Chapter 6: A Tour of the Cell

BIOL 1020 – CHAPTER 6 LECTURE NOTES Chapter 6: A Tour of the Cell 1. What are the 3 main tenets of cell theory? 2. What are the major lines of eviden...
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BIOL 1020 – CHAPTER 6 LECTURE NOTES

Chapter 6: A Tour of the Cell 1. What are the 3 main tenets of cell theory? 2. What are the major lines of evidence that all presently living cells have a common origin? 3. What is surface area to volume ratio, and why is it an important consideration for cells? 4. What (usually) happens to surface area to volume ratio as cells grow larger? 5. Compare and contrast:  LM and EM  SEM and TEM Include the terms resolution and magnification in your discussions. 6. Describe cell fractionation. Why is it done, and how is it done? Include the terms lyse, centrifugation, pellet, and supernatant in your discussion. 7. How do prokaryotic cells and eukaryotic cells differ from each other in typical size and general organization? 8. Describe cytoplasm, cytosol, nucleoplasm, and the general role of membranes in cells. 9. List as many organelles as you can think of. Describe their structures and key functions. 10. Draw and label a typical animal cell and a typical plant cell, including organelles. 11. Describe the nuclear envelope, nuclear pores, chromatin, chromosomes, and nucleoli in terms of structures and key functions. 12. Name something that you KNOW must get out of the nucleus for cells to function. 1 of 12

BIOL 1020 – CHAPTER 6 LECTURE NOTES

13. Describe the structure and function of ribosomes. 14. What is the endomembrane system (include organelle components)? 15. Diagram and describe the pathway from synthesis to final destination for a secreted protein. Then do the same for a plasma membrane protein. 16. Diagram the cisternal maturation model for the Golgi. 17.        

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

18. Draw a mitochondrion in cross-section and describe its structure and functions. 19. Draw a chloroplast in cross-section and describe its structure and functions. 20. Describe the endosymbiont theory. Include evidence for it, including predictions that have proven true. 21. What are the functions of the cytoskeleton? 22. What are the three main types of cytoskeleton? Describe the structure and function(s) of each type. 23.    

Describe the structure and function(s) of: motor proteins MTOCs centrosomes centrioles 2 of 12

BIOL 1020 – CHAPTER 6 LECTURE NOTES

 cilia and flagella 24. Describe the outer part and outside interface of a: A. typical prokaryotic cell B. typical plant cell C. typical fungal cell D. typical animal cell 25. Diagram and describe the animal cell glycocalyx and ECM interaction (include collagen, fibronectin, and integrin).

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

II.

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

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.

2.

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

cell shape varies depending both on function and surface area requirements 3 of 12

III.

BIOL 1020 – CHAPTER 6 LECTURE NOTES 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 LM, at about 30x mag

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 (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 4 of 12

V.

2.

BIOL 1020 – CHAPTER 6 LECTURE NOTES other small DNA molecules (plasmids) are often present, found throughout the cell

3.

plasma membrane is usually enclosed in a cell wall that is often covered with a capsule (layer of proteins and/or sugars)

4.

do not completely lack organelles; the plasma membrane and ribosomes are both present and are considered organelles

5.

AKA bacteria, prokaryotic cells are typically 1-10 m in diameter

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

VI.

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)

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

VII.

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

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, serve as the sites of translation

B. prokaryotic ribosome subunits are both smaller than the corresponding subunits in eukaryotes 5 of 12

BIOL 1020 – CHAPTER 6 LECTURE NOTES 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

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 6 of 12



BIOL 1020 – CHAPTER 6 LECTURE NOTES 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



F.

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

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

4.



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

5.

contractile vacuoles – used by many protozoa for removing excess water

G. microbodies – small membrane-bound organelles that carry out specific cellular functions; examples: 7 of 12

1.

BIOL 1020 – CHAPTER 6 LECTURE NOTES 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 cell

3. IX.



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

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

4.

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

5.

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 8 of 12

4.

BIOL 1020 – CHAPTER 6 LECTURE NOTES 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



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) 9 of 12



BIOL 1020 – CHAPTER 6 LECTURE NOTES 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

2.

made of -tubulin and -tubulin dimers

3.

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

4.

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

5.

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

6.

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 10 of 12

8.

BIOL 1020 – CHAPTER 6 LECTURE NOTES 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; 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

XI.

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

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 11 of 12

1.

BIOL 1020 – CHAPTER 6 LECTURE NOTES 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) 



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

12 of 12