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Chapter 6 A Tour of the Cell. AP Biology Smiley. Basic Structure of every Organism. Based on 1 of 2 types of cells Prokaryotic Eukaryotic. Basic Structure of every Organism. Based on 1 of 2 types of cells Prokaryotic ‘pro’ =before ‘ karyon ’ = kernel Eukaryotic ‘ eu ’ = true

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basic structure of every organism
Basic Structure of every Organism
  • Based on 1 of 2 types of cells
    • Prokaryotic
    • Eukaryotic
basic structure of every organism1
Basic Structure of every Organism
  • Based on 1 of 2 types of cells
    • Prokaryotic
      • ‘pro’ =before
      • ‘karyon’ = kernel
    • Eukaryotic
      • ‘eu’ = true
      • ‘karyon’ = kernel
basic structure of every organism2
Basic Structure of every Organism
  • Based on 1 of 2 types of cells
    • Prokaryotic
      • Only exist in domains of Bacteria or Archaea
basic structure of every organism3
Basic Structure of every Organism
  • Based on 1 of 2 types of cells
    • Prokaryotic
      • Only exist in domains of Bacteria or Archaea
    • Eukaryotic
      • Protists, fungi, animals, and plants
basic common feature of both
Basic Common Feature of Both
  • Bound by selective barrier (plasma membrane)
  • Have cytosol (jellylike substance)
    • Where organelles and other components are found
  • Contain chromosomes
    • Carry genes in the form of DNA
  • Have ribosomes
different features of both
Different Features of Both
  • Location of DNA
    • Eukaryotes
      • Most DNA is in nucleus
      • Nucleus is bound by double membrane
        • “true kernel”
    • Prokaryotes
      • DNA is concentrated in region not membrane-enclosed
        • Nucleoid
  • Cytoplasm
different features of both1
Different Features of Both
  • Cytoplasm
    • Eukaryotes
      • Region between the nucleus and plasma membrane
      • Contains a variety of organelles of specialized form and function
    • Prokaryotes
      • Interior of prokaryotic cell
different features of both2
Different Features of Both
  • Organelles
    • Eukaryotes
      • Membrane- bound organelles are Present
      • Specialized form and function
    • Prokaryotes
      • Absence of organelles
different features of both3
Different Features of Both
  • Size
    • Eukaryotes
      • Generally Larger than prokaryotes
      • Size relates to function
      • Logistics of carrying out cellular metabolism limits cell size
      • 10 – 100um in diameter
      • Metabolic requirements limit size practicality of cells
    • Prokaryotes
      • Smallest cells known
      • 1 – 5 um in diameter
plasma membrane
Plasma Membrane
  • Acts as a selective barrier
  • Allows sufficient passage of oxygen, nutrients, and wastes to service entire cell
  • Example:
    • For 1 um2 of membrane, only a limited amount of particular substance can cross per second
      • SA to V ratio is critical
plasma membrane1
Plasma Membrane
  • As a cell increases in size, its volume grows proportionately more than surface area
    • Area is proportional to linear dimension square
    • Volume is proportional to linear dimension cubed
    • THEREFORE, smaller object has greater ratio of SA to V
how does this relate to the size of cells1
How does this relate to the size of cells?
  • Specialized cells
    • Some longer, shorter, thinner depending on function
    • Sometimes there are more of one type instead of an increase in size
when would you need a higher sa v1
When would you need a higher SA:V?
  • Cells that exchange a lot of material with surroundings
  • May have projections from surface (microvilli)
    • This increases SA without increasing volume
villi and microvilli on the interior of the small intestine




Vein carrying blood

to hepatic portal



(brush border)

Villi and Microvilli on the interior of the small intestine





Muscle layers

Epithelial cells









Intestinal wall

eukaryotic cells
Eukaryotic Cells
  • Focus of this chapter
  • Contains: Nuclear envelope, nucleolus, and chromatin.
  • Nuclear envelope: double membrane enclosing the nucleus; perforated by pores; continuous with ER
  • Nucleolus: structure involved in production of ribosomes; a nucleus has one or more nucleoli.
  • Chromatin: material consisting of DNA and proteins; visible as individual chromosomes in a dividing cell.



1 µm



Nuclear envelope:

Inner membrane


Outer membrane

Nuclear pore



Rough ER

Surface of nuclear envelope


1 µm

0.25 µm

Close-up of nuclear


Pore complexes (TEM)

Nuclear lamina (TEM)

  • contains most of the genes in the eukaryotic cell
  • Chromatin: material consisting of DNA and proteins; visible as individual chromosomes in a dividing cell.
  • DNA is organized into discrete units called chromosomes
  • Each chromosome is made up of chromatin
  • typical human cell has 46 chromosomes in its nucleus
  • rRNA is synthesized from instructions in the DNA is here
  • proteins imported from cytoplasm are assembled with rRNA into ribosomal subunits here
ribosomes and rna
Ribosomes and RNA
  • Ribosomes translate messenger RNA (mRNA) into a protein.
    • A ribosome binds to the 5’ end of the mRNA.
    • Transfer RNA attached to an amino acid carries a codon (3 nucleotide sequences) to bind to the mRNA.
    • This process continues with more tRNA and amino acids forming peptide bonds.
    • The process stops when a codon reaches a stop codon.
    • By then a protein is formed, releases itself from the ribosome and curls up into a secondary or tertiary structure.
free and bound ribosomes
Free and Bound Ribosomes
  • Both free and bound ribosomes are structurally the same (both make proteins)
  • Bound Ribosomes (attached to the ER)
    • Make proteins that are to be inserted into membranes, secreted or packaged
  • Free Ribosomes (free in the cytosol)
    • Make proteins and release them into the cytosol
endomembrane system1
Endomembrane System
  • Encompasses the variety of different membranes
what is it responsible for
What is it responsible for?
  • Synthesis of proteins
  • Transport of proteins into membranes and organelles or out of cell
  • Metabolism and movement of lipids
  • Detoxification of poisons
endomembrane system2
Endomembrane System
  • Related through direct contact or through transfer of vesicles
what is a vesicle
What is a vesicle?
  • Sac made up of membrane
endomembrane system3
Endomembrane System
  • Pieces are not identical
    • Vary in structure and function
  • Vary in chemical reactions carried out in the given membrane
endomembrane system4
Endomembrane System
  • Includes:
    • the Nuclear envelope
    • Golgi Apparatus
    • Lysosomes
    • Vacuoles
    • Plasma Membrane
  • The endoplasmic reticulum (ER) is a network of flattened sacs and branching tubules that extends throughout the cytoplasm in plant and animal cells.
  • The endoplasmic reticulum manufactures, processes, and transports a wide variety of biochemical compounds for use inside and outside of the cell.
  • Accounts for more than half the total membranes in many eukaryotic cells
smooth er
Smooth ER
  • The smooth ER functions in diverse metabolic processes, which vary with cell type
  • Lacks ribosomes
  • (Barbiturates, alcohol, and many other drugs induce the proliferation of smooth ER and its associated detoxification enzymes thus increasing the rate of detoxification)-increase tolerance to other helpful drugs
function of smooth er
Function of Smooth ER
  • Process includes synthesis of Lipids, metabolism or carbohydrates, and detoxification of drugs and poisons (in Liver cells)
  • In animal cells the steroids produced are the sex hormones of vertebrates and the various steroid hormones secreted by the adrenal glands
  • Detoxification usually involves adding Hydroxyl groups to drug molecules making them more soluble and easier to flush from the body
function of smooth er1
Function of Smooth ER
  • Stores Calcium
    • Important to muscle cells
    • When stimulated, calcium ions rush back across the ER membrane into the cytosol and trigger contraction of the muscle cell
rough er
Rough ER
  • • A complex membrane bound organelle that is composed of a greatly convoluted but flattish sealed sac that is continuous with the nuclear membrane.
  • • Called a ROUGH Endoplasmic Reticulum because it is studded on the outside with ribosomes.
  • • Found in eukaryotic cells - the cells of plants, animals, and humans.
function of rough er
Function of Rough ER
  • • The RER is involved in transport of proteins made by ribosomes on its surface.
  • • The Rough ER changes with the needs of the cells. When the cell is actively making proteins, the rough ER can enlarge and become more complex.
  • • Ribosomes on the rough endoplasmic reticulum are called 'membrane bound' and are responsible for the assembly of many proteins. This process is called translation.

After leaving the ER, transport vesicles go to the golgi apparatus

  • FedEx
    • Manufacturing
    • Warehousing
    • Sorting
    • Shipping
  • Here, products of the ER (such as proteins) are modified and stored and then sent to other destinations
  • In a lot of cells used for secretion
  • Flattened membranous sacs called cisternae
  • Looks like a stack of pita bread
  • Distinct structural polarity
    • Membranes of cisternae on opposite sides of the stack differ in thickness and molecular composition
      • Cis face and trans face
        • Cis: receiving; trans: shipping
      • Cis face—located near the ER
  • Transport vesicles move material from the ER to the Golgi apparatus
  • A vesicle that buds from the ER can add its membrane and the contents of its lumen to the cis face by fusing with a Golgi membrane
  • The trans face gives rise to vesicles, which pinch off of the golgi body and travel to other sites.
  • Products of the ER are usually modified during their transit from the cis region to the trans region of the Golgi
non protein golgi products
Non-protein Golgi Products
  • In addition, the Golgi apparatus manufactures certain macromolecules by itself.
  • Many polysaccharides secreted by cells are Golgi products
    • Including pectins and certain other noncellulose polysaccharides
  • Non-protein Golgi products that will be secreted depart from the trans face inside transport vesicles
cis to trans
Cis to Trans
  • The Golgi manufactures and refines its products in stages, with different cisternae containing unique teams of enzymes
  • The cisternae of the Golgi actually progress forward from the cis to the trans face of the Golgi, carrying and modifying their cargo as they move
    • Good example in book on page 106, Figure 6.13
before exiting
Before exiting…
  • Before a Golgi stack dispatches its products by budding vesicles from the trans face, it sorts these products and targets them for various parts of the cell
  • Molecular identification tags, such as phosphate groups added to the Golgi products, aid in sorting
    • act like ZIP codes on mailing labels
  • Transport vesicles budded from the Golgi may have external molecules on their membranes that recognize “docking sites” on the surface of specific organelles or on the plasma membrane, thus targeting the vesicles appropriately
lysosomes the cell s garbage disposal
Lysosomes: the cell’s garbage disposal
  • Break down old organelles
  • Destroy invaders
    • Viruses
    • bacteria
  • Break down macromolecules
    • Proteins
    • Carbohydrates
    • Nucleic acids
    • lipids
lysosomal acid hydrolysis
Lysosomal Acid Hydrolysis
  • Contain about 50 degradative enzymes
    • Hydrolyze proteins, DNA, RNA, lipids
  • Lysosomes maintain an acidic pH (5)
    • Controlled by a hydrogen ion pump
    • Uses ATP hydrolysis
  • Double protection
    • Enzymes only active in acidic pH
  • Enzymatic genetic diseases
    • “lysosomal storage diseases”
    • Gaucher’s affects breakdown of glycolipids
lysosome formation
Lysosome formation
  • Cell membrane buds
  • Becomes an early endosome
  • Introduction of hydrolases and enzymes
    • Created by the ER then transferred to the Golgi bodies
  • Becomes a late endosome
    • Lowering of pH
  • New lysosomes are formed with acquisition of adequate hydrolases
phagocytosis and autophagy
Phagocytosis and Autophagy
  • Phagocytes fuse with lysosomes
    • Becomes phagolysosome
    • Digests extracellular substances
    • Ex: bacteria, viruses, food substances
  • Autophagosomes fuse with lysosomes
    • Endoplasmic reticulum encloses old organelles
    • Vesicle fuses with lysosome

1 µm




Lysosome contains

active hydrolytic



enzymes digest

food particles

Food vacuole

fuses with








Food vacuole

Phagocytosis: lysosome digesting food

  • Two types:
    • Food
      • Formed by phagocytosis
    • Contractile
      • Pumps excess water out of the cell
      • Helps maintain a suitable concentration of ions
  • Different in Plants and Animals
  • Animal
    • General description
  • Plant
    • Versatile
    • Take the job of lysosomes
      • Carry out hydrolysis
    • Disposal site for metabolic by-products
    • Contain pigments
    • Contain unpalatable compounds
    • Aid in growth


Intermembrane space






in the









100 nm

mitochondria an organelle
Mitochondria: An Organelle
  • Mitochondria are important to the cell because they are the “powerhouse” of the cell.
  • Mitochondria are the sites of cellular respiration; cellular respiration is the metabolic process by which ATP is produced.
  • Mitochondria are enclosed by membranes, however, they are not considered part of the endomembrane system.
mitochondria an organelle1
Mitochondria: An Organelle
  • Mitochondria are unique in the sense that they have two membranes in order to function correctly.
  • Found only in Eukaryotic cells.
  • Mitochondria are typically 0.5 to 1.0 micrometer in length.
  • Amount of mitochondria in the cell varies depending on the type of tissue the cell is found in and on the organism that the cell is found in.











energy processing
Energy Processing
  • “Powerhouse of the cell”
  • site of cellular respiration
  • converts energy from sugar to forms that cell can use
  • involved in other cell processes
  • semiautonomous
  • Cellular Respiration
  • Glycolysis
  • Citric acid cycle
what are chloroplasts
What are Chloroplasts?
  • Specialized member of a family of closely related plant organelles called plastids
  • Lens shaped organelles, 2-5 micrometers
  • Found in leaves, green organs of plants, and algae
  • Contain:
    • The green pigment chlorophyll
    • Enzymes
    • Molecules that function in the photosynthetic production of sugar
the structure
The Structure
  • Enclosed by two membranes separated by a intermembrane space
    • Outer compartment
  • Second, inner compartment holding the fluid or stroma
    • surrounds the thylakoid space
  • Membranous system in the form of connected, flattened disks called thylakoids
    • Stacked like poker chips which is called granum
  • Chloroplasts are one of the many different types of organelles in the plant cell.
  • Considered to have originated from cyanobacteria through endosymbiosis—when a eukaryotic cell engulfed a photosynthesizing cyanobacterium which remained and became a permanent resident in the cell. 
  • Mitochondria are thought to have come from a similar event, where a aerobicprokaryote was engulfed.
  • This origin of chloroplasts was first suggested by Konstantin Mereschkowski in 1905after Andreas Schimper observed that chloroplasts closely resemble cyanobacteria in 1883.
  • Chloroplasts are similar to mitochondria in that they both originate from an endosymbiotic event, but chloroplasts are found only in plants and some protists.
  • A network of fibers
  • Gives mechanical support
  • Stabilized by a system of opposing forces
  • Aids in cell motility
  • Interact with motor proteins
  • Three main types of fibers
    • Microtubules
    • Microfilaments
    • Intermediate filaments
  • Three main types of fibers
    • Microtubules
      • Hollow rods
      • Globular protein called tubulin
      • Grow out from centrosome
        • Within there are a pair of centrioles
      • Examples:
        • Cilia
        • flagella
  • Three main types of fibers
    • Microtubules
    • Microfilaments
      • Built from Molecules of actin
      • Double chain of actin subunits
  • Three main types of fibers
    • Microtubules
    • Microfilaments
    • IntermediateFilaments
      • Larger than microfilaments
      • Smaller than microtubules
extra cellular matrix ecm






Extra Cellular Matrix(ECM)