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. Chapter 6: A Tour of the Cell Cell theory Cell theory Cell organization and homeostasis Cell organization and homeostasis Studying cells – microscopy.

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Presentation on theme: ". Chapter 6: A Tour of the Cell Cell theory Cell theory Cell organization and homeostasis Cell organization and homeostasis Studying cells – microscopy."— Presentation transcript:

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

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

3 . What are the main tenets of cell theory? What are the major lines of evidence that all presently living cells have a common origin?

4 . Cell theory All living organisms are composed of cells All living organisms are composed of cells smallest “building blocks” of all multicellular organisms 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 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 specialized structures with the cell are called organelles; many are membrane-bound

5 . Cell theory Today, all new cells arise from existing cells Today, all new cells arise from existing cells All presently living cells have a common origin All presently living cells have a common origin all cells have basic structural and molecular similarities all cells have basic structural and molecular similarities all cells share similar energy conversion reactions all cells share similar energy conversion reactions all cells maintain and transfer genetic information in DNA all cells maintain and transfer genetic information in DNA the genetic code is essentially universal the genetic code is essentially universal

6 . What are the main tenets of cell theory? What are the major lines of evidence that all presently living cells have a common origin?

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

8 . 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?

9 . Cell organization and homeostasis Plasma membrane surrounds cells and separates their contents from the external environment Plasma membrane surrounds cells and separates their contents from the external environment Cells are heterogeneous mixtures, with specialized regions and structures (such as organelles) Cells are heterogeneous mixtures, with specialized regions and structures (such as organelles)

10 . Cell organization and homeostasis Cell size is limited Cell size is limited surface area to volume ratio puts a limit on cell size surface area to volume ratio puts a limit on cell size food and/or other materials must get into the cell food and/or other materials must get into the cell waste products must be removed from the cell waste products must be removed from the cell cells need a high surface area to volume ratio 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 BUT volume increases faster than surface area as cells grow larger…so cells usually must divide

11 . Fig. 5.4

12 .

13 . Cell organization and homeostasis cell shape varies depending both on function and surface area requirements cell shape varies depending both on function and surface area requirements

14 . 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?

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

16 . Compare and contrast: –LM and EM –SEM and TEM Include the terms resolution and magnification in your discussions.

17 . Studying cells – microscopy Most cells are large enough to be resolved from each other with light microscopes (LM) Most cells are large enough to be resolved from each other with light microscopes (LM) cells were discovered by Robert Hooke in 1665 cells were discovered by Robert Hooke in 1665 he saw the remains of cell walls in cork with a LM he saw the remains of cell walls in cork with a LM his microscope had about 30x magnification his microscope had about 30x magnification modern LMs can reach up to 1000x modern LMs can reach up to 1000x

18 . Fig. 5.2a

19 . Fig. 5.2b

20 . Fig. 5.2c

21 . Studying cells – microscopy LM resolution is limited LM resolution is limited LM resolution (clarity) is limited LM resolution (clarity) is limited about 1  m about 1  m due to the wavelength of visible light due to the wavelength of visible light only about 500 times better than the human eye, even at maximum magnification only about 500 times better than the human eye, even at maximum magnification small cells (such as most bacteria) are ~1  m across, just on the edge of resolution small cells (such as most bacteria) are ~1  m across, just on the edge of resolution modifications of LMs and some treatments of cells allow observation of subcellular structure in some cases modifications of LMs and some treatments of cells allow observation of subcellular structure in some cases

22 . Studying cells – microscopy Resolution of most subcellular structure requires electron microscopy (EM) Resolution of most subcellular structure requires electron microscopy (EM) electrons have a much smaller wavelength than light (resolve down to under 1 nm) electrons have a much smaller wavelength than light (resolve down to under 1 nm) magnification up to 250,000x or more magnification up to 250,000x or more resolution over 500,000 times better than the human eye resolution over 500,000 times better than the human eye

23 Light microscope Transmission electron microscope Scanning electron microscope Light beam Ocular lens Objective lens Specimen Condenser lens Light source Electron gun Electron beam First condenser lens (magnet) Specimen Projector lens (magnet) Secondary electrons Film or screen Specimen Second condenser lens Scanning coil Final (objective) lens Cathode ray tube synchronized with scanning coil Electron detector (a)(b)(c)

24 . Studying cells – microscopy transmission electron microscopy (TEM) transmission electron microscopy (TEM) electron passes through sample electron passes through sample need very thin samples (100 nm or less thick) need very thin samples (100 nm or less thick) samples embedded in plastic and sliced with a diamond knife samples embedded in plastic and sliced with a diamond knife

25 . Studying cells – microscopy scanning electron microscopy (SEM) scanning electron microscopy (SEM) samples are gold-plated samples are gold-plated electrons interact with the surface electrons interact with the surface images have a 3-D appearance images have a 3-D appearance

26 .

27 . Compare and contrast: –LM and EM –SEM and TEM Include the terms resolution and magnification in your discussions.

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

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

30 . Studying cells – fractionation Cells can be broken and fractionated to separate cellular components 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 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 grinding and other physical force may be required, especially if cell walls are present centrifugation is used to separate cellular components centrifugation is used to separate cellular components

31 . Studying cells – fractionation centrifugation is used to separate cellular components centrifugation is used to separate cellular components samples are spun at high speeds samples are spun at high speeds results in a centrifugal force thousands to hundreds of thousands times “normal” gravity results in a centrifugal force thousands to hundreds of thousands times “normal” gravity after spinning: after spinning: pellet – what gets packed down to the bottom (densest material) pellet – what gets packed down to the bottom (densest material) supernatant – solution above the pellet supernatant – solution above the pellet

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

33 . Studying cells – fractionation density gradients can be used to subdivide pellet components density gradients can be used to subdivide pellet components based on their density based on their density can be used to better separate similar organelles from each other, for example Golgi complex from ER can be used to better separate similar organelles from each other, for example Golgi complex from ER

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

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

36 . 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.

37 . Eukaryotic vs. prokaryotic cells prokaryotic cells do not have internal membranes (thus no nuclear membrane) 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 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 other small DNA molecules (plasmids) are often present, found throughout the cell

38 . Eukaryotic vs. prokaryotic cells prokaryotic cells prokaryotic cells plasma membrane is typically enclosed in a cell wall 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 often the cell wall is covered with a sticky layer of proteins and/or sugars called a capsule do not completely lack organelles; have: do not completely lack organelles; have: plasma membrane plasma membrane ribosomes ribosomes generally just called bacteria generally just called bacteria prokaryotic cells are typically 1-10  m in diameter prokaryotic cells are typically 1-10  m in diameter

39 . Eukaryotic vs. prokaryotic cells eukaryotic cells have internal membranes and a distinct, membrane- enclosed nucleus eukaryotic cells have internal membranes and a distinct, membrane- enclosed nucleus typically 10-100  m in diameter typically 10-100  m in diameter

40 . 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.

41 . 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.

42 .

43 .

44 . 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.

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

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

47 . 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.

48 . Compartments in eukaryotic cells two general regions inside the cell: cytoplasm and nucleoplasm two general regions inside the cell: cytoplasm and nucleoplasm cytoplasm – everything outside the nucleus and within the plasma membrane cytoplasm – everything outside the nucleus and within the plasma membrane contains fluid cytosol and organelles contains fluid cytosol and organelles nucleoplasm – everything within the nuclear membrane nucleoplasm – everything within the nuclear membrane

49 . Compartments in eukaryotic cells membranes separate cell regions membranes separate cell regions have nonpolar regions that help form a barrier between aqueous region have nonpolar regions that help form a barrier between aqueous region allow for some selection in what can cross a membrane (more details later) allow for some selection in what can cross a membrane (more details later)

50 . nucleus – the control center of the cell typically large (~5  m) and singular typically large (~5  m) and singular nuclear envelope nuclear envelope double membrane surrounding the nucleus double membrane surrounding the nucleus nuclear pores – protein complexes that cross both membranes and regulate passage nuclear pores – protein complexes that cross both membranes and regulate passage

51 . nucleus – the control center of the cell chromatin – DNA-protein complex chromatin – DNA-protein complex have granular appearance; easily stained for microscopy (“chrom-” = color) have granular appearance; easily stained for microscopy (“chrom-” = color) “unpacked” DNA kept ready for message transcription and DNA replication “unpacked” DNA kept ready for message transcription and DNA replication proteins protect DNA and help maintain structure and function proteins protect DNA and help maintain structure and function chromosomes – condensed or “packed” DNA ready for cell division (“-some” = body) chromosomes – condensed or “packed” DNA ready for cell division (“-some” = body)

52 . nucleus – the control center of the cell nucleoli – regions of ribosome subunit assembly nucleoli – regions of ribosome subunit assembly appears different due to high RNA and protein concentration (no membrane) appears different due to high RNA and protein concentration (no membrane) ribosomal RNA (rRNA) transcribed from DNA there ribosomal RNA (rRNA) transcribed from DNA there proteins (imported from cytoplasm) join with rRNA at a nucleolus to form ribosome subunits proteins (imported from cytoplasm) join with rRNA at a nucleolus to form ribosome subunits ribosome subunits are exported to the cytoplasm through nuclear pores ribosome subunits are exported to the cytoplasm through nuclear pores (note singular: nucleolus; plural: nucleoli)

53 . 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.

54 . Describe the structure and function of ribosomes.

55 . ribosomes – the sites of protein synthesis ribosomes are granular bodies with three RNA strands and about 75 associated proteins ribosomes are granular bodies with three RNA strands and about 75 associated proteins two main subunits, large and small 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 perform the enzymatic activity for forming peptide bonds, and serve as the sites of translation of genetic information into protein sequences

56 . ribosomes – the sites of protein synthesis prokaryotic ribosome subunits are both smaller than the corresponding subunits in eukaryotes prokaryotic ribosome subunits are both smaller than the corresponding subunits in eukaryotes in eukaryotes in eukaryotes the two main subunits are formed separately in the nucleolus and transported separately to the cytoplasm 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) some are free in the cytoplasm while others are associated with the endoplasmic reticulum (ER)

57 . Describe the structure and function of ribosomes.

58 . What is the endomembrane system (include organelle components)?

59 . Diagram the cisternal maturation model for the Golgi.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.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:Describe the structure and function of: - ER- microbodies in general - vesicles- lysosomes - vacuoles- peroxisomes - Golgi apparatus- glyoxysomes

60 . endomembrane system endomembrane system – a set of membranous organelles that interact with each other via vesicles 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 includes ER, Golgi apparatus, vacuoles, lysosomes, microbodies, and in some definitions the nuclear membrane and the plasma membrane

61 . endomembrane system endoplasmic reticulum (ER) – membrane network that winds through the cytoplasm endoplasmic reticulum (ER) – membrane network that winds through the cytoplasm winding nature of the ER provides a lot of surface area winding nature of the ER provides a lot of surface area many important cell reactions or sorting functions require ER membrane surface many important cell reactions or sorting functions require ER membrane surface ER lumen – internal aqueous compartment in ER ER lumen – internal aqueous compartment in ER separated from the rest of the cytosol separated from the rest of the cytosol typically continuous throughout ER and with the lumen between the nuclear membranes 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 enzymes within lumen and imbedded in lumen side of ER differ from those on the other side, thus dividing the functional regions

62 . endomembrane system smooth ER – primary site of lipid synthesis, many detoxification reactions, and sometimes other activities 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 rough ER – ribosomes that attach there insert proteins into the ER lumen as they are synthesized

63 . endomembrane system rough ER – ribosomes that attach there insert proteins into the ER lumen as they are synthesized 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) 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 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 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 SRP leaves, protein synthesis resumes (now into the ER lumen), and the signal peptide is cut off

64 . endomembrane system proteins inserted into the ER lumen may be membrane bound or free 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 often modified in the lumen (example, carbohydrates or lipids added) proteins are transported from the ER in transport vesicles proteins are transported from the ER in transport vesicles vesicles – small, membrane-bound sacs vesicles – small, membrane-bound sacs buds off of an organelle (ER or other) buds off of an organelle (ER or other) contents within the vesicles (often proteins) transported to another membrane surface 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 vesicles fuses with membranes, delivering contents to that organelle or outside of the cell

65 . Fig. 5.16d (TEArt) Vesicle budding from rough endoplasmic reticulum Fusion of vesicle with Golgi apparatus Migrating transport vesicle Protein Ribosome

66 . 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] 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 not contiguous with ER, and lumen of each sac is usually separate from the rest has three areas: cis, medial, and trans has three areas: cis, medial, and trans

67 . 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 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 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 ) 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 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 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 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

68 . endomembrane system

69 . lysosomes – small membrane-bound sacs of digestive enzymes lysosomes – small membrane-bound sacs of digestive enzymes serves to confine the digestive enzymes and their actions serves to confine the digestive enzymes and their actions allows maintenance of a better pH for digestion (often about pH 5) 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 formed by budding from the Golgi apparatus; special sugar attachments to hydrolytic enzymes made in the ER target them to the lysosome

70 . endomembrane system lysosomes – small membrane-bound sacs of digestive enzymes lysosomes – small membrane-bound sacs of digestive enzymes used to degrade ingested material, or in some cases dead or damaged organelles 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 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 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 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 found in animals, protozoa; debatable in other eukaryotes, but all must have something like a lysosome

71 . endomembrane system vacuoles – large membrane-bound sacs that perform diverse roles; have no internal structure vacuoles – large membrane-bound sacs that perform diverse roles; have no internal structure distinguished from vesicles by size distinguished from vesicles by size in plants, algae, and fungi, performs many of the roles that lysosomes perform for animals 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 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 usually formed from fusion of many small vacuoles in immature plant cells storage sites for water, food, salts, pigments, and metabolic wastes storage sites for water, food, salts, pigments, and metabolic wastes important in maintaining turgor pressure important in maintaining turgor pressure tonoplast – membrane of the plant vacuole 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 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 contractile vacuoles – used by many protozoa for removing excess water

72 . endomembrane system microbodies – small membrane- bound organelles that carry out specific cellular functions; examples: microbodies – small membrane- bound organelles that carry out specific cellular functions; examples: lysosomes could be consider a type of microbody lysosomes could be consider a type of microbody peroxisomes – sites of many metabolic reactions that produce hydrogen peroxide (H 2 O 2 ), which is toxic to the rest of the cell peroxisomes – sites of many metabolic reactions that produce hydrogen peroxide (H 2 O 2 ), which is toxic to the rest of the cell peroxisomes have enzymes to break down H 2 O 2, protecting the cell peroxisomes have enzymes to break down H 2 O 2, protecting the cell peroxisomes are abundant in liver cells in animals and leaf cells in plants peroxisomes are abundant in liver cells in animals and leaf cells in plants normally found in all eukaryotes normally found in all eukaryotes example: detoxification of ethanol in liver cells occurs in peroxisomes example: detoxification of ethanol in liver cells occurs in peroxisomes glyoxysomes – in plant seeds, contains enzymes that convert stored fats into sugar glyoxysomes – in plant seeds, contains enzymes that convert stored fats into sugar

73 . What is the endomembrane system (include organelle components)?

74 . Diagram the cisternal maturation model for the Golgi.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.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:Describe the structure and function of: - ER- microbodies in general - vesicles- lysosomes - vacuoles- peroxisomes - Golgi apparatus- glyoxysomes

75 . Energy Converting Organelles energy obtained from the environment is typically chemical energy (in food) or light energy 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 mitochondria are the organelles where chemical energy is placed in a more useful molecule chloroplasts are plastids where light energy is captured during photosynthesis chloroplasts are plastids where light energy is captured during photosynthesis

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

77 . Energy Converting Organelles mitochondria – the site of aerobic respiration mitochondria – the site of aerobic respiration recall aerobic respiration: recall aerobic respiration: sugar + oxygen  carbon dioxide + water + energy sugar + oxygen  carbon dioxide + water + energy the “energy” is actually stored in ATP the “energy” is actually stored in ATP

78 . Energy Converting Organelles - mitochondria mitochondria have a double membrane mitochondria have a double membrane space between membranes = intermembrane space space between membranes = intermembrane space inner membrane is highly folded, forming cristae; provides a large surface area inner membrane is highly folded, forming cristae; provides a large surface area inner membrane is also a highly selective barrier inner membrane is also a highly selective barrier the enzymes that conduct aerobic respiration are found in the inner membrane 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 inside of inner membrane is the matrix, analogous to the cytoplasm of a cell

79 . Energy Converting Organelles – mitochondria mitochondria have their own DNA, and are inherited from the mother only in humans 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 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 some cells require more mitochondria than others mitochondria can leak electrons into the cell, allowing toxic free radicals to form mitochondria can leak electrons into the cell, allowing toxic free radicals to form mitochondria play a role in initiating apoptosis (programmed cell death) mitochondria play a role in initiating apoptosis (programmed cell death)

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

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

82 . Energy Converting Organelles plastids – organelles of plants and algae that produce and store food 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) 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) 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 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 numbers and types of plastids vary depending on the organism and the role of the cell

83 . Energy Converting Organelles – plastids (chloroplasts) chloroplasts get their green color from chlorophyll, the main light harvesting pigments involved in photosynthesis 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 chloroplasts have a double membrane the region within the inner membrane is the stroma; it is analogous to the mitochondrial matrix 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 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 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 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 carotenoids in the chloroplast serve as accessory pigments for photosynthesis

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

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

86 . Energy Converting Organelles endosymbiont theory mitochondria and plastids evolved from prokaryotic cells that took residence in larger cells and eventually lost their independence 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) 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)

87 . Energy Converting Organelles endosymbiont theory supporting evidence supporting evidence the size scale is right - mitochondria and plastids are on the high end of the size of typical bacteria 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 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 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 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 there are other known, more modern endosymbiotic relationships: algae in corals, bacteria within protozoans in termite guts

88 . Energy Converting Organelles endosymbiont theory some genes appear to have been shuttled out of the endosymbionts to the nucleus 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 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 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) 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) 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) 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)

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

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

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

92 . Describe the structure and function(s) of: –motor proteins –MTOCs –centrosomes –centrioles –cilia and flagella

93 .Cytoskeleton eukaryotic cells typically have a size and shape that is maintained 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 cytoskeleton is a dense network of protein fibers that provides needed structural support the network also has other functions the network also has other functions a scaffolding for organelles a scaffolding for organelles cell movement and cell division (dynamic nature to the protein fibers is involved here) cell movement and cell division (dynamic nature to the protein fibers is involved here) transport of materials within the cell transport of materials within the cell the cytoskeleton is composed of three types of protein filaments: microtubules, microfilaments, and intermediate filaments the cytoskeleton is composed of three types of protein filaments: microtubules, microfilaments, and intermediate filaments

94 .

95 . microtubules are the thickest filaments of the cytoskeleton microtubules are the thickest filaments of the cytoskeleton hollow, rod -shaped cylinders about 25 nm in diameter hollow, rod -shaped cylinders about 25 nm in diameter made of  -tubulin and  -tubulin dimers made of  -tubulin and  -tubulin dimers dimers can be added or removed from either end (dynamic nature) dimers can be added or removed from either end (dynamic nature) one end (plus end) adds dimers more rapidly than the minus end 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 can be anchored, where an end is attached to something and can no longer add or lose dimers

96 . microtubule-organizing centers (MTOCs) serve as anchors centrosome in animal cells centrosome in animal cells centrosome has two centrioles in a perpendicular arrangement centrosome has two centrioles in a perpendicular arrangement centrioles have a 9x3 structure: 9 sets of 3 attached microtubules forming a hollow cylinder 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 used for assembly of microtubules for use throughout the cell

97 . microtubule-organizing centers (MTOCs) serve as anchors centrioles are duplicated before cell division centrioles are duplicated before cell division play an organizing role for microtubule spindles in 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 other eukaryotes must use some alternative MTOC during cell division; still incompletely described

98 . microtubules are involved in moving organelles motor proteins (such as kinesin or dynein) attach to organelle and to microtubule 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 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 microtubule essentially acts as a track for the motor protein motor proteins are directional; kinesin moves toward the plus end, dynein away from it motor proteins are directional; kinesin moves toward the plus end, dynein away from it

99 . cilia and flagella are made of microtubules thin, flexible projections from cells thin, flexible projections from cells used in cell movement, or to move things along the cell surface 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) 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 central stalk covered by cell membrane extension, and anchored to a basal body 9x3 structure 9x3 structure stalk has two inner microtubules surrounded by nine attached pairs of microtubules stalk has two inner microtubules surrounded by nine attached pairs of microtubules 9+2 arrangement 9+2 arrangement

100 . cilia and flagella are made of microtubules stalk has two inner microtubules surrounded by nine attached pairs of microtubules stalk has two inner microtubules surrounded by nine attached pairs of microtubules 9+2 arrangement 9+2 arrangement dynein attached to the outer pairs actually fastens the pair to its neighboring pair 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 dynein motor function causes relative sliding of filaments; this produces bending movement of the cilium or flagellum

101 . microfilaments are solid filaments about 7 nm in diameter composed of two entwined chains of actin monomers composed of two entwined chains of actin monomers linker proteins cross-link the actin chains with each other and other actin associated proteins 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 actin monomers can be added to lengthen the microfilament or removed to shorten it; this can be used to generate movement

102 . microfilaments are solid filaments about 7 nm in diameter important in muscle cells; in conjunction with myosin, they are responsible for muscle contraction important in muscle cells; in conjunction with myosin, they are responsible for muscle contraction used for many cell movements such as: used for many cell movements such as: contractile structures contractile structures forming cell extensions forming cell extensions “pinching in” during cell division “pinching in” during cell division

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

104 . intermediate filaments not easily disassembled, thus more permanent not easily disassembled, thus more permanent a web of intermediate filaments reinforces cell shape and positions of organelles (they give structural stability) a web of intermediate filaments reinforces cell shape and positions of organelles (they give structural stability) prominent in cells that withstand mechanical stress prominent in cells that withstand mechanical stress form the most insoluble part of the cell form the most insoluble part of the cell

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

106 . Describe the structure and function(s) of: –motor proteins –MTOCs –centrosomes –centrioles –cilia and flagella

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

108 . 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).

109 . Outside the Cell Most prokaryotes have a cell wall, an outer envelope, and a capsule (capsule is also called glycocalyx or cell coat) 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 Most eukaryotic cells produce materials that are deposited outside the plasma membrane but that remain associated with it

110 . Outside the Cell plants have thick, defined cell walls made primarily of cross- linked cellulose fibers 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 growing plant cells secrete a primary cell wall, which is thin and flexible growth ends  primary cell wall is usually thickened and solidified 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 often a secondary cell wall is then produced between the primary cell wall and the plasma membrane still contains cellulose still contains cellulose typically has more strengthening material (for example, lignin in wood) typically has more strengthening material (for example, lignin in wood)

111 . Outside the Cell fungi typically have thinner cell walls than plants, made primarily of cross-linked chitin fibers fungi typically have thinner cell walls than plants, made primarily of cross-linked chitin fibers

112 . 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) 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 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 typically functions in cell recognition and communication, cell contacts, and structural reinforcement often works through direct interaction with the ECM often works through direct interaction with the ECM

113 . Outside the Cell ECM: a gel of carbohydrates and fibrous proteins; several different molecules can be involved ECM: a gel of carbohydrates and fibrous proteins; several different molecules can be involved main structural protein is tough, fibrous collagen main structural protein is tough, fibrous collagen fibronectins are glycoproteins in the ECM that often bind to both collagen and integrins 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 integrins are proteins in the plasma membrane that typically receive signals from the ECM

114 . 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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