1.

1: Cell Theory
- Before microscope, organisms were thought of as complete and inseparable into smaller
parts
- Inability to see smaller structures w/o optical instruments like the microscope
- Robert Hooke → microscope → looked at cork
- Honeycomb structure → called the spaces ‘cells’
- Nonliving so no nuclei, organelles, or cell membrane
- Anton van Leeuwenhoek → first to view living cell under microscope
- Researchers noted that cells
- could be separated
- Each cell was a distinct structure
- Tissues were made of cells and the function of tissue was dependent upon the
function of the cells from which it was formed
- Rudolph Virchow → diseased cells could arise from normal cells in normal tissue
- Cell theory
- All living things are composed of cells
- The cell is the basic functional unit of life
- Cells arise only from preexisting cells
- Cells carry genetic information in the form of deoxyribonucleic acid (DNA)
- This genetic material is passed from parent to daughter cell
- Viruses violate the cell theory so they are not living
- Contain genetic material but cannot produce on their own
- violates 3rd tenet bc virions can only replicate by invading other
organisms
- Violated 4th tenet bc they may contain ribonucleic acid (RNA)

1.2: Eukaryotic Cells

- Living organisms can be composed of eukaryotic or prokaryotic cells
- Eukaryotic cells can be unicellular or multicellular
- Eukaryotic cells contain a true nucleus contained in a membrane
- Prokaryotic cells do not contain a nucleus
- Eukaryotic cells also contain organelles in their cytoplasm
- Membrane bound organelles
- Each cell has cell membrane enclosing semifluid cytosol in which organelles are
suspended
- In eukaryotic cells, most organelles are membrane bound → allows
compartmentalization of functions
- Membranes of eukaryotic cells consists of a phospholipid bilayer
 - Hydrophilic surfaces that electrostatically interacts with the aqueous
environments inside and outside of the cell
- Hydrophobic inner portion which provides a highly selective barrier
between the interior of the cell and the external environment

- Cytosol allows for diffusion of molecules throughout the cell

- Within the nucleus, genetic material is encoded in DNA which is organized into
chromosomes
- Eukaryotic cells reproduce by mitosis → formation of identical daughter cells
- Nucleus
- Control center of the cell
- Contains all of the genetic material necessary for replication of the cell
- Surrounded by the nuclear membrane (envelope)
- Double membrane that maintains a nuclear environment separate and
distinct from the cytoplasm
- Nuclear pores in the membrane allow selective two-way exchange of material
between the cytoplasm and the nucleus
- DNA contains genes (sections of nucleotides)
- Linear DNA is wound around organizing proteins called histone and then further
wound into chromosomes
- DNA in the nucleus → compartmentalization of DNA transcription (DNA →
RNA)
- Keeps transcription separate from RNA translation (RNA → protein)
- Nucleolus (subsection of the nucleus)
- Ribosomal rRNA is synthesized in this region
- 25% of the nucleus
- Dark spot of the nucleus
- Mitochondria
- Power house of the cell bc of its important metabolic functions
- Two layers
- Outer membrane
- Barrier between cytosol and inner environment of the mitochondria
- Inner membrane
 - Consists of many foldings called cristae
- Highly folded structures that increases SA so that more
electron transport enzymes can be there
- Contains molecules and enzymes needed for electron transport
chain
- Intermembrane space: Space between the outer and inner membrane
- Matrix: space inside the inner membrane
- Protons are pumped from the matrix to the intermembrane space then through
ATP synthase to generate ATP during oxidative phosphorylation
- Semi Autonomous
- Contain some of their own genes and replicate independently of the
nucleus via binary fission
- Cytoplasmic (extranuclear) inheritance: transmission of genetic
material independent of the nucleus
- Endosymbiosis theory
- Thought to have evolved from an anaerobic prokaryote engulfing an
aerobic prokaryote and establishing a symbiotic relationship
- Capable of killing the cell by the release of enzymes from the ETC
- Kick-starts apoptosis (programmed cell death)
- Lysosomes
- Membrane bound structures
- Contains hydrolytic enzymes that are capable of breaking down many different
substrates
- Can function in conjugation with endosomes
- transport, package, and sort cell material travelling to and from the cell
membrane
- Capable of transporting material to the trans golgi, cell membrane, or
lysosomal pathway for degradation
- Lysosomal membrane sequesters these enzymes to prevent damage to the cell
- Release of enzymes can occur in process called autolysis → apoptosis
- Released enzymes directly lead to degradation of cell components
- Endoplasmic Reticulum (ER)
- Series of interconnected membranes that are contiguous (share a border) with the
nuclear envelope
- Double membrane folded into numerous invaginations → complex structures
with a central lumen
- Rough ER
- Studded with ribosomes
- permit translation of proteins destined for secretion directly into its
lumen
 - Smooth ER
- Lacks ribosomes
- Lipid synthesis
- Detoxification of certain drugs and poisons
- Transports proteins from RER to the Golgi apparatus
- Golgi Apparatus
- Stacks of membrane-bound sacs
- Material from the ER are transferred to the Golgi in vesicles
- Modifies cellular proteins by
- adding different groups (i.e. carbohydrates, phosphates, etc)
- Adds signal sequences
- Directs the proteins to a specific location
- Cellular products are repackaged into vesicles after being modified and
transferred to their correct location
- Secretion → vesicle to cell membrane → merge with the membrane →
contents released via exocytosis
- Peroxisomes
- Contain hydrogen peroxide
- Breakdown very-long-chain fatty acids via beta-oxidation
- Participate in the synthesis of phospholipids
- Contains some enzymes involved in the pentose phosphate pathway
- Cytoskeleton
- Provides structure to the cell and helps its maintain shape
- Provides tracks for transportation of material around the cell
- Three components of the cytoskeleton
- Microfilaments
- Made of actin
- Actin filaments are organized into bundles and networks and are
resistant to compression and fracture
- Actin filaments use ATP to generate force for movement by
interacting with myosin
- Role in cytokinesis (division of material between daughter cells)
- During mitosis, a cleavage furrow is formed from
microfilaments which organize as a ring at the site of
division between the two new daughter cells
- Actin filaments in the ring contract → ring becomes
smaller → pinching off the connection between the two
daughter cells
- Microtubules
- Made of tubulin proteins
 - Radiate throughout the cell → primary pathway along which
motor proteins like kinesin and dynein carry vesicles
- Cilia and flagella are motile structures composed of microtubules
- Cilia are projections from the cell that are involved in
movement of material along the surface of the cell
- Flagella are structures involved in movement of the cell
itself
- Cilia and flagella have the same structure (9+2 structure)
- Nine doublets of microtubules forming the outer ring
- two microtubules in the center
- 9+2 structure is only seen in eukaryotic organelles of motility
- Bacterial flagella have different structure with different
chemical composition
- Centrioles are found in the centrosome (region of the cell)
- Organizing centers for microtubules
- Structured as nine triplets of microtubules with a hollow
center
- During mitosis, centrioles migrate to opposite poles of
dividing cell and organize mitotic spindle (microtubules)
- Microtubules coming from the centriole attach to the
chromosome via kinetochores and exert force on the
sister chromatid → pulling them apart
- Intermediate filaments
- Diverse group of filamentous proteins
- ex: keratin, desmin, vimentin, and lamins
- Involved in cell-cell adhesion or maintenance of overall integrity
of cytoskeleton
- Able to withstand large amount of tension → cell structure rigid
- Help anchor other organelles
- Identity of intermediate filament proteins within a cell is specific to
the cell and tissue type
- Tissue Formation
- Eukaryotic cells can come together and form tissue with division of labor
- Different cells in a tissue may carry out different functions
- Four types of tissue
- Muscle tissue
- Nervous tissue
- Epithelial tissue
- Covers the body and lines the cavities
 - Provides protection against pathogen invasions and desiccation
- Involved in absorption, secretion, and sensation
- Tightly joined by to each other and to an underlying layer of
connective tissue (basement membrane)
- Epithelial cells are highly diverse and have different functions
depending on the organ they are in
- Epithelial cells are polarized
- One side faces a lumen or the outside world while the other
side interacts with underlying blood vessels and structural
cells
- Epithelia can be classified according to number of layers and shape
of their cells
- Simple: one layer
- Stratified : multiple layers
- Psuedostratified: appear to have multiple layers due to
differences in cell height but are really just one layer
- Cuboidal: cube-shapes
- Columnar: long and thin
- Squamous: flat and scalelike
- Connective tissue
- Supports the body
- provides a framework for the epithelial cells to carry out their
functions
- Main contributors to the stroma (support structure) of the organ
- Examples: bone, cartilage, tendons, ligaments, adipose tissue, and
blood
- Most cells in connective tissue produce and secrete materials
like collagen and elastin → formation of the extracellular matrix

1.3: Classification and Structure of Prokaryotic Cells

- Prokaryotes are the simplest of all organisms and include all bacteria
- Prokaryotes
- Do not contain membrane-bound organelles
- Genetic material is organized into a single circular molecule of DNA concentrated
in the nucleoid region (area of the cell)
- Simple but diverse
- Can cause infection in humans
- Prokaryotic domains
- Three domains into which all life is classified: archaea, bacteria, and eukarya
- Archaea and bacteria contain prokaryotes
 - Used to be one kingdom (Monera) until modern genetics and biochemical
techniques indicated the significant difference in evolutionary pathways
- Archaea
- Single-celled organisms
- Look like bacteria
- contain genes and metabolic pathways that are more similar to eukaryotes
than bacteria
- Extremophiles
- Found in harsh environments
- High temps, high salinity, or no light
- Can be found in a variety of environments (i.e. the human body)
- Can use alternative sources of energy
- Photosynthetic or chemosynthetic (generate energy from inorganic
compounds)
- Similarities to the eukaryotes → possible common origin
- Start translation with Met
- Contain similar RNA polymerases
- Associate DNA with histones
- Differences
- Single circular DNA
- Divide by binary fission
- Share similar structure to bacteria
- Resistant to many antibiotics
- Bacteria
- Contain cell membrane and cytoplasm
- Have flagella or fimbriae (similar to cilia)
- Bacteria and eukaryotes can share analogous structures → hard to
develop meds that only affect bacteria
- Even similar structures can have enough biochemical differences
to allow targeting of one organism over the other
- Outnumber human cells in the body
- Different relationships between bacteria and humans
- Mutualistic symbiotes
- Both human and bacteria benefit from the relationship
- Pathogens or parasites
- Provide no advantage or benefit to the host but rather cause
disease
- Can live intracellularly or extracellularly
- Classification of Bacteria By Shape
- Cocci: spherical bacteria
 - Bacilli: rod-shaped bacteria
- Spirilla: spiral-shaped bacteria

- Aerobes and Anaerobes

- Obligate aerobes: bacteria that require oxygen for metabolism
- Anaerobes: bacteria that use some other form of cellular metabolism that does not
require oxygen
- Obligate anaerobes: cannot survive in an oxygen-containing environment
- Presence of oxygen → production of reactive oxygen-containing
radicals → cell death
- Facultative anaerobes: bacteria that can use oxygen for metabolism when
present and switch to anaerobic metabolism if oxygen is not present
- Aerotolerant anaerobes: unable to use oxygen for metabolism but are not
harmed by its presence
- Prokaryotic cell structure

- Prokaryotes lack a nucleus and membrane-bound organelles

- Prokaryotes are single-celled organisms, so each cell must perform all of the
function needed for life
- Prokaryotes can live in colonies with other cells and may signal these cells to
share info about the environment
- Cell wall
- Single-cell so each bacterium is responsible for protecting itself from the
environment
- Cell wall forms the outer barrier of the cell
- The cell membrane (plasma membrane) is the next layer
- Composed of phospholipids
- Cell wall + cell membrane = envelope
- Provides structure
 - Controls movement of solutes into and out of the bacterium
- Allows the cell to maintain concentration gradients relative to the
environment
- May protect pathogen from the human immune system
- Types of cell walls in bacteria
- Gram + cell wall
- Thick layer of peptidoglycan (polymeric substance made of
amino acids and sugars)
- Lipoteichoic acid (unknown function, but may activate
human immune system)
- Absorbs crystal violet stain and appears dark purple
- Gram - cell wall
- Very thin
- Small amount of peptidoglycan
- Adjacent to cell membrane and separated from membrane
by the periplasmic space
- Outer membranes containing phospholipids and
lipopolysaccharides (triggers large immune response in
humans)
- Absorbs safranin counterstain and appears pink-red

- Flagella
- Long, whiplike structures that can be used to propel the entire cell
- Bacteria can have one, two, or many (depends on species)
- Important for chemotaxis (ability to detect chemical stimuli and move
toward or away from it)
- Bacteria can sense food and move toward it or toxins and move
away from it
- Composed of filament, basal body, and a hook
- Filament
- Hollow, helical structure composed of flagellin
- Basal body
 - complex structure that anchors the flagellum to the
cytoplasmic membrane
- Motor of the flagellum
- Hook
- Connects the filament and the basal body so that the basal
body rotates and exerts torque on the filament
- Structure is similar in both types of cell walls, but slightly differences due
to chemical composition differences of the cell walls
- NOTE: Archaea contain flagella but they are different from bacteria
flagella

- Other organelles
- Prokaryotes concentrate DNA in nucleoid region but do not contain a
nuclear envelope
- Prokaryotic DNA is carried on circular chromosome which can be found
coiled around histone-like proteins in some bacteria
- True histones in archaea
- DNA acquired from external sources may be carried on smaller circular
structures (plasmids)
- Carry DNA that is not necessary for survival of the prokaryote (not
part of the genome of bacterium) but may give some advantage
- Prokaryotes lack mitochondria
- Cell membrane is used for ETC and generation of ATP in prokaryotes
- Prokaryotes contain primitive cytoskeleton compared to eukaryotes
- Contains ribosomes (different size from eukaryotes)
- Important for drug development bc bacterial (prokaryotic)
ribosomes can be specifically targeted

1.4: Genetics and Growth of Prokaryotic Cells

- Prokaryotes reproduce via asexual reproduction in a form of binary fission
- Prokaryotes are capable of acquiring genetic material from outside the cell and using that
genetic material (plasmids)
- Binary fission
 - Simple form of asexual reproduction seen in prokaryotes
- Circular chromosomes attaches to the cell wall and replicates while the cell
continues to grow in size
- Eventually, the plasma membrane and cell wall begin to grow inward along
the midline of the cell → produce two identical daughter cells
- Process requires fewer events than mitosis → proceeds more rapidly

- Genetic recombination
- Single circular chromosome contains the info that is needed for the cell to survive
and reproduce
- Some bacteria contain plasmid (circular structure that carries extracellular genetic
material)
- Plasmids can
- carry genes that impart some benefit to the bacteria
- Increase virulence factors (things that increase how pathogenic a
bacterium is)
- Episomes (subset of plasmids) are capable of integrating into the genome of the
bacterium
- Bacterial genetic recombination helps increase bacterial diversity and this permits
evolution of bacterial species
- Recombination processes in bacteria
- Transformation
- Integration of foreign genetic material into the host genome
- Foreign material usually comes from some other bacteria that
spilled its contents close to the bacteria capable of transformation
- Many gram - neg rods are able to do this
- Conjugation
- Bacterial form of mating
- Two cells forming a conjugation bridge between them that allows
the transfer of genetic material
- Transfer is unidirectional
- Donor male (+) to the recipient (-)
 - Bridge is made from appendages called sex pili that are found on
the donor male
- To form the pilus, bacteria must contain sex factors (plasmids that
contain the necessary genes)
- i.e. F (fertility) factor in E. coli
- + means they have the sex factor while - means they do not
have the sex factor
- During conjugation between an + and - cell, the + replicates its
sex factor and donates the copy to the - → now there are two +
cells
- Enables both cells to transfer stuff
- Allows for rapid acquisition of different genetic material
- The sex factor is a plasmid but it can become integrated into the
host genome through transformation
- When conjugation occurs, the donor copy its hold genome
and try to transfer it
- Bridge usually breaks before fll DNA is transferred
- Cells that have the sex factor in their genome are indicated by Hfr
(high frequency of recombination)

- Transduction
- Requires a vector (virus that carries genetic material from one
bacterium to another)
- Viruses are obligate intracellular pathogens
- Cannot reproduce outside of a host cell
- Bacteriophages (viruses that infect bacteria) can trap segment of
host (bacteria) DNA during assembly
- When the bacteriophage infects another bacterium, it can release
the trapped DNA into the new host cell
- Transferred DNA can then integrate into the genome →
additional genes in new host
 - Transposons
- Genetic elements capable of inserting and removing themselves
from the genome
- Can occur in prokaryotes and eukaryotes
- If inserted within a coding region of a gene, the gene may be
disrupted
- Growth
- Bacteria reproduce via binary fission
- Implies that all bacteria are the same in a local colony (Assuming no mutations or
recombinations ) and no bactering will be dividing faster than the others
- Bacteria can grow in a series of phases
- In a new environment,
- Bacteria must adapt to new local conditions (lag phase)
- As the bacteria adapt, growth increases → exponential growth
(exponential phase or log phase)
- As number grow, resources become reduced → slowed reproduction →
stationary phase
- Bacteria exceed the ability of the environment to support the number of
bacteria, the death phase occurs (resources in the environment have been
depleted)

1.5: Viruses and Subviral Particles

- Viruses
- nonliving because they are acellular
- Lack organelles
- Viral structure
 - Composed of
- Genetic material
- DNA or RNA
- Circular or linear
- Single or double stranded
- Protein coat (capsid)
- Envelope containing lipids (sometimes)
- Surrounds the capsid
- Composed of phospholipids and virus specific proteins
- Sensitive to heat, detergents, and desiccation
- Viruses with envelope are easier to kill for this reason
- Viruses without envelope are more resistant to sterilization
and are likely to persist on surfaces for extended time
periods
- Cannot reproduce independently → obligate intracellular parasites
- Must express and replicate genetic info within a host cell bc they lack
ribosomes to carry out protein synthesis
- Use the host cell’s machinery to reproduce
- After taking over host cells machinery, the virus will replicate and produce
viral progeny (virions) → can be released to infect additional cells
- Bacteriophages (viruses that specifically target bacteria)
- Do not actually enter the bacteria
- Inject genetic material leaving the remaining structures outside the
infected cell
- Two additional structures
- Tail sheath: injects material into a bacterium
- Tail fibers: recognition and connection to correct host cell

- Viral Genomes
- Variety of shapes and sizes with different numbers of genes
- Viral genomes may be made of either DNA or RNA
- Can be single-stranded or double-stranded
- Single-stranded RNA viruses may be positive or negative sense
 - Positive sense: genome may be directly translated to functional protein by
the ribosome of the host cell just like mRNA
- Negative sense: virus requires synthesis of RNA strand complementary to
the negative sense RNA strand which can then be used as a template for
protein synthesis
- Must carry a RNA replicase in the virion to ensure that the
complementary strand is synthesized
- Retroviruses
- Enveloped, single-stranded RNA viruses
- Virions contains two identical RNA molecules
- Carry reverse transcriptase
- Synthesizes DNA from single-stranded RNA
- DNA synthesized from reverse transcriptase can then be integrated into
the host cell’s genome where it will replicate and transcribe as if it were
the host’s DNA
- Cell is permanently infected since the DNA is integrated
- Only way to cure is by killing the infected cell itself
- Viral life cycle
- Infection
- Viruses can only infect a specific set of cells
- Virus has to bind to specific receptors on the host cell
- Without the receptors, the cell is invisible to the virus
- Once bound, additional interactions occur between the virus and the host
cell
- Enveloped viruses fuse with the plasma membrane → entry of the
virion into the host cell
- Host cell can mistake the virus as nutrient or some other beneficial
substance and bring the virus in via endocytosis
- Bacteriophages use tail fibers to anchor to the cell membrane and then
inject their viral genome into the host bacterium using the tail sheath
- Some tail fibers have enzymatic activity → allows penetration of
cell wall and formation of pores in the cell membrane
- Different portions of the virion will be inserted into the host cell (depends
on the virus)
- Envolvoped cells fuse with the membrane and enter the cell intact while
bacteriophages insert genetic material into the cell and leaves capsids
outside the host cell
- Translation and progeny assembly
- Translation of viral genetic material must occur in order for the virus to
reproduce
 - Requires translocation of the genetic material to the correct location in the
cell
- Most DNA viruses go to the nucleus to be transcribed into mRNA →
mRNA to cytoplasm for translation to proteins
- Genetic material from positive sense RNA viruses stays in the cytoplasm
for direct translation into protein
- Negative sense RNA viruses’ genetic material needs to synthesize
complementary RNA strand via RNA replicase which can then be
translated into protein
- DNA formed through reverse transcriptase in retroviruses travels to the
nucleus where it will be integrated into the host genome
- Viral RNA is translated to protein using host cell’s ribosomes, tRNA,
AAs, and enzymes
- Many of the proteins produced are structural capsids and allow for the
creation of new virions in the cytoplasm in the host cell
- Once viral genome is replicated, it can be packaged within the capsid
- Viral genome must be returned to original form before packaging
- Single virus many virions within a single host cell
- Progeny release
- Different ways to release
- Viral invasion may initiate cell death → soulling of viral
progeny
- Disadvantage for the virus bc it can no longer use the cell’s
machinery to carry out its life cycle
- Host cell may lyse due to large number of virions
- Disadvantage for the virus bc it can no longer use the cell’s
machinery to carry out its life cycle
- Virus can leave by fusing with the plasma membrane (extrusion)
- Keeps the host cell alive → continued use of the host by
the virus
- Virus is said to be in productive cycle when it is
continually using a host cell
- Lytic and Lysogenic cycles
- Bacteriophage can enter a lytic or lysogenic cycle depending on growth
conditions and virus
- Lytic cycle (virulent)
- Maximal use of the cell’s machinery
- Little regard for the survival of the host cell
 - Host cell swells with virions → cell lyses → other bacteria can be
infected
- Lysogenic cycle
- If the virus does not lyse the host cell, it may integrate into the host
genome as a provirus or prophase
- Virus will be replicated as the bacterium reproduces since it is apart of the
host’s genome
- Environmental factors can cause the provirus to leave the genome and
revert back to lytic cycle
- Trapping of bacterial genome can occur when the provirus is leaving
the host bacterium → transduction of genes from one bacteria to
another
- Infection with one strain of phage makes bacteria less susceptible to
superinfection (simultaneous infection)
- Provirus is innocuous there may be some evolutionary advantage to this
association

- Prions and Viroids

- Prions
- Infectious proteins
- Nonliving
- Triggers misfolding in other proteins
- alpha-helical structures to beta sheets
- Reduces solubility of protein and ability of cell to degrade the misfolded
protein
- Proteins starts to aggregate → reduced function of cell
- Viroids
- Small pathogens consisting of short circular single-stranded RNA that
infect plants
- Bind to large number of RNA sequences and will silence genes in the
plant genome
- Prevents synthesis of necessary proteins and cause metabolic/structural
derangements in the plant cell
- Usually plant pathogens, but humans viroids exist