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.
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
· 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
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 LM, at about 30x mag
2. modern LMs can reach up to 1000x
3. LM resolution (clarity) is limited to about 1 mm 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 mm 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 mm 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 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 mm 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 mm) 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, serve as the sites of translation
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
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 (H2O2), which is toxic to 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