Ch. 1: The Cell Flashcards
what was Robert Hooke’s first vision of the structure of a cell?
looked at cork under a microscope
honeycomb-like
the spaces are like small rooms of a monastery (known as cells)
no nuclei, organelles, or cell membranes
what are the three basic tenets of the original form of cell theory?
- all living things are composed of cells
- the cell is the basic functional unit of life
- cells arise only from preexisting cells
what is the fourth tenet of cell that was added in modern times?
- cells carry genetic info in the form of DNA
this genetic material is passed on from parent to daughter cell
why don’t viruses follow the 4 tenets of cell theory, and thus are not considered as living organisms?
violate tenet 3 and 4 because they:
can only replicate by invading other organisms (violating tenet 3 “cells arise only from preexisting cells”)
may use RNA as their genetic info (violating tenet 4 “cells carry genetic info in the form of DNA”)
difference + definition: prokaryotic vs. eukaryotic cells (the first major distinction we can make between living organisms)
PROKARYOTIC
- always single celled
- do not contain a nucleus
EUKARYOTIC
- can be unicellular or multicellular
- contain a true nucleus enclosed ina membrane
provide a brief summary of how a eukaryotic cell is structured (not detailed) (2)
- each cell has a MEMBRANE enclosing a semifluid CYTOSOL in which the ORGANELLES are suspended (many organelles are membrane bound)
- membranes consist of a phospholipid bilayer
what does having organelles be membrane bound allow for?
compartmentalization of functions
is the outer portion or inner portion of the cell membrane hydrophilic or hydrophobic? pair and explain the impact!
- INNER = HYDROPHOBIC
- SURFACES = HYDROPHILIC (electrostatically interacting with the aqueous environments inside and outside of the cell)
Provides a highly selective barrier between the interior of the cell and external environment
what is the function of the cytosol?
allows for diffusion of molecules throughout the cell
NUCLEUS
- what is contained in the nucleus?
- what surrounds the nucleus?
- all of the genetic material necessary for replication of the cell
- the nuclear membrane/envelope
defn + func: nuclear membrane/envelope
a double membrane that maintains a nuclear environment separate and distinct from the cytoplasm
defn + func: nuclear pores
holes in the nuclear membrane that allow selective two-way exchange of material between the cytoplasm and the nucleus
defn: genes vs. DNA vs. chromosomes
GENES are coding regions contained within DNA
DNA is genetic material
CHROMOSOMES are the linear strands that DNA is organized into
defn + func: histones
organizing proteins that linear DNA is wound around
defn + func: nucleolus
how much of the nucleus does the nucleolus take up?
why does the nucleolus exist?
where ribosomal RNA (rRNA) is synthesized
takes up about 25 % of the nucleus volume
exists because DNA transcription is separate from RNA translation because the DNA is localized in the nucleus and the RNA is localized in the nucleolus
if the mitochondria is the power plant of the cell, what is the nucleus?
the CONTROL center of the cell
why is the mitochondria the power plant of the cell?
they have important metabolic functions
what are the four main divisions of space of the mitochondria and what are their distinct functions?
OUTER MEMBRANE = a barrier between the cytosol and the mitochondrion’s inner environment
INTER-MEMBRANE SPACE = the space between the outer and inner membranes
INNER MEMBRANE = contains molecules and enzymes of the ETC
MITOCHONDRIAL MATRIX = the space inside the inner membrane
the inner membrane of the mitochondrion is arranged into numerous infoldings
what are the called and what is their purpose?
CRISTAE
increase the surface area available for electron transport chain enzymes
how are mitochondria unique from other parts of the cell?
they are semi-autonomous
what does it mean that mitochondria are semi-autonomous? (2)
what phenomenon does this make them prime examples of?
- contain some of their own genes
- replicate independently of the nucleus via binary fission
- great example of cytoplasmic or extranuclear inheritance (the transmission of genetic material independent of the nucleus)
main 2 func of the mitochondria
- keep the cell alive by providing energy
- can kill the cell by release of ETC enzymes (which kickstarts apoptosis = programmed cell death)
defn + func: lysosomes
membrane-bound structures containing HYDROLYTIC enzymes (break down many different substrates, including substances ingested by endocytosis and cellular waste products)
what structure do lysosomes often function with? what does this structure do?
ENDOSOMES
transport, package, and sort cell material traveling to and from the membrane
where are endosomes capable of transporting materials to? (3)
- trans-golgi
- cell membrane
- lysosomal pathway for degradation
defn + effect: autolysis
the release of enzymes by lysosomes
leads directly to cellular component degradation
defn + char + func: endoplasmic reticulum
a series of interconnected membranes contiguous with the nuclear envelope
folded into numerous invaginations (creates complex structures with a central lumen)
what are the differences between the smooth (3) and rough (1) ER?
ROUGH ER
- studded with ribosomes
SMOOTH ER
- lacks ribosomes
- utilized mostly for lipid synthesis and drug and poison detoxification
- transports proteins from the RER to the Golgi
what is the functions of the ribosomes that dot the rough ER?
permit the translation of proteins destined for secretion directly into its lumen
defn + func + char: Golgi apparatus
stacked membrane-bound sacs
receives materials from the ER in vesicles, then modifies these cellular products
what are the modifications (2) that the Golgi apparatus can make to cellular products?
- group addition (carbohydrates, phosphates, and sulfates)
- introduction of signal sequences (direct the delivery of the product to a specific cellular location)
what happens to cellular products after they are modified by the Golgi apparatus?
they are repackaged in vesicles and directed to the correct cellular location
defn: exocytosis
if a product is destined for secretion, the secretory vesicle from the Golgi merges with the cell membrane and its contents are released
defn + func (3): peroxisomes
cellular structures that contain hydrogen peroxide
functions:
1. breakdown of long chain fatty acids via beta-oxidation
2. participate in phospholipid synthesis
3. contain some enzymes involved in the pentose phosphate pathway
func: cytoskeleton (2)
components (3)
- provides structure to the cell, helps it to maintain its shape
- provides a conduit for the transport of materials around the cell
components
1. microfilaments
2. microtubules
3. intermediate filaments
what are microfilaments made of?
how are these materials organized and why?
solid polymerized rods of actin
these actin filaments are organized into bundles and networks and are resistant to compression and fracture (provide cell protection)
how and why do actin filaments use ATP?
to generate force for movement by interacting with myosin
like in muscle contraction
what role do microfilaments play in cytokinesis (the division of materials between daughter cells)
the cleavage furrow is formed from microfilaments which organize as a ring at the site of division between the two new daughter cells
what are microtubules made of?
what is their function?
made of hollow polymers of tubulin proteins
radiate throughout the cell to provide the primary pathways along which motor proteins like kinesin and dynein carry vesicles
what is the commonality between cilia and flagella?
they are motile structures composed of microtubules
defn + func + ex: cilia vs. flagella
CILIA
- projections from a cell
- primarily involved in the movement of materials along the surface of the cell
- ex: cilia line the respiratory tract, involved in mucus movement
FLAGELLA
- involved in the movement of the cell itself
- ex: movement of sperm cells through the reproductive tract
defn + application: 9 + 2 structure
seen only in eukaryotic organelles of motility
structure used in cilia and flagella
nine pairs of microtubules forming an outer ring with two microtubules in the center
defn + char + location: centrioles
found in the CENTROSOME (cell region)
organizing centers for microtubules
nine triplets of microtubules with a hollow center
char (2) + func (3) + examples (4): intermediate fliaments
a diverse group of filamentous proteins
KERATIN, DESMIN, VIMENTIN, LAMINS
- involved in cell-cell adhesion
- involved in cytoskeleton integrity maintenance
- help anchor other organelles
- can withstand a lot of tension (increases cell’s structural rigidity)
- identity within a cell is specific to the cell and tissue type
what are the 4 tissue types?
- epithelial
- connective
- muscle
- nervous
func: epithelial tissues (2)
- cover the body and line its cavities (protection against pathogen invasion and dessication)
- involved in absorption, secretion, and sensation in certain organs
what is the function of the basement membrane of epithelial tissues?
epithelial cells are tightly joined to each other and to an underlying layer of connective tissue (the basement membrane)
to remain as one cohesive unit
defn: parenchyma
the functional parts of the organ
usually composed of epithelial cells
what does it mean that epithelial cells are often polarized?
one side faces the lumen (the hollow inside of an organ or tube) or the outside world
the other side interacts with underlying blood vessels and structural cells
defn: simple vs. stratified vs. pseudostratified epithelia
SIMPLE = one layer of cells
STRATIFIED = multiple layers of cells
PSEUDOSTRATIFIED - appear to have multiple layers due to cell height differences, but are only one layer in reality
defn: cuboidal vs. columnar vs. squamous epithelial cells
CUBOIDAL = cube-shaped
COLUMNAR = long and thin
SQUAMOUS = flat and scale-like
func: connective tissue
supports the body and provides a framework for the epithelial cells to carry out their functions
defn: stroma
support structure of an organ
mainly composed of connective tissue
what are 6 examples of connective tissues?
- bone
- cartilage
- tendons
- ligaments
- adipose tissue
- blood
what is the extracellular matrix composed of?
collagen and elastin (which are secreted and products by most cells in connective tissue)
what are prokaryotes and what are 2 characteristics of them?
prokaryotes include all bacteria
- do not contain any membrane-bound organelles
- genetic material is organized into a single circular molecule of DNA concentrated in an area of the cell (the nucleoid region)
what are the 3 overarching domains into which all life can be classified? which 2 of these contain prokaryotes?
- Archaea (includes prokaryotes)
- Bacteria (includes prokaryotes)
- Eukarya
defn: Archaea
single-celled organisms that are visually similar to bacteria, but contain genes and several metabolic pathways that are more similar to eukaryotes than to bacteria
what is a notable feature of Archaea?
their ability to use alternative sources of energy
- some are photosynthetic
- many are chemosynthetic (can generate energy from inorganic compounds, including sulfur- and nitrogen-based compounds)
how are Archaea similar to Bacteria? (3)
contain a single circular chromosome
divide by binary fission or budding
share a similar overall structure
how are Archaea similar to Eukarya? (3)
start translation with methionine
contain similar RNA polymerases
associate their DNA with histones
what are 2 things that all bacteria contain and 2 things that some contain?
ALL
1. cell membrane
2. cytoplasm
SOME
1. flagella
2. fimbriae (similar to cilia)
defn: mutualistic symbiotes
both humans and the bacteria benefit from the relationship
defn: pathogens (parasites)
bacteria that provide no advantage or benefit to the host, but rather cause disease
may live intracellularly or extracellularly
what are the three shapes that most bacteria exist in?
- COCCI = spherical bacteria
- BACILLI = rod-shaped bacteria
- SPIRILLI = spiral-shaped bacteria
defn: obligate aerobes vs. anaerobes
OBLIGATE AEROBES = bacteria that require oxygen for metabolism
ANAEROBES = bacteria that use fermentation (or some other form of cellular metabolism that does not require oxygen)
what are the 3 types of anaerobes?
- obligate anaerobes
- facultative anaerobes
- aerotolerant anaerobes
defn: obligate vs. facultative vs. aerotolerant anaerobes
OBLIGATE ANAEROBES = anaerobes that cannot survive in an oxygen-containing environment
FACULTATIVE ANAEROBES = bacteria that can toggle between metabolic processes, using oxygen for aerobic metabolism if it is present, and switching to anaerobic metabolism if it is not
AEROTOLERANT ANAEROBES = anaerobes that are unable to use oxygen for metabolism, but are not harmed by its presence in the environment
why can’t obligate anaerobes survive in an oxygen-containing environment?
the presence of oxygen leads to the production of reactive oxygen-containing radicals in these species, which leads to cell death
defn + func: bacterial cell wall (4)
- forms the outer barrier of the cell
- provides structure
- controls the movement of solutes into and out of the bacterium (allows the cell to maintain a concentration gradient relative to the environment)
- specific components of the cell wall can trigger an inflammatory response
what is the next layer of bacteria after the cell wall and what is it composed of?
the cell membrane (or plasma membrane)
composed of phospholipids
defn: bacterial envelope
the cell wall and the cell membrane
what are the two main types of bacterial cell wall and how is the type determined?
gram positive and gram negative
Gram staining process
explain the process and results of Gram staining
a crystal violet stain followed by a counterstain with a substance called safranin
if the envelope absorbs the crystal violet stain = appears deep purple = GRAM POSITIVE
if the envelope does NOT absorb the crystal violet stain, but absorbs the safranin counterstain = appears pink-red = GRAM NEGATIVE
what are two substances that gram positive cell walls contain? what is each substances role?
- peptidoglycan (thick layer) = a polymeric substance made from amino acids and sugars
ROLE = aids a bacterial pathogen in providing protection from a host organism’s immune system
- lipoteichoic acid
ROLE = unclear, but human immune system may be activated by exposure to it
what is the structural organization and components of gram-negative cell walls? (4)
- very thin
- contain peptidoglycan but in smaller amounts
- separated from the cell membrane by the PERIPLASMIC SPACE
- have outer membranes containing phospholipids and lipopolysaccharides
what is the part of gram-negative cell walls that triggers an immune response in human beings?
how strong is this immune response in comparison to the immune response triggered by lipoteichoic acid in gram-positive bacteria?
lipopolysaccharides
MUCH STRONGER THAN inflammatory response to lipoteichoic acid
struct (2) + func (3): flagella
long, whip-like structures
bacteria may have 1, 2, or many
- propulsion
- move toward food
- move away from toxins or immune cells
defn: chemotaxis
the ability of a cell to detect chemical stimuli and move toward or away from them
what are the 3 structural components of flagella? describe each.
- FILAMENT = hollow, helical structure composed of flagellin
- BASAL BODY = a complex structure that anchors the flagellum to the cytoplasmic membrane; is also the motor of the flagellum
- HOOK = connects the filament and the basal body so that, as the basal body rotates, it exerts torque on the filament, which spins and propels the bacterium forward
are flagella the same in gram-positive and gram-negative bacteria?
they are similar, but there are slight differences due to the physical structure and chemical composition of the envelope
how is DNA stored in prokaryotes? (3)
- concentrate DNA in a region of the cell known as the nucleoid (which does not contain a nuclear envelope)
- DNA is carried on a single circular chromosome (which can be found coiled around histone-like proteins in some bacteria)
- DNA acquired from external sources may also be carried on smaller circular structures (plasmids)
what type of DNA do plasmids carry?
DNA acquired from external sources that is not necessary for survival of the prokaryote (and therefore is not considered part of the genome of the bacterium), but may confer an advantage (like antibiotic resistance)
extrachromosomal (extragenomic) material is what is contained
Since prokaryotes don’t have mitochondria, what structures is used for the generation of ATP and the ETC?
the cell membrane
do prokaryotes contain a cytoskeleton?
yes, but it is primitive and much less complex than the one found in eukaryotes
what is the difference between the prokaryotic and eukaryotic ribosome?
PROKARYOTIC = 30S and 50S subunits
EUKARYOTIC = 40S and 60S subunits
defn + 2 main steps: binary fission
a simple form of asexual reproduction seen in prokaryotes, can proceed very rapidly bc few steps
- the circular chromosome 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 to produce two identical daugher cells
what are 3 other things that plasmids can contain?
- virulence factors (traits that increase pathogenicity)
- projections that allow attachment to certain kinds of cells
- features that allow evasion of the host’s immune system
defn: episome
a subset of plasmids that are capable of integrating into the genome of the bacterium
what is a benefit of bacterial genetic recombination?
helps increase bacterial diversity –> permits evolution of a bacterial species over time
what are the 3 types of bacterial genetic recombination?
- transformation
- conjugation
- transduction
defn + char: transformation (3)
- results from the integration of foreign genetic material into the host genome
- this material generally comes from other bacteria that, upon lysing, spill their contents into the vicinity of a bacterium capable of transformation
- common in gram-negative rods
defn + char: conjugation (3)
- the bacterial form of mating (sexual reproduction)
- involves 2 cells forming a conjugation bridge between them that facilitates the transfer of genetic material
- unidirectional transfer from the donor male (+) to the recipient female (-)
what is the conjugation bridge in bacterial conjugation made of? how are these formed?
sex pili found on the donor male
for pilus to be formed, bacteria must contain plasmids known as sex factors that contain the necessary genes
defn + char: F factor
fertility factor
the best studied sex factor (plasmid)
in E.Coli
bacteria with this: F+ cells
bacteria without this: F- cells
explain what happens with the F factor during conjugation
the F+ cell replicates its F factor and donates the copy to the F- cell, converting it into an F+ cell
this enables the cell obtaining the new plasmid to then transfer copies to other cells
what does conjugation specifically allow for?
rapid acquisition of antibiotic resistance or virulence factors throughout a colony because other plasmids can also be passed through the conjugation bridge
explanation: Hfr (high frequency of recombination)
sometimes the sex factor becomes integrated into the host genome
then, if conjugation occurs, the entire genome replicates because it now contains the sex factor
the donor cell will try to transfer an entire copy of its genome into the recipient, however the bridge usually breaks before the full DNA sequence can be moved
defn + char: transduction
the only genetic recombination process that requires a vector
VECTOR = a virus that carries genetic material from one bacterium to another
defn: bacteriophage + how do they work
viruses that infect bacteria
they target bacteria, but do not actually enter them
they just inject their genetic material, leaving the remaining structures outside the infected cell
explain how bacteriophages are involved in transduction
viruses are obligate intracellular pathogens (they cannot reproduce outside of a host cell)
thus bacteriophages can accidentally incorporate a segment of host DNA during assembly
when the bacteriophage infects another bacterium, it can release this trapped DNA into the new host cell, which can then integrate into the genome
defn: transposon
genetic elements capable of inserting and removing themselves from the genome
(can be in prokaryotes or eukaryotes)
what is the series of phases by which bacteria reproduce/grow? (4) describe them
- LAG PHASE = bacteria adapt to new local conditions in a new environment
- EXPONENTIAL (LOG) PHASE = as the bacteria adapt, the rate of division increases, causing an exponential increase in the number of bacteria in the colony
- STATIONARY PHASE = as the number of bacteria grows, resources are often reduced, which slows reproduction
- DEATH PHASE = after the bacteria have exceeded the ability of the environment to support the number of bacteria, marks the depletion of resources
what are the 3 main components of viruses?
- genetic material
- a protein coat
- sometimes an envelope containing lipids
what are the characteristics of the genetic info in viruses?
may be circular or linear
may be single or double stranded
may be composed of either DNA or RNA
defn: capsid
the protein coat of a virus
char: envelope (virus)
- what does it surround?
- what is it composed of?
- what are they sensitive to? what does this imply?
surrounds the capsid
composed of phospholipids and virus-specific proteins
sensitive to heat, detergents, and dessication –> easier to kill
what is true of viruses without an envelope that is not true of viruses with an envelope?
they are more resistant to sterilization and are likely to persist on surfaces for an extended period of time
why do viruses need a host cell? what for?
they cannot reproduce independently (they are obligate intracellular parasites)
they must express and replicate genetic info within a host cell because they lack ribosomes to carry out protein synthesis
defn: virion
viral progeny
are produced when a virus hijacks a cell’s machinery and replicates
can be released to infect additional cells
what are the three physical components of a bacteriophage? what are their purposes?
- CAPSID = protein coat
- TAIL SHEATH = can act like a syringe, injects genetic material into a bacterium
- TAIL FIBERS = help the bacteriophage recognize and connect to the correct host cell
defn: positive vs. negative sense (single-stranded) RNA viruses
POSITIVE SENSE = the genome may be directly translated to functional proteins by the ribosomes of the host cell
NEGATIVE SENSE = the negative-sense RNA strand acts as a template for synthesis of a complementary strand, which can then be used as a template for protein synthesis
what must negative sense RNA viruses have that positive sense RNA viruses don’t? why?
they must carry an RNA replicase in the virion to ensure the complementary strand is synthesized
defn: retrovirus
enveloped, single-stranded RNA viruses in the family Retroviridae
usually the virion contains 2 identical RNA molecules
explain the mechanism by which retroviruses function (2)
- carry an enzyme: reverse transcriptase (synthesizes DNA from single-stranded RNA)
- DNA integrates into the host cell genome where it is replicated and transcribed as if it were the host’s own DNA
why are retroviruses so difficult to treat? what is an example of a retrovirus?
integration of the genetic material into the host cell genome allows the cell to be infected indefinitely
the only way to remove the infection is to kill the infected cell
example: HIV
what are the 4 main parts of the viral life cycle?
- infection
- translation and progeny assembly
- progeny release
- lytic and lysogenic cycles
what are the 3 types of progeny release? explain them
- viral invasion may initiate cell death – results in viral progeny spilling
- host cell may lyse as a result of being filled with extremely large numbers of virions
- EXTRUSION = a virus can leave the cell by fusing with its plasma membrane
why is lysis a disadvantage for the virus?
why is extrusion good for the virus?
LYSIS –> the virus can no longer use the cell to carry out its life cycle
EXTRUSION –> it keeps the host cell alive and thus allows for the continued use of the host cell by the virus
what is the state of a virus in extrusion?
the productive cycle
what 2 factors determine if bacteriophages may enter a lytic or lysogenic life cycle?
- growth conditions
- the specific virus
defn: lytic cycle
the bacteriophage maximizes the use of the cell’s machinery with little regard for the survival of the host cell
once the host is swollen with new virions, the cell lyses, and other bacteria can be infected
defn: virulent
viruses in the lytic phase
defn: prophage/provirus
in the event that the virus does not lyse the bacterium, it may integrate into the host genome as this
defn: lysogenic cycle
initiated when a prophage/provirus integrates into the host genome
the virus will be replicated as the bacterium reproduces because it is now part of the host’s genome
what may cause a provirus to leave a genome? what happens to it then?
environmental factors (radiation, light, chemicals)
reverts to a lytic cycle
what is a benefit of integration of a bacteriophage into the host genome for the bacterial host?
infection with one strain of phage generally makes the bacterium less susceptible to superinfection (simultaneous infection) with other phages
what category do prions and viroids belong to?
very small, subviral particles that can cause disease under certain circumstances
defn: prion
infectious proteins (nonliving)
how do prions cause disease?
by triggering protein misfolding (usually through conversion of a protein from an alpha-helical structure to a beta-pleated sheet)
this drastically reduces the protein’s solubility, as well as the cell’s ability to degrade the protein
eventually, protein aggregates form, which interferes with cell function
what are 3 diseases caused by prions?
- mad cow disease
- Creutzfeldt-Jakob disease
- familial fatal insomnia
defn: viroids
small pathogens consisting of a very short circular single-stranded RNA that infect plants
how do viroids work?
they can bind to a large number of RNA sequences and can silence genes in the plant genome
this prevents synthesis of necessary proteins –> results in metabolic disruption and structural damage to the cell
