounding the protoplast is the bacterial envelope. The component of the

envelope, adjacent to the plasma membrane is the cell wall. One of the functions
of the cell wall is to prevent the protoplast from bursting!!! Most bacteria
(prokaryote) are hypertonic (hypotonic solution) to their environment (this
means that the aqueous solution of their cytosol contains more particles than the
aqueous solution surrounding them. The resulting osmotic pressure causes a net
movement of water into of the cell). Compare isotonic where the cytosol contains
the same amount of particles and hypotonic (hypertonic solution) where the
cytosol contains less particles. 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. If the cell wall is
removed, the plasma membrane cannot withstand the pressure. Osmosis describes
the movement of water.

Note: Think of Osmotic pressure as the pulling into a solution and

hydrostatic pressure as the pressure pushing out
Movement of water can be described in three cases:

1) isotonic solution- The concentration of solute inside and outside the

cell is the same and hence there is no movement of water.
2) hypotonic solution- The concentration of solute in the outside
environment is smaller than the concentration within the cell, as a
result water moves into the cell and the cell potentially burst
3) hypertonic solution- The concentration of solute in the outside
environment is more than the concentration within the cell. As result,
water leaves the cell and thus the cell shrivels.

Peptidoglycan, also known as murein, is a polymer consisting of sugars and

amino acids that forms a mesh-like layer outside the plasma membrane of bacteria,
forming the cell wall. The polymers are crosslinked by an interbridge of more
amino acids. It is porous, so it allows large molecules to pass through!!!

Recall: Archaea don’t have peptidoglycan cell walls!!

 Note: Peptidoglycan is more elastic than cellulose, which as we recall is
carbohydrate formed by plants and contains Beta linkages
(only bacteria eat Beta linkages and is part of the plants cell wall)

The structure of peptidoglycan

Some antibacterial drugs such as penicillin interfere with the production of

peptidoglycan by binding to bacterial enzymes which make the crosslinks.

Lysozyme, an enzyme produced naturally by humans, attacks the crosslinks

as well!!! In both cases the cell wall is disrupted and the cell lyses killing the
bacterium.

- Don’t confuse this with a lysosome which are organelles containing

digestive enzymes

Capsules: This type of surface layer is composed primary of polysaccharides. If

the layer is strongly adhered to the cell wall, it is called a capsule; if not, it is
called a slime layer. Not all bacteria have this!!

- These layers provide resistance to phagocytosis and serve as

antigenic determinants.
One method of classification of bacteria is according to the type of cell wall
that they possess. A staining technique, called gram staining, used to prepare
bacteria for viewing under the light microscope, stains two major cell walls
differently

The first type is called gram-positive bacteria. Gram-positive bacteria are those that
are stained dark blue or violet by Gram staining. This is in contrast to Gram-
negative bacteria, which cannot retain the crystal violet stain, instead taking up the
counterstain and appearing red or pink.

- Gram-positive organisms are able to retain the crystal violet stain

because of the high amount of peptidoglycan in the cell wall.

- Thick peptidoglycan layer!!

 - Stain blue/violet!!

. Gram-Positive Envelope

The space between the peptidoglycan layer and the plasma membrane is known as
the periplasmic space and it contains proteins that help the bacteria
acquire nutrition!!

Gram-negative bacteria appear red or pink in color when gram stained. Many
species of Gram-negative bacteria are pathogenic, meaning that they can cause
disease in a host organism. This pathogenic capability is usually associated with
certain components of Gram-negative cell walls, in particular the
lipopolysaccharide (also known as LPS or endotoxin) layer

The following characteristics are displayed by Gram-negative bacteria:

1. Thin peptidoglycan layer (which is present in much higher levels in

Gram-positive bacteria)
2. Outer membrane containing lipopolysaccharide (LPS) (can form a
protective barrier from antibodies and many antibiotics) outside the
 peptidoglycan layer, this outer membrane is also more permeable
than the inner, even allowing molecules the size of glucose to
pass through
3. Porins exist in the outer membrane, which act like pores for
particular molecules
4. A lipoprotein in the outer membrane called Braun’s lipoprotein
points inward toward the cell wall and attaches covalently to the
peptidoglycan!!!
5. There are two spaces between the layer of peptidoglycan and the two
membranes
6. Stain red/pink!!
7. The periplasmic space is the space between the two membranes.

Some gram-negative bacteria possess fimbrie or pili (not to be confused with the
sex pilus discussed below). Fimbriae are short tentacles that can attach a
bacterium to a solid surface. They are NOT involved in cell motility!!!

Bacterial flagella are long, hollow, rigid, helical cylinders made from a
globular protein called flagellin; these shouldn’t be confused with
eukaryotic flagella which are made up of microtubules!!
 - They rotate counterclockwise!!!
- When they are rotated clockwise, the bacterium tumbles. This
tumbling acts to change the orientation of the bacterium allowing
it to move forward in a new direction.

The movement of a bacterium toward or away from a particular stimulus is called

taxis. Such stimuli include chemicals (chemotaxis) and light (phototaxis)

Note: The flagellum is propelled using the energy from a proton

gradient rather than by ATP!!

Bacterial Reproduction

Bacteria (prokaryotes) CAN’T undergo meiosis or mitosis, don’t have

centrioles, and they can ONLY undergo Asexual Reproduction. The type of
cell division they are capable of undergoing is called binary fission, which
exhibits exponential growth.

In binary fission, the circular DNA is replicated in a process similar to replication

in eukaryotes. Two DNA polymerases begin at the same point on the circle (ORI)
and move in opposite directions making complementary single strands that
combine with their template strands to form two complete DNA double stranded
circles. The cell then divides, leaving one circular chromosome in each daughter
cell. The daughter cells are genetically identical.
There are three types of genetic recombination that can occur in bacterium:

1) Conjugation – requires that one of the bacterium have a plasmid with

the gene that codes for the sex pilus. If the plasmid can integrate into
the chromosome of the host it’s called an episome!!!

In order for a bacterium to initiate conjugation, it must contain a

conjugative plasmid. Conjugative plasmids possess the gene for the
sex pilus. The sex pilus a hollow protein tube that connects the two
bacteria to allow the passage of DNA. The plasmid replicates
differently than the circular chromosome. One strand is nicked, and one
end of this strand begins to separate from its complement as its
 replacement is replicated. The loose strand is then replicated and fed
through the pilus.

Two plasmids of interest are: the F plasmid and the R plasmid. The F
plasmid is called the fertility factor or F factor. It allows the
production of the sex pilus. A bacterium with an F factor is
designated as F+, and one without it is designated F-. The F plasmid
can be in the form of an episome and if the sex pilus is made while the F
factor is integrated into the chromosome, then some or the entire
chromosome may be replicated and transferred. R-plasmids often
contain resistance genes coding for multiple antibiotic resistance. As
well as resistance transfer genes, they also code for the production
of a conjugation (sex) pilus. The conjugation pilus enables the donor
bacterium to transfer a copy of the R-plasmid to a recipient bacterium,
making it also multiple antibiotic resistant and able to produce a
conjugation pilus

Conjugation is conservative because the donor retains a complete

original copy of the plasmid after the transfer is complete!!

Conjugation diagram 1- Donor cell produces pilus. 2- Pilus attaches to recipient cell,
brings the two cells together. 3- The mobile plasmid is nicked and a single strand of DNA
 is then transferred to the recipient cell. 4- Both cells recircularize their plasmids,
synthesize second strands, and reproduce pili; both cells are now viable donors

2) Transformation – is the process by which bacteria may incorporate

DNA from the external environment into their genome.

3) Sometimes the capsid of a bacteriophage will mistakenly encapsulate a

DNA fragment of the host cell. When these new virions infect a new
bacterium, they inject harmless bacterial DNA fragments instead of
virulent viral DNA fragments. This type of genetic recombination is
called transduction. The virus mediates that mediates transduction is
called the vector. This can be done artificially in a lab.

Mnemonic for transduction : the bacteriophage induces a change

Growth is shown as L = log(numbers) where

numbers is the number of colony forming units
per ml, versus T (time.)

Bacterial growth in batch culture can be modeled with four different phases:

lag phase (A), exponential or log phase (B), stationary phase (C), and death
phase (D).

1. During lag phase, bacteria adapt themselves to growth conditions. It is the

period where the individual bacteria are maturing and not yet able to divide.
During the lag phase of the bacterial growth cycle, synthesis of RNA,
enzymes and other molecules occurs.
2. Exponential phase (sometimes called the log phase) is a period
characterized by cell doubling. The number of new bacteria appearing per
unit time is proportional to the present population. If growth is not limited,
doubling will continue at a constant rate so both the number of cells and the
rate of population increase doubles with each consecutive time period. For
 this type of exponential growth, plotting the natural logarithm of cell
number against time produces a straight line. The slope of this line is the
specific growth rate of the organism, which is a measure of the number
of divisions per cell per unit time. The actual rate of this growth (i.e. the
slope of the line in the figure) depends upon the growth conditions, which
affect the frequency of cell division events and the probability of both
daughter cells surviving. Exponential growth cannot continue indefinitely,
however, because the medium is soon depleted of nutrients and enriched
with wastes.
3. During stationary phase, the growth rate slows as a result of nutrient
depletion and accumulation of toxic products. This phase is reached as the
bacteria begin to exhaust the resources that are available to them. This
phase is a constant value as the rate of bacterial growth is equal to the
rate of bacterial death.
4. At death phase, bacteria run out of nutrients and die.

Endospores

An endospore is a dormant, tough, and non-reproductive structure produced by

Gram-positive bacteria which forms when a bacterium produces a thick
internal wall that encloses its DNA and part of its cytoplasm.

- Remember that Gram + bacteria produce endospores!!

The primary function of most endospores is to ensure the survival of a

bacterium through periods of environmental stress. They are therefore resistant
to ultraviolet and gamma radiation, desiccation, lysozyme, temperature, starvation,
and chemical disinfectants.

In endospore formation, the bacterium divides within its cell wall. One side then
engulfs the other side. The chemistry of the cell wall of the engulfed
bacterium changes slightly to form the cortex of the endospore.

Several protein layers lie over the cortex to form the resistant structure called
the spore coat. A delicate covering called the exosporium, sometimes surrounds
the spore coat. The outer cell then lyses, releasing the dormant endospore. The
endospore must be activated before it can be germinated and grow.
 - Activation usually involves heat
- Germination is triggered by nutrients.

Fungi

Fungi represent a distinct kingdom of organisms with tremendous diversity and

are eukaryotes but have characteristics of both prokaryotes and eukaryotes (such
as a cell wall). Three divisions exist within this kingdom: Zygomycota,
Ascomycota and Basidiomycota. Fungi, like plants, are separated into divisions
not phyla.

Note: If something contains “mycota” in its division then it’s a fungus

 Note: All cells of Zygomycota are haploid, except for the zygospore
and don’t have cell walls except in their sexual structures

Note: Oomycota, which are slime molds and water molds, are not true
fungus but are part of the Protista kingdom.

All fungi are eukaryotic heterotrophs that obtain their food by absorption rather
than by ingestion: they secrete their digestive enzymes outside their bodies and
then absorb the products of digestion. Although most fungi are considered
saprophytic (live off dead matter), many fungi do not distinguish between living
and dead matter, and thus can be potential pathogens.

- Fungi are larger than bacteria.

Characteristics of Fungi:

1) With the exception of yeasts, fungi are multicellular.

- Yeasts are unicellular fungi

2) Most fungi possess cell walls, called septa, made up of the

polysaccharide, chitin.
a) Chitin is more resistant to microbial attack than is cellulose!!!
Note: Arthopods’s (insects and crustaceans) exoskeleton is
made up of chitin as well

3) Septa is usually perforated to allow exchange of cytoplasm between

cells, called cytoplasmic streaming.
a) This allows for rapid growth

4) A fungal cell can contain multiple nuclei!!!

a) The nuclei, in a single cell, may or may not be identical

5) Fungi lack centrioles (as well as prokaryotes), mitosis takes place

entirely within the nucleus, and their nuclear membranes don’t
disappear during mitosis!!

6) In the growth state, fungi consist of a tangle mass (called mycelium) of

multiply branched thread-like structures called hyphae (haploid).

Fungal Reproduction and Life Cycle

Like most organisms, fungi alternate between haploid and diploid stages in their
life cycle; however, the haploid stage predominates, and is their growth stage.
Hyphae are haploid and some hyphae may form reproductive structures called
sporangiophores. By far the most important type of asexual reproduction is that
of spore formation. Asexual reproduction is extremely important to fungi. It is
responsible for the production of large numbers of spores throughout the year

Note: These structures release haploid spores that give rise to new
mycelia in asexual reproduction!!!

Note: Spore formation is NOT always via asexual reproduction!!!

Note: Haploid spores can form and spread faster and more efficiently
than diploid zygotes because they don’t undergo meiosis!!!

Yeasts rarely reproduce sexually by producing spores!!! More often in yeasts,

asexual reproduction occurs via budding. (also called cell fission), in which a
smaller cell pinches off from the single parent cell.

When sexual reproduction occurs it is between hyphae from two mycelia of

different mating types + and -. These two hyphae (haploid) grow towards one
another eventually touching and forming a conjugation bridge, and becomes a
gamete producing cell, called a gametangium. In Zygomycota, the gametangia
remain attached to the parent hyphae and the nuclei fuse with one another to
produce a diploid zygote, called a zygospore. After its formed it usually goes
dormant, but when it is activated, the zygospore undergoes meiosis to produce
haploid cells, one of which immediately grows a short sporangiophore to asexually
reproduce many spores.

Recall: sporangiophores release haploid spores that give rise to new

mycelia in asexual reproduction
 Note: Except for the zygospore all cell in Zygomycota are haploid, so
they undergo mitosis.

The important thing to understand about fungal reproduction is that asexual

reproduction (Ex. Budding or mitosis) normally occur when conditions are
good; Sexual reproduction (meiosis) occur when conditions are tough!!

Haploid state  asexual reproduction (mitsosis/budding (cell fission))

 conditions are good

Diploid state (zygospore)  sexual reproduction (meiosis)  conditions

are bad

Recall: Homologous chromosomes are chromosomes in a biological cell

that pair (synapse) during meiosis. The pair are non-identical
chromosomes that both contain information for the
same biological features and contain the same genes at the same
loci but possibly each have different alleles (that is, different
genetic information) at those genes.

- Any cell that contains homologous chromosomes are called diploid

- Any cell that doesn’t contain homologous chromosomes are called
haploid
Lichens are composite organisms consisting of a symbiotic association of a
fungus with a photosynthetic partner usually either a green alga or cyanobacterium

Note: The mixture of organisms regularly found at any anatomical site is

referred to as the normal flora.