cell theory, cells and organelles, cytoskeleton

characteristics of life

1. cell organization/order

2. reproduction

3. heredity

4. growth and development

5. metabolism

6. response to stimuli

7. homeostasis

8. evolutionary adaptation

___ are the simplest units which constitute life and are capable of replication

cells

cells were first identified and named by ____ in 1665 using a simple microscope and a thin slice of cork

• saw dead plant cells

Robert Hooke

cell theory (1838)

1. all organisms are composed of cells

2. cells are the smallest living things

3. cells arise only from pre-existing cells

all cells today are believed to represent

a continuous line of descent from the first living cells

modern cell theory

1. all known living things are made up of cells

2. the cell is the fundamental structural and functional unit of all living things

3. all cells come from pre-existing cells by division (no spontaneous generation occurs)

4. cells contain hereditary info which is passed from cell to cell during cell division

5. all cells are basically the same in chemical composition

6. all energy flow (metabolism and biochemistry) of life occurs within cells

7. the activity of an organism depends on the total activity of independent cells

all cells in nature share these 4 common structural features

1. a plasma membrane (boundary)

2. cytoplasm/cytosol (intracellular matrix)

3. chromosome(s) of DNA (genetic material)

4. ribosomes (translation machinery)

cytoplasm vs cytosol

cytosol: the fluid component of the cytoplasm, rich in nutrients, salts, and proteins

cytoplasm: contents inside the structure of the cell

• includes the liquid part (cytosol) and any organelles/membrane-bound structures

all cells also share the same 4 primary macromolecules

nucleic acids, proteins, lipids, carbohydrates

• comprise the cell’s structure, key properties of life, and basic principles of biochemistry and heredity

all living things are believed to come from a common ancestor called

protobionts (“proto-life”)

3 domains of living things

1. Bacteria (prokaryotes)

2. Archaea (prokaryotes)

3. Eukarya (eukaryotes)

6 kingdoms of living things

bacteria —→ eubacteria

archaea —→ archaea

eukarya ——→ protista, fungi, plantae, animalia

viruses

an infectious non-living obligate intracellular parasite

• NOT cells

structure of a virus

capsid: protein coat (shell) protecting the genome, may carry accessory proteins

envelope: host-derived lipid bilayer membrane (optional); protects genome, helps evading recognition by immune cells, facilitates virus entry

genome: RNA or DNA, varies considerably in size and organization (controls the virus replication strategy)

attachment protein (spikes): recognizes one or more specific host cell receptors (controls viral tropism or host range)

host range / tropism

the spectrum of cells of a host that a virus may infect

• ex: bacteriophages are viruses with a specific bacterial tropism

properties viruses share with life

1. exhibit structural organization

2. adaptation

3. replication/reproduction

properties of life that viruses lack

since viruses don’t have cytoplasm…

1. metabolism/growth - require host cell products

2. homeostasis - need a host for replication

3. response to stimuli - they remain inert outside of a host

why do viruses remian inert outside of a host

they do not have ribosomes to produce proteins

• this is why they need the host cells

virus particles outside of a host are called

virions

• exhibit no biological activity

• only referred to as a virus when inside of a host

why are viruses NOT cells?

they lack fundamental structures and functions of living cells such as

• cytoplasm/cytosol

• ribosomes

cannot do anything with their genetic material by themselves. need a host cell!

why are viruses NOT living organisms?

they can’t independently carry out life processes like growing, responding to stimuli, or maintaining homeostasis

scientists often study cellular and molecular biology by means of

model organisms

• instead of testing on humans!

• ex: bacteria, yeast, fruit fly, plant, mouse

human limit of detection (for seeing cells with the naked eye)

100 μm

erythrocytes / red blood cells are among the _____ eukaryotic cells

smallest

prokaryotic cells are ______ than eukaryotic cells and viruses are _____ than bacteria

smaller

smaller

is there a correlation between the size of a cell/microorganism, its ecological niche, and its disease potential?

no!

• ex: COVID = super small in size but had a huge impact/disease potential

prokaryote vs eukaryote

prok:

• simple and small, reproduce quickly

• oldest

• single-celled

• no nucleus

• no membrane-bound organelles

• DNA is circular and located in nucleoid region

• have a cell wall made of polysaccharides

euk:

• evolved from prok.

• larger and more complex

• have a nucleus

• either single or multicellular

• have membrane-bound organelles

• linear DNA

what do prokaryotes and eukaryotes have in common?

• both have DNA/genetic material

• have ribosomes

• have cytoplasm

• have a plasma membrane

3 “boundary layers” of a prokaryotic cell

from outermost to innermost:

• capsule

• cell wall

• plasma membrane

capsule

an organized glycocalyx (thick, sticky gel-like sugar coat surrounding the cell) permanently affixed to the cell

• function: protection and attachment

3 kinds of attachments on the capsule

fimbriae: small, hair-like projections used for attachment to surfaces (kind of like fingers to use for gripping)

flagellum/flagella: long filament(s) used for taxis (stimulus directed movement)

pili: long hair-like projection used for some motility, also used for DNA transfer btween bacteria mating pair

• ^ during conjunction or “parasexual mode of reproduction” via a conjugative pilus

pili of separate bacteria cells can form a _______ through which they transfer plasmids

microtunnel/pilus

cell wall

semi-rigid structure responsible for maintaining cell shape

• immediately below the glycocalyx

• provide structure and protection from lysis (destruction)

• made of peptidoglycan (protein, carb)

2 main types of cell wall

gram positive and gram negative

gram positive: cell wall made of a thick layer of peptidoglycan (network of cross-linked sugar molecules)

gram negative: cell wall made of thin layer of peptidoglycan, but also has an outer layer of lipopolysaccharides (LPS) - membrane layer loaded with sugar molecules

why is gram staining of a bacterial cell important?

determines if a bacteria is gram+ or gram-

• identify the bacteria’s cell wall structure & composition

• can help determine which antibiotic would most effectively target it

• not all antibiotics can affectively destroy every bacteria/burst their cell walls

plasma membrane

phospholipid bilayer located directly beneath cell wall

• controls what biomolecules can enter/exit!

prokaryotic cytoplasm typically only contains the following components

• cytosol

• ribosomes

• genetic material - chromosomal DNA and plasmids

the genome of a bacterium is located in the nuceloid region and is usually a double-stranded, circular piece of DNA that encodes…

all the essential genes, and therefore proteins, that are required for bacterial growth

plasmids

• bonus DNA!

• acquired from other cells or from the enviornment

• frequently copied

• bacteria often carry one or more

• small, circular pieces of DNA that encode non-essential genes, and therefore non-essential proteins

• not essential, but help bacteria thrive

plasmids often have genes that

confer beneficial traits for cell survival

• ex: antibiotic resistance, tolerance of toxic metals, virulence factors (toxins) that help bacteria attach to hosts

do bacteria have a preference for which plasmids they pick up?

no

• collect the harmful, neutral, and beneficial

• beneficial traits are seen/those plasmids survive because of “natural selection”

what do bacteria and archaea have in common

• lack a true nucleus

• circular chromosomes made of DNA

• Asexual reproduction (binary fission) and horizontal gene transfer

• unicellular form

archaea are NOT ____ with bacteria

interchangeable

• archaea are as distantly related from bacteria as they are from eukaryotes

unique characteristics of archaea

• lack peptidoglycan in cell walls

• use of histones in DNA packaging

• use of met instead of fMet during translation initiation

• translation and transcription are similar to those of eukarya

• preference for extreme environmental conditions

4 primary kingdoms of eukaryotic life

1. Protists: predominately small unicellular aquatic organisms

2. Fungi: uni or multicellular organisms

3. Plants: multicellular organisms

4. Animals: multicellular organisms

eukaryotic cell structure - cell wall

cell wall: a rigid, outer cell boundary present in plants, fungi, and many protists

• provide structure & stability

• comprised of carbohydrate polymers

In plants: primary and secondary cell walls made of cellulose

In fungi: single cell wall comprised of a carbohydrate called chitin

In protists: if any cell wall, there is generally a single one made of cellulose, modified sugars, or proteins. thin cell wall in moving protists is a protein-made pellicle

cytoplasm and its contents - eukaryotic cell

cytoplasm: the intracellular space between the plasma membrane and the nucleus

• cytosol

• organelles

• inclusions - vary with cell type (ex: glycogen granules, pigments, liquid droplets, vacuoles, crystals)

ALL cells have

cytoplasm and ribosomes

free vs membrane-bound ribosomes

free: synthesize soluble proteins for cytosol or other organelles, freely floating

membrane-bound: bound to ER, synthesize proteins to be trafficked

• the same ribosome can go from free, to bound, to free again in its lifespan

endomembrane system

represents the membrane-associated structures of the cell which compartmentalize functions and facilitate intracellular trafficking

• like a maze that proteins travel through!

where is protein created in all cells?

the cytoplasm

6 major components of the endomembrane system

proteins travel in this order:

1. nucelus (nuclear envelope)

2. endoplasmic reticulum

3. golgi apparatus

4. lysosomes

5. vesicles/vacuoles

6. cell membrane

• “Ninjas Eat Giant Lasagna, Very Carefully”

• all 6 are comprised of lipid membranes, but the composition of the membranes differ and play a key role in membrane trafficking!

nucelus, nucleolus, nuclear envelope

nucleus: membrane-enclosed, contains genomic DNA in the form of chromatin, site of DNA replication and transcription, “command center of the cell”

nucleolus: small dense spherical structure inside the nucelus (during interphase) associated with rRNA synthesis and ribosome assembly

nuclear envelope: a membrane phospholipid bilayer surrounding the nucleus, contains nuclear pores to regulate what enters and exits

nucleoplasm, nuclear lamina, nuclear matrix/chromosome territories

nuceloplasm: inner contents of the nucleus

nuclear lamina: dense, fibrous protein network that provides structure to the nucleus and facilitates its disassembly during cell division (disappears in prophase, reappears in telophase)

nuclear matrix/chromosome territories: network of fibers within the nucleus serving as a scaffold to establish designated chromosome territories

endoplasmic reticulum (ER)

network of membrane sacs which synthesize and store proteins and other molecules

• connected to nuclear envelope

rough: covered with ribosomes, involved in synthesis and modification (through glycosylation) of proteins for trafficking w/in the cell ——→ plasma membrane ————> potentially out of the cell

smooth: no ribosomes on the surface, site of lipid (fats and steroids) synthesis modifications, some carb metabolism, and detoxification

• stores calcium!

• think smooth —> skim milk —→ milk has calcium

golgi apparatus

network of flattened membrane sacs, aka cisternae, which modify proteins and lipids received from the ER and ship them throughout the cell in small sacs called transport vesicles

AKA post office of the cell

transport vesicles

small, membrane-bound sacs w/in a cell that function to move molecules, like proteins, from one part of the cell to another

• bud off from one organelle, carry their cargo, then fuse with another organelle to release their contents at the right destination

lysosomes

small membrane-bound vesicles produced by the golgi

• contain acidic conditions and hydrolytic enzymes to break down molecules (for recycling)

• can be used to destroy bacteria ingested by cells through phagocytosis

primary functions of the cell membrane in eukaryotic cells

• protect the cell

• maintain ion concentrations (osmotic balance) of various substances

• selectively permeable

• facilitate cell communication

• cell adhesion

what is NOT part of the endomembrane system

• mitochondria

• chloroplasts

• peroxisomes

• vacuoles

mitochondria

double membrane-enclosed structures that generate ATP in all types of eukaryotic cells by cellular respiration

• have their own ribosomes and DNA

• can self replicate (divide by simple fission)

• outer mitochondrial membrane is separated from the inner by the inner membrane space

• inner membrane has folds called cristae - increases surface area for cell resp.

• matrix: inner most region present in the inner membrane of mitochondria

chloroplast

double membrane-enclosed structures containing chlorophyll (make them appear green)

• used for photosynthesis

• present in plants and some animal cells

• have their own DNA and ribosomes

• inside of the chloroplast is called the stroma and is filled with flattened sacs called thylakoids, which form columns called grana

—> thylakoids contain photosynthetic pigments, primarily chlorophyll

endosymbiotic theory

suggests that eukaryotes, and their membrane-bound organelles, evolved from prokaryotic cells

main evidence to support:

1. mitochondria and chloroplasts resemble modern aerobic and photosynthetic bacteria, respectively

2. mitochondria and chloroplasts have their own DNA (which is most similar to bacteria) and perform their own, autonomous functions

3. bacteria are known to form symbiotic relationships with eukaryotic cells

peroxisomes

membrane-bound vesicles found in both plant and animal cells that are involved in lipid metabolism and the reduction of toxic materials in the cell (like hydrogen peroxide)

vacuoles

large membrane-bound sacs (much larger than vesicles) that are used for storing excess materials like fat or water

central vacuole

very large vacuole found in plant cells occupying 70% of the cell’s volume

• holds water, materials, nutrients, pigments, wastes

• regulate cell pressure

contractile vacuole

large vacuole found in protists that plays a similar role to the central vacuole in plants

food/digestive vacuole

organelle found in protists that essentially performs a lysosome’s function: digestion and excretion for the cell

plants don’t have lysosomes. they have ______ instead

lytic vacuoles

animal cells do have little vacuoles, but only plant cells have ____

a large central vacuole

both plant and animal cells have

peroxisomes, microtubules, and secretory vesicles

some characteristics that only animal cells have vs only plant cells

animal only:

• lysosomes

• centrioles

plant only:

• cell wall

• central vacuole

• chloroplast

3 types of extracellular structures for eukaryotic cells

flagella: similar to prokaryotic flagella, long, hair-like projections for motility

• composition of flagella is different for eukaryotic and prokaryotic cells

cilia: small, hair-like projections used for motility and movement of substances

• cillia on cells in respiratory tract to keep particulates out of the lungs

• protists require cilia for their movement

microvilli: minute, finger-like extensions of plasma membrane

• increase surface area for absorption purposes!

cytoskeleton

a complex network of fibers which perform numerous functions in the cell including providing cell structure, facilitating motility, and mediating intracellular transport of materials

• 3 types: microfilaments (aka actin filaments), intermediate filaments, microtubules

• most cytoskeletal elements exhibit dynamic instability - the constant assembly and disassembly to alter cell structure and function

microfilaments

• smallest fibers (made of mostly actin) which are associated with the plasma membrane

• provide cell shape and aid in small local changes in the membrane for motility

intermediate filaments

• intermediate in size

• toughest and most durable of the 3 types

• involved in positioning of organelles

• provide structural support for the cell and help facilitate cell-to-cell connections

• comprised of several different types of proteins

• not involved in motility

• not found in plants

different proteins that comprise intermediate filaments

keratins: epithelial cells, cytoplasmic, most diverse by structure

vimentin, desmin: connective tissue, muscles, cytoplasmic

neurofilaments, nestin: neurons, cytoplasmic

lamins: nuclei of all animal cells

assembly of intermediate filaments

pair of helical monomers twist —→ dimers twist ——> tetramers bind to generate rope-like final filament

• plectins: class of proteins that crosslink and connect these elements to other cytoskeletal elements (act as a link between all 3 main components of the cytoskeleton)

function of intermediate filaments

• provide mechanical strength to cells

• help resist stretching forces so the cells remain intact and together

• form a scaffold structure within cells to anchor the cytoskeleton

• play little to no role in movement/motility

ex of improper function: “butterfly children” / epidermolysis bullosa

• connective tissue disorder

• issues with anchoring between epidermis and dermis

• slightest touch or stretching causes rupture

• associated with mutations to keratin genes

nuclear lamina

the inner membrane/core structure of the nuclear membrane

• type of intermediate filament

• comprised of linked proteins called lamins that form a cross-linked network

• meshwork instead of rope-like (the other intermediate filaments are rope-like!)

• disassemble and reform the nucleus with every cell division

which cells employ lamins in the nuclear structure

all animal cells!!!

• NOT present in plants, fungi, or microorganism

hutchinson-gilford progeria syndrome

rare autosomal dominant genetic disease associated with premature aging due to a point mutation in the LMNA gene resulting in failure to produce lamin A

• nucelus can’t form correctly or disassemble correctly, so cell division/mitosis is greatly hindered

• shortened lifespan

microtubules

• largest filaments

• comprised primarily of polymers of the protein tubulin

• undergo polymerization and depolymerization (assemble and disassemble)

• make up several cell structures like: centrioles/centrosomes, mitotic spindle fibers, flagella, cilia

functions of microtubules

• intracellular trafficking

• organelle positioning

• cell locomotion (cilia and flagella)

• nuclear division, formation of spindle apparatus, separation of chromosome pairs

• providing structural support

microtubule structure & assembly

• made of tubulin heterodimers (have one alpha and one beta tubulin monomer)

• tubulin heterodimers stack to create protofilaments

• in humans, 1 microtubule contains 13 protofilaments

• protofilaments come together to form the microtubule and its lumen structure

• each microtubule tube has polarity and orientation (plus and minus end)

the heterodimers add to the ___ end of the microtubule tubes

plus

microtubule organizing center (MTOC)

• structure found in eukaryotic cells (especially animal)

• major assembly site of microtubules

• two main functions:

1. help organize microtubules for motility structures (flagella and cilia)

2. organize mitotic spindle during cell division

gamma-tubulin rings on the surface of the centrosome serve as nucleation sites for building new microtubules

^ where the minus end is attached!!

centrosome

the most prominent MTOC!!!

main MTOC of the animal cell

• inside the center of the centrosome are two centrioles

• centrioles are comprised of microtubule triplets

• the centrioles are surrounded by a dense, highly structured mass of protein called the pericentriolar material (PCM)

pericentriolar material/PCM

• contains proteins responsible for microtubule nucleation and anchoring

• gamma-tubulin, pericentrin, ninein

the polymerization/assembly of microtubules requires __ as an energy source

GTP

• GTP is bound to the tubulin dimers to provide the energy for attachment

• GTP hydrolysis to GDP promotes the depolymerization/disassembly

• 50% of tubulin dimers in the cell are in polymerized microtubules and 50% are free

capping the microtubules for stabilization

• minus end is capped by centrosome and MTOCs

• capping proteins are on the plus end and prevent any changes to microtubule structure or length

• capped microtubules play a larger role in structure and shape rather than motility

• capping microtubules on one end of the cell can lead to cell polarization or distinct morphological poles of the cell

microtubule motor proteins

traffic materials/cargo throughout the cell

cargo: proteins, vesicles, organelles, etc

2 major types:

1. dyneins: move towards minus end, retrograde

2. kinesins: move towards the plus end, anterograde

what energy do motor proteins require

ATP

• the head utilizes ATP energy to facilitate motion via ATP hydrolysis and binds to microtubules

• tail region of the proteins bind specific cargo

anterograde vs retrograde motion

anterograde: movement of substances away from the cell nucleus, motion towards the positive end, use kinesins

retrograde: movement of substances towards the cell nucleus, motion towards the negative end, use dyneins

_____ causes microtubule bending in normal flagellum, allowing for motion

dynein

^ motor protein

• apply forces on cross-linked microtubules

actin polymerization

like tubulin, about ½ is polymerized and ½ is free

ATP-bound actin polymerizes at the plus end of a growing microfilament

as ATP is slowly hydrolyzed to ADP, the actin monomers become more fragile and more likely to dissociate from the minus end

actin microfilament treadmilling

the overturn of actin on both ends

• adding subunits at the barbed end, losing them at the pointed end —> no net change in length

• whole point of actin isn’t to grow, but to move/allow cell to move

microfilament associated amoeboid movement

• extending a portion of the plasma membrane and forming a contact, then pulling the cell forward

• contractile forces for pulling are associated with myosin

• cell extensions used for movement include: pseudopodia, lamellipodia (flattened extension), filopodia (pointy extensions)

• cell uses actin rearrangement to ensure movement occurs

• ex: macrophages use amoeboid movement to move in and out of the bloodstream