Chapter 6: A Tour of the Cell

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Chapter 6: A Tour of the Cell Cell theory Cell organization and homeostasis Studying cells – microscopy and fractionation Eukaryotic vs. prokaryotic cells Compartments in eukaryotic cells (cell regions,

organelles) Cytoskeleton Outside the cell

http://www.auburn.edu/academic/classes/biol/1020/bowling/

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• What are the main tenets of cell theory?

• What are the major lines of evidence that all presently living cells have a common origin?


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Cell theory All living organisms are

composed of cells smallest “building blocks” of all

multicellular organisms

all cells are enclosed by a surface membrane that separates them from other cells and from their environment

specialized structures with the cell are called organelles; many are membrane-bound


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Cell theory Today, all new cells arise from

existing cells All presently living cells have a

common origin all cells have basic structural and

molecular similarities all cells share similar energy

conversion reactions all cells maintain and transfer

genetic information in DNA the genetic code is essentially

universal


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• What are the main tenets of cell theory?

• What are the major lines of evidence that all presently living cells have a common origin?


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• What is surface area to volume ratio, and why is it an important consideration for cells?

• What (usually) happens to surface area to volume ratio as cells grow larger?


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Cell organization and homeostasis

Plasma membrane surrounds cells and separates their contents from the external environment

Cells are heterogeneous mixtures, with specialized regions and structures (such as organelles)


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Cell size is limited surface area to volume ratio puts a limit on cell

size food and/or other materials must get into the cell

waste products must be removed from the cell

cells need a high surface area to volume ratio

BUT volume increases faster than surface area as cells grow larger…so cells usually must divide


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Fig. 5.4


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cell shape varies depending both on function and surface area requirements


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• What is surface area to volume ratio, and why is it an important consideration for cells?

• What (usually) happens to surface area to volume ratio as cells grow larger?


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• Compare and contrast:– LM and EM– SEM and TEM

• Include the terms resolution and magnification in your discussions.


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Studying cells – microscopy Most cells are large enough to be

resolved from each other with light microscopes (LM)

cells were discovered by Robert Hooke in 1665

he saw the remains of cell walls in cork with a LM

his microscope had about 30x magnification

modern LMs can reach up to 1000x


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Fig. 5.2a


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Fig. 5.2b


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Fig. 5.2c


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Studying cells – microscopy LM resolution is limited LM resolution (clarity) is limited

about 1 mm due to the wavelength of visible light only about 500 times better than the human eye, even at

maximum magnification

small cells (such as most bacteria) are ~1 mm across, just on the edge of resolution

modifications of LMs and some treatments of cells allow observation of subcellular structure in some cases


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Studying cells – microscopy Resolution of most subcellular structure

requires electron microscopy (EM) electrons have a much smaller wavelength

than light (resolve down to under 1 nm)

magnification up to 250,000x or more

resolution over 500,000 times better than the human eye


Lightmicroscope

Transmissionelectron

microscope

Scanningelectron

microscope

Light beam

Ocular lens

Objective lens

Specimen

Condenser lens

Light source

Electron gunElectron beam

First condenserlens (magnet)

Specimen

Projectorlens (magnet)

Secondaryelectrons

Film or screen

Specimen

Second condenserlens

Scanning coil

Final (objective)lensCathode ray tubesynchronized with

scanning coil

Electrondetector

(a) (b) (c)

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Studying cells – microscopy transmission

electron microscopy (TEM)

electron passes through sample

need very thin samples (100 nm or less thick)

samples embedded in plastic and sliced with a diamond knife


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Studying cells – microscopy

scanning electron microscopy (SEM)

samples are gold-plated

electrons interact with the surface

images have a 3-D appearance


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• Compare and contrast:– LM and EM– SEM and TEM

• Include the terms resolution and magnification in your discussions.


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• Which is SEM, and which TEM? How can you tell?


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• Describe cell fractionation. Why is it done, and how is it done? Include the terms lyse, centrifugation, pellet, and supernatant in your discussion.


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Studying cells – fractionation Cells can be broken and

fractionated to separate cellular components cells are broken (lysed) by

disrupting the cell membrane, often using some sort of detergent

grinding and other physical force may be required, especially if cell walls are present

centrifugation is used to separate cellular components


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Studying cells – fractionation centrifugation is used to

separate cellular components samples are spun at high speeds results in a centrifugal force

thousands to hundreds of thousands times “normal” gravity

after spinning: pellet – what gets packed down to

the bottom (densest material) supernatant – solution above the

pellet


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Studying cells – fractionation cell components will end up in

either the pellet or the supernatant depending on their individual properties and the details of the centrifugation

intact membrane-bound organelles often wind up in pellets (denser once first)

special treatments can determine whether a component ends up in the pellet or supernatant


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Studying cells – fractionation density gradients can be used to subdivide

pellet components based on their density can be used to better separate similar organelles

from each other, for example Golgi complex from ER


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• Describe cell fractionation. Why is it done, and how is it done? Include the terms lyse, centrifugation, pellet, and supernatant in your discussion.


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• How do prokaryotic cells and eukaryotic cells differ from each other in typical size and general organization?

• Describe cytoplasm, cytosol, nucleoplasm, and the general role of membranes in cells.


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Eukaryotic vs. prokaryotic cells prokaryotic cells

do not have internal membranes (thus no nuclear membrane)

main DNA molecule (chromosome) is typically circular; its location is called the nuclear area

other small DNA molecules (plasmids) are often present, found throughout the cell


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Eukaryotic vs. prokaryotic cells prokaryotic cells

plasma membrane is typically enclosed in a cell wall

often the cell wall is covered with a sticky layer of proteins and/or sugars called a capsule

do not completely lack organelles; have:

plasma membrane ribosomes

generally just called bacteria prokaryotic cells are typically

1-10 mm in diameter


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Eukaryotic vs. prokaryotic cells

eukaryotic cells have internal membranes and a distinct, membrane-enclosed nucleus

typically 10-100 mm in diameter


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• How do prokaryotic cells and eukaryotic cells differ from each other in typical size and general organization?

• Describe cytoplasm, cytosol, nucleoplasm, and the general role of membranes in cells.


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• List as many organelles as you can think of. Describe their structures and key functions.

• Draw and label a typical animal cell and a typical plant cell, including organelles.


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• List as many organelles as you can think of. Describe their structures and key functions.

• Draw and label a typical animal cell and a typical plant cell, including organelles.


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How do proteins get outside of a cell?How do proteins get into a cell membrane?How does a cell digest its food?How does a cell commit suicide?Why would a cell commit suicide?


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• Describe the nuclear envelope, nuclear pores, chromatin, chromosomes, and nucleoli in terms of structures and key functions.

• Name something that you KNOW must get out of the nucleus for cells to function.


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Compartments in eukaryotic cells

two general regions inside the cell: cytoplasm and nucleoplasm cytoplasm – everything outside the nucleus and

within the plasma membrane contains fluid cytosol and organelles

nucleoplasm – everything within the nuclear membrane


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Compartments in eukaryotic cells membranes separate cell regions

have nonpolar regions that help form a barrier between aqueous region

allow for some selection in what can cross a membrane (more details later)


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nucleus – the control center of the cell

typically large (~5 mm) and singular

nuclear envelope double membrane

surrounding the nucleus

nuclear pores – protein complexes that cross both membranes and regulate passage


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chromatin – DNA-protein complex

have granular appearance; easily stained for microscopy (“chrom-” = color)

“unpacked” DNA kept ready for message transcription and DNA replication

proteins protect DNA and help maintain structure and function

chromosomes – condensed or “packed” DNA ready for cell division (“-some” = body)


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nucleoli – regions of ribosome subunit assembly

appears different due to high RNA and protein concentration (no membrane)

ribosomal RNA (rRNA) transcribed from DNA there

proteins (imported from cytoplasm) join with rRNA at a nucleolus to form ribosome subunits

ribosome subunits are exported to the cytoplasm through nuclear pores

(note singular: nucleolus; plural: nucleoli)


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• Describe the nuclear envelope, nuclear pores, chromatin, chromosomes, and nucleoli in terms of structures and key functions.

• Name something that you KNOW must get out of the nucleus for cells to function.


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• Describe the structure and function of ribosomes.


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ribosomes – the sites of protein synthesis

ribosomes are granular bodies with three RNA strands and about 75 associated proteins

two main subunits, large and small perform the enzymatic activity for forming peptide bonds, and

serve as the sites of translation of genetic information into protein sequences


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ribosomes – the sites of protein synthesis

prokaryotic ribosome subunits are both smaller than the corresponding subunits in eukaryotes

in eukaryotes the two main subunits are formed separately in the nucleolus and

transported separately to the cytoplasm some are free in the cytoplasm while others are associated with the

endoplasmic reticulum (ER)


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• Describe the structure and function of ribosomes.


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• What is the endomembrane system (include organelle components)?


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• Diagram the cisternal maturation model for the Golgi.

• Diagram and describe the pathway from synthesis to final destination for a secreted protein. Then do the same for a plasma membrane protein.

• Describe the structure and function of: - ER - microbodies in general- vesicles - lysosomes- vacuoles - peroxisomes- Golgi apparatus - glyoxysomes


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endomembrane system endomembrane system – a set of

membranous organelles that interact with each other via vesicles

includes ER, Golgi apparatus, vacuoles, lysosomes, microbodies, and in some definitions the nuclear membrane and the plasma membrane


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endomembrane system endoplasmic reticulum (ER) – membrane

network that winds through the cytoplasm winding nature of the ER provides a lot of surface

area many important cell reactions or sorting functions

require ER membrane surface ER lumen – internal aqueous compartment in ER

separated from the rest of the cytosol typically continuous throughout ER and with the

lumen between the nuclear membranes enzymes within lumen and imbedded in lumen side

of ER differ from those on the other side, thus dividing the functional regions


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endomembrane system smooth ER – primary site

of lipid synthesis, many detoxification reactions, and sometimes other activities

rough ER – ribosomes that attach there insert proteins into the ER lumen as they are synthesized


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endomembrane system rough ER – ribosomes that attach there insert proteins into the ER

lumen as they are synthesized ribosome attachment directed by a signal peptide at the amino end of

the polypeptide (see Ch. 17.4, p.326) a protein/RNA signal recognition particle (SRP) binds to the signal

peptide and pauses translation at the ER the assembly binds to an SRP receptor protein SRP leaves, protein synthesis resumes (now into the ER lumen), and the

signal peptide is cut off


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endomembrane system proteins inserted into the ER lumen may be

membrane bound or free proteins are often modified in the lumen

(example, carbohydrates or lipids added) proteins are transported from the ER in

transport vesicles vesicles – small, membrane-bound sacs

buds off of an organelle (ER or other) contents within the vesicles (often proteins)

transported to another membrane surface vesicles fuses with membranes, delivering

contents to that organelle or outside of the cell


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Fig. 5.16d (TEArt)

Vesiclebuddingfrom roughendoplasmicreticulum

Fusionof vesiclewith Golgiapparatus

Migratingtransportvesicle

Protein

Ribosome


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endomembrane system Golgi apparatus (AKA Golgi complex) – a stack of flattened

membrane sacs (cisternae) where proteins further processed, modified, and sorted [the “post office” of the cell]

not contiguous with ER, and lumen of each sac is usually separate from the rest

has three areas: cis, medial, and trans


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endomembrane system cis face: near ER and receives vesicles from it; current model (cisternal maturation model)

holds that vesicles actually coalesce to continually form new cis cisternae medial region: as a new cis cisterna is produced, the older cisternae mature and move away

from the ER in this region proteins are further modified (making glycoproteins and/or lipoproteins where appropriate,

and ) maturing cisternae may make other products; for example, many polysaccharides are made in the Golgi some materials are needed back a the new cis face and are transported there in vesicles

trans face: nearest to the plasma membrane; a fully matured cisterna breaks into many vesicles that are set up to go to the proper destination (such as the plasma membrane or another organelle) taking their contents with them


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endomembrane system


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endomembrane system lysosomes – small membrane-bound sacs of digestive enzymes

serves to confine the digestive enzymes and their actions

allows maintenance of a better pH for digestion (often about pH 5)

formed by budding from the Golgi apparatus; special sugar attachments to hydrolytic enzymes made in the ER target them to the lysosome


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endomembrane system lysosomes – small membrane-bound sacs of digestive enzymes

used to degrade ingested material, or in some cases dead or damaged organelles

ingested material is found in vesicles that bud in from the plasma membrane; the complex molecules in those vesicles is then digested

can also fuse with dead or damaged organelles and digest them

digested material can then be sent to other parts of the cell for use found in animals, protozoa; debatable in other eukaryotes, but all must have

something like a lysosome


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endomembrane system vacuoles – large membrane-bound sacs

that perform diverse roles; have no internal structure

distinguished from vesicles by size in plants, algae, and fungi, performs many

of the roles that lysosomes perform for animals

central vacuole – typically a single, large sac in plant cells that can be 90% of the cell volume

usually formed from fusion of many small vacuoles in immature plant cells

storage sites for water, food, salts, pigments, and metabolic wastes

important in maintaining turgor pressure tonoplast – membrane of the plant vacuole

food vacuoles – present in most protozoa and some animal cells; usually bud from plasma membrane and fuse with lysosomes for digestion

contractile vacuoles – used by many protozoa for removing excess water


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endomembrane system microbodies – small membrane-

bound organelles that carry out specific cellular functions; examples:

lysosomes could be consider a type of microbody

peroxisomes – sites of many metabolic reactions that produce hydrogen peroxide (H2O2), which is toxic to the rest of the cell

peroxisomes have enzymes to break down H2O2, protecting the cell

peroxisomes are abundant in liver cells in animals and leaf cells in plants

normally found in all eukaryotes example: detoxification of ethanol in

liver cells occurs in peroxisomes glyoxysomes – in plant seeds,

contains enzymes that convert stored fats into sugar


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• What is the endomembrane system (include organelle components)?


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• Diagram the cisternal maturation model for the Golgi.

• Diagram and describe the pathway from synthesis to final destination for a secreted protein. Then do the same for a plasma membrane protein.

• Describe the structure and function of: - ER - microbodies in general- vesicles - lysosomes- vacuoles - peroxisomes- Golgi apparatus - glyoxysomes


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Energy Converting Organelles energy obtained from the environment is

typically chemical energy (in food) or light energy

mitochondria are the organelles where chemical energy is placed in a more useful molecule

chloroplasts are plastids where light energy is captured during photosynthesis


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• Draw a mitochondrion in cross-section and describe its structure and functions.


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Energy Converting Organelles mitochondria – the site of aerobic respiration

recall aerobic respiration:

sugar + oxygen carbon dioxide + water + energy the “energy” is actually stored in ATP


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Energy Converting Organelles - mitochondria

mitochondria have a double membrane

space between membranes = intermembrane space

inner membrane is highly folded, forming cristae; provides a large surface area

inner membrane is also a highly selective barrier

the enzymes that conduct aerobic respiration are found in the inner membrane

inside of inner membrane is the matrix, analogous to the cytoplasm of a cell


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Energy Converting Organelles – mitochondria

mitochondria have their own DNA, and are inherited from the mother only in humans

mitochondria have their own division process, similar to cell division; each cell typically has many mitochondria, which can only arise from mitochondrial division

some cells require more mitochondria than others

mitochondria can leak electrons into the cell, allowing toxic free radicals to form

mitochondria play a role in initiating apoptosis (programmed cell death)


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• Draw a mitochondrion in cross-section and describe its structure and functions.


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• Draw a chloroplast in cross-section and describe its structure and functions.


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Energy Converting Organelles plastids – organelles of plants and algae that produce and

store food include amyloplasts (for starch storage), chromoplasts (for color,

often found in petals and fruits), and chloroplasts (for photosynthesis)

like mitochondria, have their own DNA (typically a bit larger and more disk-shaped than mitochondria, however)

derive from undifferentiated proplastids, although role of mature plastids can sometimes change

numbers and types of plastids vary depending on the organism and the role of the cell


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Energy Converting Organelles – plastids (chloroplasts)

chloroplasts get their green color from chlorophyll, the main light harvesting pigments involved in photosynthesis

carbon dioxide + water + light energy food (glucose) + oxygen

chloroplasts have a double membrane the region within the inner membrane is the stroma; it is analogous to the mitochondrial matrix inner membrane is contiguous with an interconnected series of flat sacks called thylakoids that are

grouped in stacks called grana the thylakoids enclose aqueous regions called the thylakoid lumen

chlorophyll is found in the thylakoid membrane, and the reactions of photosynthesis take place there and in the stroma

carotenoids in the chloroplast serve as accessory pigments for photosynthesis


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• Draw a chloroplast in cross-section and describe its structure and functions.


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• Describe the endosymbiont theory. Include evidence for it, including predictions that have proven true.


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Energy Converting Organellesendosymbiont theory

mitochondria and plastids evolved from prokaryotic cells that took residence in larger cells and eventually lost their independence

the cells containing the endosymbionts became dependent upon them for food processing, and in turn provide them with a protected and rich environment (a mutualistic relationship)


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supporting evidence the size scale is right - mitochondria and plastids are on the high end

of the size of typical bacteria

endosymbionts also have their own DNA and their own “cell” division; in many ways they act like bacterial cells

the DNA sequence and arrangement (circular chromosomes)of endosymbionts is closer to that of bacteria than to that found in the eukaryotic nucleus

endosymbionts have their own ribosomes, which are much like bacterial ribosomes

there are other known, more modern endosymbiotic relationships: algae in corals, bacteria within protozoans in termite guts


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some genes appear to have been shuttled out of the endosymbionts to the nucleus

many of the proteins used by endosymbionts are actually encoded by nuclear genes and translated in the cytoplasm (or on rough ER) and transported to the endosymbionts

DNA sequencing of endosymbionts is being used to trace the evolutionary history of the endosymbionts

appears that endosymbiosis began about 1.5 to 2 billion years ago (around when the first eukaryotic cells appeared)

mitochondria appear to have a monophyletic origin (one initial endosymbiotic event, giving rise to all mitochondria in eukaryotic cells today)

plastids appear to have a polyphyletic origin (more than one initial endosymbiotic event giving rise to different plastid lines present today in algae and plants)


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• Describe the endosymbiont theory. Include evidence for it, including predictions that have proven true.


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• What are the functions of the cytoskeleton?

• What are the three main types of cytoskeleton? Describe the structure and function(s) of each type.


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• Describe the structure and function(s) of:

– motor proteins– MTOCs– centrosomes– centrioles– cilia and flagella


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Cytoskeleton eukaryotic cells typically have a size and shape that is maintained

the cytoskeleton is a dense network of protein fibers that provides needed structural support

the network also has other functions a scaffolding for organelles cell movement and cell division (dynamic nature to the protein fibers is involved

here) transport of materials within the cell

the cytoskeleton is composed of three types of protein filaments: microtubules, microfilaments, and intermediate filaments


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microtubules are the thickest filaments of the cytoskeleton

hollow, rod -shaped cylinders about 25 nm in diameter

made of a-tubulin and b-tubulin dimers

dimers can be added or removed from either end (dynamic nature)

one end (plus end) adds dimers more rapidly than the minus end

can be anchored, where an end is attached to something and can no longer add or lose dimers


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microtubule-organizing centers (MTOCs) serve as anchors

centrosome in animal cells

centrosome has two centrioles in a perpendicular arrangement

centrioles have a 9x3 structure: 9 sets of 3 attached microtubules forming a hollow cylinder

used for assembly of microtubules for use throughout the cell


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microtubule-organizing centers (MTOCs) serve as anchors

centrioles are duplicated before cell division

play an organizing role for microtubule spindles in cell division

other eukaryotes must use some alternative MTOC during cell division; still incompletely described


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microtubules are involved in moving organelles

motor proteins (such as kinesin or dynein) attach to organelle and to microtubule

using ATP as an energy source, the motor proteins change shape and thus produce movement

microtubule essentially acts as a track for the motor protein

motor proteins are directional; kinesin moves toward the plus end, dynein away from it


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cilia and flagella are made of microtubules

thin, flexible projections from cells used in cell movement, or to move

things along the cell surface share the same basic structure;

called cilia if short (2-10 mm typically) and flagella if long (typically 200 mm)

central stalk covered by cell membrane extension, and anchored to a basal body

9x3 structure stalk has two inner microtubules

surrounded by nine attached pairs of microtubules

9+2 arrangement


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cilia and flagella are made of microtubules

stalk has two inner microtubules surrounded by nine attached pairs of microtubules

9+2 arrangement

dynein attached to the outer pairs actually fastens the pair to its neighboring pair

dynein motor function causes relative sliding of filaments; this produces bending movement of the cilium or flagellum


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microfilaments are solid filaments about 7 nm in diameter

composed of two entwined chains of actin monomers

linker proteins cross-link the actin chains with each other and other actin associated proteins

actin monomers can be added to lengthen the microfilament or removed to shorten it; this can be used to generate movement


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microfilaments are solid filaments about 7 nm in diameter

important in muscle cells; in conjunction with myosin, they are responsible for muscle contraction

used for many cell movements such as:

contractile structures forming cell extensions “pinching in” during cell division


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intermediate filaments typically just a bit wider than microfilaments, this is

the catch-all group for cytoskeletal filaments composed of a variety of other proteins

the types of proteins involved differ depending on cell types and on the organism; apparently limited to animal cells and protozoans


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intermediate filaments not easily disassembled, thus more permanent a web of intermediate filaments reinforces cell shape and

positions of organelles (they give structural stability) prominent in cells that withstand mechanical stress form the most insoluble part of the cell


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• What are the functions of the cytoskeleton?

• What are the three main types of cytoskeleton? Describe the structure and function(s) of each type.


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• Describe the structure and function(s) of:

– motor proteins– MTOCs– centrosomes– centrioles– cilia and flagella


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• Describe the outer part and outside interface of a:

– typical prokaryotic cell– typical plant cell– typical fungal cell– typical animal cell

• Diagram and describe the animal cell glycocalyx and ECM interaction (include collagen, fibronectin, and integrin).


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Outside the Cell Most prokaryotes have a cell wall, an outer envelope, and a

capsule (capsule is also called glycocalyx or cell coat)

Most eukaryotic cells produce materials that are deposited outside the plasma membrane but that remain associated with it


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Outside the Cell plants have thick, defined cell

walls made primarily of cross-linked cellulose fibers

growing plant cells secrete a primary cell wall, which is thin and flexible

growth ends primary cell wall is usually thickened and solidified

often a secondary cell wall is then produced between the primary cell wall and the plasma membrane

still contains cellulose typically has more strengthening

material (for example, lignin in wood)


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Outside the Cell

fungi typically have thinner cell walls than plants, made primarily of cross-linked chitin fibers


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Outside the Cell animals do not have cell walls, but their cells secrete

varying amounts of compounds that can produce a glycocalyx and an extracellular matrix (ECM)

glycocalyx: polysaccharides attached to proteins and lipids on the outer surface of the plasma membrane

typically functions in cell recognition and communication, cell contacts, and structural reinforcement

often works through direct interaction with the ECM


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Outside the Cell ECM: a gel of carbohydrates and fibrous proteins;

several different molecules can be involved main structural protein is tough, fibrous collagen fibronectins are glycoproteins in the ECM that often

bind to both collagen and integrins

integrins are proteins in the plasma membrane that typically receive signals from the ECM


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• Describe the outer part and outside interface of a:

– typical prokaryotic cell– typical plant cell– typical fungal cell– typical animal cell

• Diagram and describe the animal cell glycocalyx and ECM interaction (include collagen, fibronectin, and integrin).


Chapter 6: A Tour of the Cell

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Transcript of Chapter 6: A Tour of the Cell