Content Category 2B: The structure, growth, physiology, and genetics of prokaryotes and viruses

Cell theory (BIO)

• History and development

o Robert Hooke observed under a microscope what appeared to be cells.
o German botanist Matthias Schleiden looked at all sorts of plants under a
microscope and noticed all had the same microscopic structure.
o German scientists Theodor Schwann looked all nervous systems of different
animals and noticed all had similar structures that were these cells.
o German physician and pathologist, Rudolph Virchow observed bacteria that
divided and formed two bacteria that were identical = binary fission.
o French scientist Louis Pasteur did a famous experiment known as the Swan-Neck
Bottle experiment proved that all cells come from preexisting cells.
• Impact on biology
o Proved that cells were the basic structural, functional, and biological unit of life
and cells come from preexisting cells.

Classification and Structure of Prokaryotic Cells (BIO)

Remember plants and animals are eukarytoic!

• Prokaryotic domains
o Archaea
§ Single-celled organisms that are visually similar to bacteria but contain
genes and several metabolic pathways that are more similar to eukaryotes
than bacteria.
§ Considered extremophiles in that they were most commonly isolated from
harsh environments with extremely high temperatures, high salinity, or no
light.
§ While some are photosynthetic, many are chemosynthetic and able to
generate energy from inorganic compounds, including sulfur- and
nitrogen-based compounds, such as ammonia
§ Due to similarities to eukaryotes, it is hypothesized that eukaryotes and
domain Archaea share a common origin. Both start translation with
methionine, contain similar RNA polymerases, and associate their DNA
with histones. However, Archaea contain a single circular chromosome,
divide by binary fission or budding, and overall share a similar structure to
bacteria. Interestingly, Archaea are resistant to many antibiotics.
o Bacteria
§ All bacteria contain a cell membrane and cytoplasm, and some have
flagella or fimbriae (similar to cilia). Because bacteria and eukaryotes
often share analogous structures, it can be difficult to develop medicines
that target only bacteria.
 § Bacterial flagella and eukaryotic flagella are distinct enough that scientists
are able to develop antibacterial vaccines that specifically target bacterial
flagella. Also, many antibiotics target the bacterial ribosome, which is
significantly smaller than the eukaryotic ribosome.
• Major classifications of bacteria by shape
o Bacilli (rod-shaped)
o Spirilli (spiral-shaped)
o Cocci (spherical)

• Lack of nuclear membrane and mitotic apparatus

o Bacteria do not have a membrane-enclosed nucleus. Their genetic material is
located in an irregular region called the nucleoid. Bacteria do not have spindles
and asters that make up the eukaryotic mitotic apparatus. Instead, the prokaryotic
cytoskeleton helps pull the replicated DNA apart.
• Lack of typical eukaryotic organelles
o Bacteria don’t have Golgi, ER, mitochondria, chloroplasts
• Presence of cell wall in bacteria
o Bacterial cell wall is made of peptidoglycan, a polysaccharide-protein molecule.
In contrast, plant cell wall is made of cellulose and fungi cell wall is made of
chitin.

• Flagellar propulsion, mechanism

o Bacterial flagella is made of flagellin. In contrast, eukaryotic flagella is made of
microtubules.
o The mechanism of the bacterial flagella is rotation. A rotor at the base of the
flagella drives the rotation, powered by a proton or sodium gradient. (Compare
this to eukaryotic flagella, which is powered directly by ATP)
Growth and Physiology of Prokaryotic Cells (BIO)

• Reproduction by fission
o DNA replicates
o Replicated DNAs separate by attached to the cell membrane as the cell elongates
(in contrast to mitosis, no spindle fibers needed)
o Cytokinesis divides the parent cell into two daughter cells

• High degree of genetic adaptability, acquisition of antibiotic resistance

o Mutation
o Transformation: bacteria take in plasmids and DNA fragments and integrates
them into the genome
o Transduction: bacteriophages undergoing lysogenic life cycle incorporate the
viral DNA into the bacterial genome
o Conjugation: bacteria transfer DNA between one another through the sex pilus
 In bacteria, reproduction can be very fast, with a generation
taking little more than a few minutes for some species. This short
generation time, together with random mutations and
the mechanisms of genetic recombination, allow bacteria (and
other prokaryotes) to evolve very quickly. These enable them to
respond to environmental changes (such as the introduction of
an antibiotic) very rapidly and consequently become resistant.
• Exponential growth
o Bacterial growth starts off being exponential because of the nature of binary
fission. Later, when food becomes short, and it gets crowded, growth slows and
eventually plateaus
Binary fission occurs rapidly, and as a result, bacteria tend to grow
exponentially. This growth, however, doesn’t come until after the bacteria
adapt to a new environment during a period known as the lag phase.
While the bacteria are growing during the log phase, there are only a
certain number of resources, which eventually causes the number of
bacteria to level off in a period known as the stationary phase. The last
stage of the cycle is the death phase, which is caused because there are no
more resources left in the environment. This growth cycle shows the rise
 and fall in number of bacteria over time. Bacterial growth is an example of
a positive feedback loop, where more bacteria formation causes even more
bacteria to spawn until the resources run out and the growth stops.
• Existence of anaerobic and aerobic variants
o Obligate aerobe = must have oxygen for growth
o Obligate anaerobe = dies when oxygen is present
o Facultative anaerobe = doesn’t need oxygen for growth, but grows better with
oxygen
• Parasitic and symbiotic
o Parasitic = bacteria benefits at the expense of the host. Disease causing bacteria
are examples of parasitic relationships.
o Mutualistic = both bacteria and host benefits. For example, the E. coli in your
gut; the natural flora on your skin
o Commensalistic = one benefits while the other has no effect
• Chemotaxis
o Movement in a direction corresponding to a gradient of increasing or decreasing
concentration of a particular substance/chemical

Genetics of Prokaryotic Cells (BIO)

• Existence of plasmids, extragenomic DNA

o Plasmids are double stranded DNA
o A plasmid can exist and replicate independently of the genomic DNA, or be
integrated into it
o Plasmids are inherited
o Plasmids are not essential for growth and reproduction in the wild
• Transformation: incorporation into bacterial genome of DNA fragments from external
medium
o When a bacterium dies, it lyses and spills many DNA fragments into the
environment
o Another bacteria encounters these DNA fragments, takes them in, and integrates
them into its own genome
o If the DNA fragments contained an a ntibiotic resistant gene, then the
transformation just made the bacteria antibiotic resistant
• Conjugation
o Transfers genetic material between bacteria via a pillus
o A bacterium able to make the pillus (F+) has a plasmid that contains the pillus
genes
o F+ bacteria can transfer the plasmid to an F-bacteria
o Conjugation can also transfer some genomic DNA (because F+ plasmid can
integrate into the chromosome)

• Transposons (also present in eukaryotic cells)

o They are a heterogeneous class of genetic elements that can insert at new
locations on chromosomes. Classified into three major groups:
§ Class I, retrotransposons; Class II, DNA transposons; Class III, miniature
inverted-repeat transposable elements
 § Class I retrotransposon translocate via copy-and-paste mechanism, class II
DNA transposons translocate via cut-and-paste mechanism, while the
mechanism for MITEs are unknown. Transposons cause chromosomal
mutations such as deletion, insertion and inversion. They are also used as
tools for gene delivery and targeted gene mutation.

o Transposons have direct repeat flanking sequences that are not part of the
transposons, and terminal inverted repeats that are part of the transposons. DNA
transposons translocate via a cut-and-paste mechanism, retrotransposons
translocate via a copy-and-paste mechanism.
o Transposons cause significant changes in genome organization and gene
sequence. They can give insertion/deletion mutant and chromosomal inversion
mutant. They are used as tools in gene delivery or targeted mutation.

Virus Structure (BIO)

• General structural characteristics (nucleic acid and protein, enveloped and
non-enveloped)
o Nucleic acid can be DNA or RNA, single stranded or double stranded
o Protein coat covers the nucleic acid
o Some viruses have an envelope derived from the host’s cell membrane, while
others lack it (non-enveloped)
§ Enveloped viruses bud off the host’s membrane
§ Non-enveloped viruses cause the host to burst to release viral particles
o Smaller than bacteria
• Lack organelles and nucleus
o Viruses don’t have any organelles or a nucleus. The genetic material is simply
packed inside a protein coat.
• Structural aspects of typical bacteriophage
o Head stores genetic material
o Sheath provides a passageway for genetic material to be injected into the host
bacteria
o Tail fibers attach to the host bacteria
• Genomic content - RNA or DNA
o Viruses can contain either RNA or DNA as their genomic content
o Out of the RNA viruses, those that convert their genome into DNA inside their
host are called retroviruses
• Size relative to bacteria and eukaryotic cells
o Viruses are roughly 100 times smaller than bacteria, and 1000 times smaller than
eukaryotic cells
Viral Life Cycle (BIO)

• Self-replicating biological units that must reproduce within specific host cell
o Viruses cannot replicate by themselves. They depend on the host’s replication
organelles to replicate. The host’s ribosomes will make the necessary protein
coats and polymerases that replicate the viral genetic material. Retroviruses
contain their own reverse polymerase to convert RNA to DNA before the host’s
polymerases take over
o
Lytic Cycle
5 stages (Attachment, Penetration, Biosynthesis, Maturation, Lysis)
During Penetration, the viral DNA enters the host cell and then kills the
host

Lysogenic Cycle
Contains Attachment and Penetration BUT...
Instead of killing the host, the phage genome integrates into the bacterial
chromosome and becomes part of the host.
The cell divides and prophage DNA is passed on to daughter cells
Under stressful conditions the prophage is excised from the bacterial
chromosome and enters the lytic cycle
Biosynthesis, Maturation, and Lysis then occurs like the lytic cycle
• Generalized phage and animal virus life cycles
o Attachment to host, penetration of cell membrane or cell wall, and entry of viral
genetic material
o Use of host synthetic mechanism to replicate viral components
§ Host’s ribosomes synthesize the necessary enzymes. Host’s ATP provides
necessary energy. The host also provides the raw materials such as
nucleotides and amino acids.
o Self-assembly and release of new viral particles
§ The coat proteins and viral genetic material will assemble into viral
particles by themselves
• Transduction: transfer of genetic material by viruses

• In the image above it can be seen that in step 1, the bacteriophage

infects the bacterial cell with viral genetic material. This causes the
bacterial cell in step 2 and 3 to reproduce the viral protein and genetic
material to make viral copies. However, when these new
 bacteriophages are made, some of them contain DNA from the host
bacterial cell. In step 4 the bacteriophage contains DNA from a
bacterial source and in step 5 and 6 when it infects a bacterial cell this
extra bacterial genetic material is incorporated into the host cells DNA,
transferring genetic material from one bacterial cell to another.

o 1. Virus infects cell: host DNA degraded into fragments, viral DNA takes over
control
o 2. Host DNA fragment gets packed into virus progeny by accident
o 3. Virus progeny infects another cell, injects previous host’s DNA fragment
o 4. Fragment enters cell, finds its homologous counterpart, and crossover
• Retrovirus life cycle: integration into host DNA, reverse transcriptase, HIV
o 1. Retrovirus enters the host
o 2. Viral reverse transcriptase converts viral RNA genome into double-stranded
DNA
o 3. Virally encoded enzyme, called integrase, adds in viral DNA into the host’s
genome at a random place
o 4. When the host replicates, the viral DNA gets replicated also
o The viral DNA will then be expressed with the original DNA into mRNA then
proteins (this mRNA is the same sequence as the viruses RNA genome)

• Prions and viroids: subviral particles

o Viroids are smaller than viruses because they’re only made of a single strand of
circular RNA. Before, they were only found to infect plants. Today, they have
been found in humans, in the case of Hepatitis D.
 § It’s thought to be catalytic RNA, meaning it can make or break covalent
bonds. It can self-cleave to create more viroids. Don’t confuse with virions
which are whole viruses.
o Prions have no genetic material, no DNA or RNA. They are only made of
proteins. A prion protein tends to be in a beta-sheet conformation (normal protein
generally in shape of an alpha helix). It’s thought that because prion protein and
normal protein made of same amino acids, they are the same protein but in a
different shape. When the beta-sheet comes in contact with the alpha-helix, it will
change the α-helix to a β-sheet. As more and more become β-sheets, this creates
protein deposits. This happens somewhere in the brain, normal cleanup still
happens. This leaves huge holes in your brain as the proteins are removed,
causing disease.