1. The Study of Cells
Light microscope (LMs) visible light passes through the specimen and then through glass lenses.
The lenses refract light such that the image is magnified into the eye or a video screen.
Low magnification and resolution.
Does not kill the specimen. ( A problem with EM’s)
Magnification is the ratio of an object’s image to its real size. (ie: 4X, 10X, 100X)
Resolution is a measure of image clarity.

2. Copyright © 2002 Pearson Education, Inc
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

3. Electron Microscopes Transmission electron microscopes (TEM)
study the internal ultrastructure of cells.
A TEM aims an electron beam through a thin section of the specimen.
Electromagnets focus and magnify specimen.
Specimens are stained with heavy metals to enhance contrast.

4. Electron Microscopes Scanning electron microscopes (SEM)
studying surface structures.
The sample surface is covered with a thin film of gold.
The beam excites electrons on the surface.
These secondary electrons are collected and focused on a screen.
Image produced by SEM appears 3-D

5. TEM
SEM

6. Studying Organelles
Light microscopes allow the study of individual cells.
The small, functional structures of cells, organelles, require the use of EM’s.
Cell fractionation separates (based on relative density) the organelles using an ultracentrifuge.

7. Cell Fractionation
Separation of organelles allows the study of their functions.

8. Isolation/Study of Organelles
Step 1: Homogenization
Gentle, mechanical disruption of the cells.
Breaks open the membranes.
Step 2: Ultracentrifugation
Spinning of cells separates the denser organelles as pellet (solid) and less dense particles remain suspended in supernatant (liquid).

9. Prokaryotic and Eukaryotic Cells
Prokaryotic Cells (ie: bacteria)
Lack a membrane bound nucleus
DNA is found in nucleoid (no membrane)
Eukaryotic Cells (ie: yeast, humans)
“True”, membrane-bound nucleus contains chromosomes.
DNA separate from rest of the cell.

10. Typical Prokaryotic Cell

11. Eukaryotic Cells vs Prokaryotic Cells
Cytoplasm– Fluid region between the cell membrane and the nuclear membrane. (All of material in prok. is cytoplasm).
Membrane bound organelles are found suspended in the cytoplasm of eukaryotic cells (absent in prokaryotes).
Eukaryotic cells are generally much bigger than prokaryotic cells. (bacteria = 1-10 microns, eukaryote = microns)

12. Why are Cells so Small?
As a cell increases in size its volume increases faster than its surface area.
Smaller objects have a greater ratio of surface area to volume.

13. Plasma Membrane
Phospholipid bilayer also containing proteins, sugars, cholesterol.
Acts as a barrier to the passage of materials into/out of the cell.

14. Importance of Surface Area
The more cytoplasm a cell has, the more gas/material exchange it needs.
Since it is the membrane that allows this exchange, it does not make sense to have large volume cells (small surface area). Therefore, cells are microscopic (best surface to volume ratio).
Therefore, large organisms have more cells, not larger cells.

15. Internal Membranes
Eukaryotic organelles tend to have secondary internal membranes.
Separate the metabolic reactions spatially.
Provide microenvironments for metabolic reactions to take place.
Enzymes are often found stored inside membrane bound structures.

16. Typical Animal Cell

17. Typical Plant Cell

18. Nucleus
The nucleus contains most DNA in eukaryotic cell (mitochondria and chloroplasts).
Approx. 5 micron diameter.
Separated from cytoplasm via double membrane.
Nuclear pore allows passage of large molecules into and out of the nucleus (ie: mRNA)

19. Nuclear Structure
Nuclear lamina (filament proteins) line the inside of the nuclear envelope and maintain shape.
DNA and associated proteins are organized into fibrous material, chromatin.
In a normal cell they appear as diffuse mass.
Cell Division- chromatin fibers coil up to be seen as separate structures- chromosomes.
All eukaryotic cells have characteristic # of chromosomes (e.g., human = 46 (23 pairs))

20. The Nucleolus Ribosomal subunits are assembled.
Subunits pass through nuclear pore to unite and form functional ribosomes in cytoplasm.

21. Nuclear Control
The nucleus controls the cell by determining which proteins are synthesized (depends on DNA).
Nucleus synthesizes mRNA and this molecule passes through nuclear pore.
mRNA works along side ribosomes to create the cell’s functional proteins.

22. Ribosomes Assemble amino acid subunits into proteins.
Found in higher numbers in cells that make lots of proteins. (ie: pancreas)
Free Ribosomes – function unattached in the cytoplasm.
Proteins made tend to function in cytoplasm.
Bound Ribosomes – Function bound to endoplasmic reticulum.
Proteins made tend to be packaged inside organelles.

23. Ribosomes rRNA and protein.
2 subunits that combine to carry out protein synthesis.
Fig. 7.10
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

24. Endomembrane System System of internal membranes in a eukaryotic cell.
Either in direct contact or connected via transfer of vesicles (sacs of membrane)
Membranes have diverse functions and structures.
Nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and the plasma membrane.

25. Endoplasmic Reticulum (ER)
Network of fluid filled tubules (cisternae)
Roughly ½ of eukaryotic membrane tissue
Continuous with the nuclear envelope
Smooth ER = lacks ribsosomes
Rough ER = ribosomes bound to cytoplasmic side of ER membrane

26. Structure of the ER

27. The Smooth ER Synthesis of lipids, steroids (ie: sex hormones)
Carb metabolism (ie: liver cells hydrolysis glycogen into glucose utilizes enzymes in smooth ER)
Detoxification of drugs/poisons (ie: smooth ER enzymes make drugs more soluble add –OH). Tolerance = more Smooth ER
Involved in Ca ion movement during muscle contraction.

28. Functions of Rough ER Attached ribosomes = protein synthesis
Abundant in cells that make proteins
Manufactured proteins are “threaded” through pore into the cisternal space of ER.
Glycoproteins – covalently bonded to carb.
Secretory proteins are packaged into transport vescicles and sent to various locations in the cell.

29. Rough ER
Also manufactures phospholipids from precursors in cytoplasm.
Assembles phospholipids and proteins into new membrane sections.
ER membrane can expand or transfer new membrane via vescicles to other parts of endomembrane system.

30. Golgi Apparatus
Responsible for modifying, packaging, and transporting products of the ER throughout the cell.
System of flattened membranous sacs (cisternae)
Has two poles; cis and trans faces.
The cis and trans faces of the golgi act as the “receiving” and “shipping” departments.

31. Golgi Function

32. Golgi Function
Products of ER are modified from cis to trans faces through golgi
Manufactures some polysaccharides (pectin)
Tags, sorts, and packages materials into transport vescicles

33. Lysosomes
Membrane-bounded sac of hydrolytic enzymes that digests macromolecules
Provide safe storage/usage of autodigestive enzymes

34. Lysosomal Enzymes
Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids.
Enzymes work best at pH 5
Proteins in the lysosomal membrane pump hydrogen ions from the cytosol to the lumen of the lysosomes.

35. The lysosomal enzymes and membrane are synthesized by rough ER and then transferred to the Golgi. Some lysosomes bud from golgi.

36. Phagocytosis
Lysosomes can fuse with food vacuoles
As the polymers are digested, monomers pass out to the cytosol to become nutrients of the cell.
Autophagy-- Lysosomes fuse with/digests another organelle or part of the cytosol. Renews cellular material.

37. Lysosome Function
Pre-programmed cell death during development and throughout cell lifetime
Pompe’s disease (liver) and Tay-Sachs disease (brain)
Serious metabolic disorders in which sufferers lack a (or many) functional hydrolytic enzyme (s).
Cells accumulate undigestible substrates in lysosomes.

38. Vacuoles Membrane bound sacs. Similar to vesicles only larger.
Three main types of vacuoles:
Food vacuoles, formed by phagocytosis, fuse with lysosomes.
Contractile vacuoles (freshwater protists)-- pump excess water out of the cell.
Central vacuoles are found in many mature plant cells.

39. Central Vacuole
Tonoplast– membrane that regulates passage into/out of the central vacoule.
Stores proteins or inorganic ions
Depositing metabolic byproducts
Storing pigments
Storing defensive compounds against herbivores
Increases surface to volume ratio for the whole cell

41. The Endomembrane System

42. Mitochondria and Chloroplasts
Convert energy into usable forms for cells.
Mitochondria are the sites of cellular respiration
Chloroplasts (plants, eukaryotic algae) are the site of photosynthesis
Have own DNA (mitochondrial used in forensics
Operate and reproduce autonomously
Mobile -- move around the cell along tracks in the cytoskeleton

43. Mitochondria
The number of mitochondria is correlated with aerobic metabolic activity
Mitochondria have a smooth outer membrane and a highly folded inner membrane, the cristae
Fluid-filled space between membranes
Cristae present ample surface area for the enzymes that synthesize ATP

44. Mitochondrial Structure
The inner membrane encloses the mitochondrial matrix, a fluid-filled space with DNA, ribosomes, and enzymes

45. Plastids Amyloplasts store starch in roots and tubers
Chromoplasts store pigments for fruits and flowers
The chloroplast produces sugar via photosynthesis
Green pigment chlorophyll
Concentrated in photosynthetic cells (ie: leaf cells)

46. Chloroplast Structure
The processes in the chloroplast are separated from the cytosol by two membranes.
Inside the innermost membrane is a fluid-filled space, the stroma, in which float membranous sacs, the thylakoids.

47. Chloroplast Structure
Stroma contain DNA, ribosomes, and enzymes for photosynthesis.
Thylakoids (flattened sacs) are stacked into grana and are critical for converting light to chemical energy.

49. Peroxisomes
Peroxisomes contain enzymes that transfer hydrogen from various substrates to oxygen
Produce H2O2 (poison) but also convert it to water
Break fatty acids down to smaller molecules that are transported to mitochondria for fuel
Detoxify alcohol and other harmful compounds

50. Split in two when they grow to certain size
Peroxisome Structure
Single membrane
Form from integration of proteins and lipids in the cytosol (most made by free ribosomes)
Split in two when they grow to certain size

51. Glyoxisomes Specialized peroxisomes
Convert fatty acids in seeds to sugars
easier energy and carbon source to transport

52. Cytoskeleton Network of fibers Run throughout cytoplasm
Maintains shape
Anchoring sites
Motility
Mechanical Support

53. Cytoskeleton and Motility
Motor molecules – specialized proteins that interact with cytoskeleton
Allow movement of cell (cilia and flagella) and movement of materials around cell (organelles, vesicles, etc.)
Muscle contractions
Cytoplasmic streaming

54. Microtubules Thickest fibers of cytoskeleton
Constructed of tubulin (globular protein)
Move chromosomes during cell division
“Tracks” that guide motor proteins carrying organelles around cell

55. Centrioles
Some microtubules are arranged into a pair of centrioles in animal cells.
During cell division, centrioles replicate.

56. Cilia and Flagella
Microtubules are the central structural supports in cilia and flagella
Propel unicellular organisms through water
Move fluid across large surfaces in multicellular organisms (ie: mucus in lungs)
Cilia occur in large numbers per cell (ie: paramecia)
Flagella are only one or two per cell (ie: sperm cell)

57. Cilia in Rabbit Pharynx

58. Flagella Undulate in order to move the cell
Force generated parallel to flagellum

59. Cilia Move Like Oars Alternating power and recovery strokes
Generate force perpendicular to cilia axis

60. Structure of Cilia and Flagella
Core of microtubules sheathed by a plasma membrane
Nine doublets of microtubules arranged around a pair at the center, the “9 + 2” pattern.
Flexible “wheels” of proteins connect outer doublets to each other and to the core.
Outer doublets connected by motor proteins.

61. Cilia and Flagella Structure
Anchored in the cell by a basal body, whose structure is identical to a centriole.

62. Dynein Motor protein Provides power to drive cilia and flagella
Addition/removal of P from ATP causes the movement of dynein
Alternately grab, move, and release microtubules of cilia/flagella
Protein cross links provide rigidity

63. Dynein

64. Microfilaments
The thinnest cytoskeletal fibers
Resist tension
Solid rods of globular protein actin (muscle cells)
Form 3-D network just inside plasma membrane

65. Microfilaments
Fig The shape of the microvilli in this intestinal cell are supported by microfilaments, anchored to a network of intermediate filaments.

66. Actin in Muscle Cells
Thousands of actin filaments are arranged parallel to one another.
Thicker filaments, composed of a motor protein, myosin, interdigitate with the thinner actin fibers.
Myosin walks along the actin filament, pulling stacks of actin fibers together and shortening the cell. (muscle contraction)

67. Muscle Contraction

68. Other Microfilaments
Microfilaments separate the cytoplasm in animal cells during cell division
Amoeba (localized contraction)
Pseudopodia -- cellular extensions
extend and contract through the reversible assembly and contraction of actin subunits into microfilaments

69. Pseudopods

70. Cytoplasmic Streaming
In plant cells (and others), actin-myosin interactions drive cytoplasmic streaming
Circular flow that speeds distribution of materials through the cell

71. Cytoplasmic Streaming

72. Intermediate Filaments
In between microtubule and microfilament diameter
Tension bearing filaments
Composed of keratins (family of proteins)
More permanent structures than other 2
Reinforce cell shape and provide strength
Fix organelle location within the cytoplasm

74. Cell Walls Surround plant cells, many prokaryotes, fungi, and protists
Protect cell
Maintain shape
Limit excessive water loss
Supports plant against gravity

75. Cellulose microfibrils embedded in protein, polysaccharide matrix
Cell Wall Structure
Cellulose microfibrils embedded in protein, polysaccharide matrix
Primary Cell Wall
Middle Lamella
Secondary Cell Wall

76. Cell Walls

77. Extracellular Matrix
The ECM provides structure to cell wall lacking animal cells.
The ECM is a network of fibrous proteins and sugars (glycoproteins). Mostly collagen.
The ECM is connected to the cytoskeleton via integrins (intermembrane proteins)
This connection allows for coordination of changes inside and outside of cell.

78. ECM

79. ECM ECM helps regulate cell activity
Embryonic cell migration follows “grain” of ECM
Can communicate with the nucleus to influence gene expression
May help coordinate cells of a tissue with one another
Receptor molecules

80. Intracellular Junctions
Neighboring cells in tissues, organs, or organ systems adhere, interact, and communicate through direct physical contact.
Plasmodesmata (plants) -- channels that allow cytosol to pass between adjacent cells

81. Plasmodesmata

82. Intercellular Junctions in Animals
Tight Junctions– Membranes of adjacent cells fused.
Desmosomes (anchoring junctions) fasten cells together into strong sheets
Gap junctions (communicating junctions) provide cytoplasmic channels between adjacent cells