BIOL 1020 – CHAPTER 6 LECTURE NOTES
Chapter 6: A tour of the Cell
I.
Cell theory
A. All living organisms are composed of cells
1. smallest “building blocks” of all multicellular organisms
2. all cells are enclosed by a surface membrane that separates them from other cells and from their environment
3. specialized structures with the cell are called organelles; many are membrane-bound
B. Today, all new cells arise from existing cells
C. All presently living cells have a common origin
1. all cells have basic structural and molecular similarities
2. all cells share similar energy conversion reactions
3. all cells maintain and transfer genetic information in DNA
4. the genetic code is essentially universal
II.
Cell organization and homeostasis
A. Plasma membrane surrounds cells and separates their contents from the external environment
B. Cells are heterogeneous mixtures, with specialized regions and structures (such as organelles)
C. Cell size is limited
1. 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
 thus, cells need a high surface area to volume ratio, but volume increases faster than surface area as cells grow larger
2. cell shape varies depending both on function and surface area requirements
III.
Studying cells – microscopy and fractionation
A. Most cells are large enough to be resolved from each other with light microscopes (LM)
1. cells were discovered by Robert Hooke in 1665; he saw the remains of cell walls in cork with a LMs, at about 30x
magnification
2. modern LMs can reach up to 1000x
3. LM resolution (clarity) is limited to about 1 m due to the wavelength of visible light (thus only about 500 times better
than the human eye, even at maximum magnification)
4. small cells (such as most bacteria) are about 1 m across, just on the edge of resolution
5. some modifications of LMs and some treatments of cells allow observation of subcellular structure in some cases
B. Resolution of most subcellular structure requires electron microscopy (EM)
1. electrons have a much smaller wavelength than light (resolve down to under 1 nm)
2. magnification up to 250,000x or more and resolution over 500,000 times better than the human eye
3. includes transmission (TEM) and scanning (SEM) forms
 transmission - electron passes through sample; need very thin samples (100 nm or less thick); samples embedded in
plastic and sliced with a diamond knife
 scanning – samples are gold-plated; electrons interact with the surface; images have a 3-D appearance
C. Cells can be broken and fractionated to separate cellular components for study
1. cells are broken (lysed) by disrupting the cell membrane, often using some sort of detergent
2. grinding and other physical force may be required, especially if cell walls are present
3. centrifugation is used to separate cellular components
 using a centrifuge, samples are spun at high speeds, resulting in exposure to a centrifugal force of thousands to
hundreds of thousands times gravity (example, 500,000 x G)
 results in a pellet and supernatant; cell components will be in one or the other depending on their individual
properties; intact membrane-bound organelles often wind up in pellets, depending on their density and the
centrifugal force reached (more dense = more likely in pellet)
 special treatments can determine whether a component ends up in the pellet or supernatant
 density gradients can also be used to subdivide pellet components based on their density; this can be used to separate
organelles from each other, for example Golgi apparatus from ER
IV.
Eukaryotic vs. prokaryotic cells
A. eukaryotic cells have internal membranes and a distinct, membrane-enclosed nucleus; typically 10-100 m in diameter
B. prokaryotic cells do not have internal membranes (thus no nuclear membrane)
1. main DNA molecule (chromosome) is typically circular; its location is called the nuclear area
2. other small DNA molecules (plasmids) are often present, found throughout the cell
3. plasma membrane is typically enclosed in a cell wall
4. often the cell wall is enclosed in an outer envelope or outer membrane
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5. do not completely lack organelles; the plasma membrane and ribosomes are both present and are considered organelles
6. AKA bacteria, prokaryotic cells are typically 1-10 m in diameter
V.
Compartments in eukaryotic cells (cell regions, organelles)
A. two general regions inside the cell: cytoplasm and nucleoplasm
1. cytoplasm – everything outside the nucleus and within the plasma membrane
 contains fluid cytosol and organelles
2. nucleoplasm – everything within the nuclear membrane
B. membranes separate cell regions
1. have nonpolar regions that help form a barrier between aqueous regions
2. allow for some selection in what can cross a membrane (more details later)
VI.
nucleus – the “control center” of the cell
A. typically large (~5 m) and singular
B. nuclear envelope
1. double membrane surrounding the nucleus
2. nuclear pores – protein complexes that cross both membranes and regulate passage
C. chromatin – DNA-protein complex
1. have granular appearance; easily stained for microscopy (“chrom-” = color)
2. “unpacked” DNA kept ready for message transcription and DNA replication
3. proteins protect DNA and help maintain structure and function
4. chromosomes – condensed or “packed” DNA ready for cell division (“-some” = body)
D. nucleoli – regions of ribosome subunit assembly
1. appears different due to high RNA and protein concentration (no membrane)
2. ribosomal RNA (rRNA) transcribed from DNA there
3. proteins (imported from cytoplasm) join with rRNA at a nucleolus to from ribosome subunits
4. ribosome subunits are exported to the cytoplasm through nuclear pores
VII. ribosomes – the sites of protein synthesis
A. ribosomes are granular bodies with three RNA strands and about 75 associated proteins
1. two main subunits, large and small
2. perform the enzymatic activity for forming peptide bonds, and serve as the sites of translation of genetic information into
protein sequences
B. prokaryotic ribosome subunits are both smaller than the corresponding subunits in eukaryotes
C. in eukaryotes
1. the two main subunits are formed separately in the nucleolus and transported separately to the cytoplasm
2. some are free in the cytoplasm while others are associated with the endoplasmic reticulum (ER)
VIII. endomembrane system – a set of membranous organelles that interact with each other via vesicles
A. includes ER, Golgi apparatus, vacuoles, lysosomes, microbodies, and in some definitions the nuclear membrane and the
plasma membrane
B. endoplasmic reticulum (ER) – membrane network that winds through the cytoplasm
1. winding nature of the ER provides a lot of surface area
2. many important cell reactions or sorting functions require ER membrane surface
3. 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
4. smooth ER – primary site of lipid synthesis, many detoxification reactions, and sometimes other activities
5. 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
 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
C. vesicles – small, membrane-bound sacs
1. buds off of an organelle (ER or other)
2. contents within the vesicles (often proteins) transported to another membrane surface
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3. vesicles fuses with membranes, delivering contents to that organelle or outside of the cell
D. 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]
1. not contiguous with ER, and lumen of each sac is usually separate from the rest
2. has three areas: cis, medial, and trans
 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
E. lysosomes – small membrane-bound sacs of digestive enzymes
1. serves to confine the digestive enzymes and their actions
2. allows maintenance of a better pH for digestion (often about pH 5)
3. formed by budding from the Golgi apparatus; special sugar attachments to hydrolytic enzymes made in the ER target
them to the lysosome
4. 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
5. digested material can then be sent to other parts of the cell for use
6. found in animals, protozoa; debatable in other eukaryotes, but all must have something like a lysosome
F. vacuoles – large membrane-bound sacs that perform diverse roles; have no internal structure
1. distinguished from vesicles by size
2. in plants, algae, and fungi, performs many of the roles that lysosomes perform for animals
3. 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
4. food vacuoles – present in most protozoa and some animal cells; usually bud from plasma membrane and fuse with
lysosomes for digestion
5. contractile vacuoles – used by many protozoa for removing excess water
G. microbodies – small membrane-bound organelles that carry out specific cellular functions; examples:
1. lysosomes could be consider a type of microbody
2. peroxisomes – sites of many metabolic reactions that produce hydrogen peroxide (H 2O2), 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
3. glyoxysomes – in plant seeds, contains enzymes that convert stored fats into sugar
IX.
energy converting organelles
A. energy obtained from the environment is typically chemical energy (in food) or light energy
B. mitochondria are the organelles where chemical energy is placed in a more useful molecule, and chloroplasts are plastids
where light energy is captured during photosynthesis
C. mitochondria –the site of aerobic respiration
1. recall aerobic respiration: sugar + oxygen  carbon dioxide + water + energy
2. the “energy” is actually stored in ATP
3. 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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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
6. some cells require more mitochondria than others
7. mitochondria can leak electrons into the cell, allowing toxic free radicals to form
8. mitochondria play a role in initiating apoptosis (programmed cell death)
D. plastids – organelles of plants and algae that produce and store food
1. include amyloplasts (for starch storage), chromoplasts (for color, often found in petals and fruits), and chloroplasts (for
photosynthesis)
2. like mitochondria, have their own DNA (typically a bit larger and more disk-shaped than mitochondria, however)
3. derive from undifferentiated proplastids, although role of mature plastids can sometimes change
4. numbers and types of plastids vary depending on the organism and the role of the cell
5. chloroplasts get their green color from chlorophyll, the main light harvesting pigments involved in photosynthesis
(carbon dioxide + water + light energy  food(glucose) + oxygen)
6. 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
E. endosymbiont theory
1. states that mitochondria and plastids evolved from prokaryotic cells that took residence in larger cells and eventually lost
their independence
2. 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)
3. 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
 the genetic code used by endosymbionts is more like that of bacteria than of eukaryotes
 there are other known, more modern endosymbiotic relationships: algae in corals, bacteria within protozoans in
termite guts
4. some genes appear to have been shuttled out of the endosymbionts to the nucleus
5. 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
6. 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 (several initial endosymbiotic events giving rise to different plastid
lines present today in algae and plants)
7. some argue that endosymbionts were simply derived within the early eukaryotic cells, along with the nuclear membrane
and the proliferation of other membrane surfaces common in eukaryotes but not prokaryotes
X.
Cytoskeleton
A. eukaryotic cells typically have a size and shape that is maintained
1. the cytoskeleton is a dense network of protein fibers that provides needed structural support
2. 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
B. the cytoskeleton is composed of three types of protein filaments: microtubules, microfilaments, and intermediate filaments
C. microtubules are the thickest filaments of the cytoskeleton
1. hollow, rod -shaped cylinders about 25 nm in diameter
4.
5.
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made of -tubulin and -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
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
 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)
7. microtubules are involved in moving organelles
 motor proteins (such as kinesin and 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
8. 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 m typically) and flagella if long (typically 200 m)
 central stalk covered by cell membrane extension, and anchored to a basal body
 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
 the basal body is very much like the centriole
 has a 9x3 structure
 replicates itself
D. microfilaments are solid filaments about 7 nm in diameter
1. composed of two entwined chains of actin monomers
2. linker proteins cross-link the actin chains with each other and other actin associated proteins
3. actin monomers can be added to lengthen the microfilament or removed to shorten it; this can be used to generate
movement
4. important in muscle cells; in conjunction with myosin, they are responsible for muscle contraction
5. also associate with myosin in many cells to form contractile structures, such as used in cell division
E. intermediate filaments
1. typically just a bit wider than microfilaments, this is the catch-all group for cytoskeletal filaments composed of a variety
of other proteins
2. the types of proteins involved differ depending on cell types and on the organism; apparently limited to animal cells and
protozoans
3. not easily disassembled, thus more permanent
4. a web of intermediate filaments reinforces cell shape and positions of organelles (they give structural stability)
5. prominent in cells that withstand mechanical stress
6. form the most insoluble part of the cell
XI.
Outside the cell
A. Most prokaryotes have a cell wall, an outer envelope, and a capsule (capsule is also called glycocalyx or cell coat)
B. Most eukaryotic cells produce materials that are deposited outside the plasma membrane but that remain associated with it
1. 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
 after a plant cell stops growing, the primary cell wall is usually thickened and solidified, or a secondary cell wall is
produced between the primary cell wall and the plasma membrane
 secondary cell walls still contain cellulose, but typically have other material as well that strengthens them further (for
example, lignin in wood)
2. fungi typically have thinner cell walls than plants, made primarily of cross-linked chitin fibers
3. animals do not have cell walls, but their cells secrete varying amounts of compounds that can produce a glycocalyx and
an extracellular matrix (ECM)
2.
3.
4.
5.
6.
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XII.
BIOL 1020 – CHAPTER 6 LECTURE NOTES
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
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
Specialized contacts (junctions) between cells
cell junctions typically connect cells and can allow special transport between connected cells
A. anchoring junctions hold cells tightly together; one common type in animals is the desmosome
 desmosomes form strong bonds between cytoskeletons,of adjacent cells and hold them together
 materials can still pass in the space between cells with anchoring junctions
 NOT involved in the transport of materials between cells
B. tight junctions between some animal cells are used to seal off body cavities
 cell plasma membranes are adjacent to each other and held together by a tight seal
 materials cannot pass between cells held together by tight junctions
 NOT involved in the transport of materials between cells
C. gap junctions between animal cells act as selective pores
 proteins connect the cells
 those proteins are grouped in cylinders of 6 subunits
 the cylinder can be opened to form a small pore (less than 2 nm), through which small molecules can pass
D. plasmodesmata act as selective pores between plant cells
 plant cell walls perform the functions of tight junctions and desmosomes
 plant cell walls form a barrier to cell-to-cell communication that must be breached by the functional
equivalent of a gap junction
 plasmodesmata are relatively wide channels (20-45 nm) across the cell wall between adjacent cells; they
actually connect the plasma membranes of the two cells, and allow exchange of some materials between the
cells
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