Cell Structure in details

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Cell Structure in details Powered By Docstoc
					Margie L. Stinson

                                STRUCTURE and FUNCTION of
                                  CELLULAR ORGANELLES


The endomembrane system includes the:
        plasma membrane
        nuclear envelope
        endoplasmic reticulum
        Golgi apparatus or Golgi bodies
        vesicles
        vaculoles
        lysosomes

The membrane of all of these is composed of two layers of phospholipids
with embedded proteins.
Membrane has a consistency of a light oil allowing its membranes to
diffuse throughout.

Autogenous hypothesis states that the endomembrane system evolved from
invagination of the plasma membrane.


PLASMA (CELL) MEMBRANE
(Meg Eppel and Doug Coppick)
   The cell membrane is possibly the most important organell in the cell. It holds the cell
   together, keeping everything intact. It is mobile & moves along paths that membranes
   follow. It is composed of a phosolipid bilayer.

    Basic Definition
    The cell membrane is the thin layer that forms the outer boundary of a living cell or of an
    internal cell compartment

    The outer boundary is the plasma membrane, and the compartments enclosed by internal
    membranes are called organelles. Cell membranes have a dual function: (1) they both
    separate important but incompatible processes conducted in the organelles and keep toxic
    substances out of the cell; and (2) they allow specific nutrients, wastes, and metabolic
    products to pass between organelles and between the cell and the outside environment.

    Main Functions ~
          Holds cell together
          Controls whats goes out of cell
          Controls what comes into cell
          Manains homeostasis.

   Composition ~ Functions
      Cell (plasma) membranes are made of lipids, proteins and carbohydrates.
              Lipids – Barrier separating the interior of the cell from its environment.Also act
                      as a barrier between the solutions inside the cell, seperating contents of
                      an organelle fromm the cell cytoplasm. For example, the nucleus is
                      surrounded by two layers of membranes that are actually extensions of
                                                                                2

        the membrane surrounding the cell. These nuclear membranes keep the
        DNA inside of the nucleus.
        Lipid molecules are called PHOSOPHOLIPIDS. ~ made of fatty acides,
        glycerol, phosphate and hydrophilic organic derivative.
             Amphipathic – one end of molecule is hydrophobic (hates water!)
             and the other side is hydrophillic (loves water!)
             Fluid, with the degree of unsaturation of fatty acds determining the
             fluidity
             Barrier to polar molecules
             Basis for the cell signaling system

Proteins –
             The proteins within the plasma membrane are the functional part of
             the membrane, allowing for transport of materials through the
             membrane AND sending and receiving signals to and from other
             cells.
             Basically these proteins can act as, pumps, gates, receptors, engery
             transducers, and enzymes OR receptors for the endocytosis of
             material and cell-cell signaling.
             The proteins associated with the outsice surface of the lipid bylayer
             are called EXTRINSIC PROTEINS. These can be easily removed.
             The proteins that are embedded in the membrane are called
             INTRINSIC PROTEINS. They can only removed with detergents that
             disrupt the cell membrane. Integral proteins also have a hydrophobic
             portion (amino acids or fatty acid tail) that spans the hydrophobic
             interior of the lipid bilayer. Some of these inner proteins also have
             INTEGRINS ~ their job is to connect the outside proteins to the
             cytoskeleton inside the cell.

Carbohydrates – Modify the lipid and protein molecules
      MODIFIED MOLECULES ARE CALLED GLYCOPROTEINS AND
      GLYCOLIPIDS
         Glycolipids are located mainly in the plasma membrane, and they are
         found only in the noncytosolic half of the bilayer. Their sugar groups
         thereforeare exposed on the exterior of the cell, where they form
         part of the protective coat of carbohydrate that surrounds most
         animal cells. This protective coat is the glycocalyx. The glycolipid
         molecules acquire their sugar groups inthe Golgi apparatus.
         The enzymes that add the sugar groups are confined to the inside
         of the Golgi apparatus so that the sugars are added to lipid
         molecules in the noncytosolic half of the lipid bilayer. Once a
         glycolipid molecule has been created in this way, it remains trapped
         in this monolayer. as there are no flippases to transfer the glycolipid
         to the cytosolic side of the membrane.

        Two broad types of glycolipids can be distinguished:
                   Glycerol-Based:
                       . Fatty acid chains attached to the glycerol molecule.
                       . A carbohydrate group linked to the 3rd carbon of
                               glycerol with no bridging phosphate group
                       . Glycerol-based glycolipids are the primary form in
                               plants and bacteria.
                   Sphingolipid-Based:
                                                                                                    3

                                         . These are based on the addition of carbohydrate units
                                         to the sphingolipid nucleus (above). This type of
                                         glycolipid is the main form in animal cell membranes.

                                 Simple glycolipids formed by the addition of a single sugar unit
                                 are called cerebrosides.

                                 The addition of straight or branched sugar chains produces
                                 gangliosides. The carbohydrates added can be have considerable
                                 variation in structure.




                                                                             Phosolipid
                                                                              Bilayer
                                                                             The Lipid Bilayer is a
                                                                             Two-dimensional
                                                                             Fluid: The aqueous
                                                                             environment inside
                                                                             and outside a cell
                                                                             prevents membrane
                                                                             lipids from escaping
                                                                             from the bilayer, but
                                                                             nothing stops these
                                                                             molecules from
                                                                             moving about and
                                                                             changing places with
                                                                             one another within
                                                                             the plane of the
                                                                             bilayer. The
                                                                             membrane therefore
behaves as a two-dimensional fluid, which is crucial for membrane function.
Membranes consist largely of a lipid bilayer, which is a double wall of phospholipid, cholesterol,
and glycolipid molecules containing chains of fatty acids. Lipids give cell membranes a fluid
character, with a consistency approaching that of a light oil. The fatty-acid chains allow many
small, fat-soluble molecules, such as oxygen, to permeate the membrane, but they repel large,
water-soluble molecules, such as sugar, and electrically charged ions, such as calcium.
Top and bottom layers of the membrane have their stems facing each other. The proteins can
stretch through the top, bottom or both layers of phosolipid bilayer. Embedded in the lipid bilayer
are large proteins, many of which transport ions and water-soluble molecules across the
membrane. Some proteins in the plasma membrane form open pores, called membrane
channels, which allow the free diffusion of ions into and out of the cell. Others bind to specific
molecules on one side of membrane and, in a process that is not clearly understood, transport
the molecules to the other side. Sometimes one protein simultaneously transports two types of
molecules in opposite directions. Most plasma membranes are about 50 percent protein by
weight, while the membranes of some metabolically active organelles are 75 percent.

The proteins in the phosolipid bilayer have 5 reasons for making it possible for the cell membrane
to perform its job.
        Used to join cells together in cell adhesion
        Attach the membrane to the cytoskeleton (keeps shape of cell and membrane in place)
        Proteins gather together as enzymes & carry out different steps of metabolic reactions
        that take place near the cell membrane
                                                                                                   4

        Act as receptors to signal the cell when to start or stop metabolic activity
        Proteins make the membrane semipermeable. Controlling movement of substances in
        and out of the membrane.


The cell membrane will only let certain substance pass through it at certain times. 4 Main
factors that determine a substance can pass through the cell membrane.
         If they are lipid or lipid soluble molecules.
         Smaller molecules will pass through easier than large molecules
         Molecules with a neutral charge will pass through easier than ions.
         Cell membrane has the ability to pass different molecules at any given time.




Attached to proteins on the
outside of the plasma
membrane are long carbohydrate molecules. Although their exact functions are unknown, they
are believed to act in the recognition of substances from the extracellular environment and from
other cells.


Study Questions to think about!
   1. What are four functions of the cell membrane?
   2. What types of molecules make up the cell membrane?
   3. What are some of the functions of the proteins?
   4. What are some of the functions of the lipids?
   5. What different types of carbohydrates are there?
   6. Summarize the bilayer aspect of the cell wall.



Cell or Plasma Membrane

  Structure:

        The plasma membrane (also called the cell membrane) forms the outer limits of the cell.
        As with other membranes, the plasma membrane is made up of proteins and lipids,
        especially phospholipids which consist of both a hydrophilic head and 2 hydrophobic fatty
        acid tails (=amphipathic). See Figure 8.26 page 131. These lipids occur in two layers,
        often called the bi-layer. The bi-layer has globular proteins that seem to float in the lipid
                                                                                              5

     layer. This type of structure is in continual motion, giving it a fluid appearance. This
     appearance is often called the fluid mosaic structure. The plasma membrane uses this
     fluid mosaic structure to control the environment of the cell.

     The lipid bilayer is the main fabric of the membrane but proteins in this lipid layer are
     very important because they carry out many of the activities that the plasma membrane
     performs. Membrane carbohydrates on surface of the plasma membrane recognize other
     cells (glycoproteins)

Functions:
    Transport proteins: allow water-soluble substances to move through their interior, which
    opens on both sides of the bi-layer. Some transport proteins hydrolyze ATP as an energy
    source to actively pump substances across the membrane.
    Enzymatic activity: A protein built into the membrane may be an enzyme with its active
    site exposed to substances in the adjacent solution.
    Signal transduction: A membrane protein may have a binding site with a specific shape
    that fits the shape of a chemical messenger, such as hormones & other extracellular
    substances that trigger changes in cellular activity
    Intercellular joining: Membrane proteins of adjacent cells may be hooked together in
    various kinds of junctions.
    Cell-cell recognition: Some glycoproteins serve as identification tags that are specifically
    recognized by other cells.
    Adhesion proteins: Microfilaments or other elements of the cytoskeleton may be bonded
    to membrane proteins, a function that helps maintain cell shape and fixes the location of
    certain membrane proteins. Proteins that adhere to the extracellular matrix (ECM) can
    coordinate extra cellular and intracellular changes.

 Fluid Mosaic Structure
     Membranes are FLUID because:
     Membranes are not static sheets, but rather held together by hydrophobic attraction (=
     weaker than covalent bonds)
     Lipids and some of proteins can drift about randomly, but rarely flip flop.
     Fluid until temperature decreases ---> solid (like bacon grease)
     Fluidity is affected by the type of bonds within the membrane.
     Membranes are MOSAIC because membrane is a collage of different proteins within the
     bi-layer.
     Proteins determine most of the specific functions of membrane Different proteins are
     found in different membranes (More than 50 kinds of proteins have been found to date
     in the plasma membrane of red blood cells, for example)

 What other organelle(s) does it connect to structurally?
   Outside: Fibers of extracellular matrix
   Inside: Filaments of cytoskeleton
                                                                                                   6

CYTOSOL = CYTOPLASM = CYTOSKELETOB
(Claudia Calderon and Laura ___)

   Cytoplasm is everything inside a cell between the plasma membrane and the nucleus.
   It is a jelly-like material that is eighty percent water and usually clear in color.
   Cytoplasm, which can also be referred to as cytosol, means cell substance. Many tiny
   structures called organelles are located in the cytoplasm except for the nucleus itself.
   Among such organelles are the mitochondria, which are the sites of energy production
   through ATP (adenosine triphosphate) synthesis; the endoplasmic reticulum, the site of lipid
   and protein synthesis; the Golgi apparatus, which packages macromolecules into vesicles for
   transport; lysosomes and peroxisomes, sacs of digestive enzymes that carry out the
   intracellular digestion of macromolecules such as lipids and proteins; the cytoskeleton, a
   network of protein fibers that give shape and support to the cell.

   The cytoskeleton is transparent in standard light and electron microscope preparations,
   therefore invisible. It is usually left out of drawings of the cell, but it is an important,
   complex, and dynamic cell component. The cytoskeleton maintains the cell's shape, anchors
   organelles in place, and moves parts of the cell in processes of growth and motility. There
   are many types of proteins that make up the cytoskeleton, but two of the most studied
   aspects are the microtubule and actin cytoskeletons. Microtubules are made of tubulin
   subunits and are often used by cells to hold their shape. Microtubules are also the major
   component of cilia and flagella. Microfilaments are made of actin subunits. These
   microfilaments are approximately the diameter of a microtubule, and are often used
   by cells to change their shapes as well as hold structures.

   The cytoplasm, as seen through an electron microscope, appears as a three-dimensional
   lattice of thin protein-rich strands. These lattices are known as microtrabecular lattice and
   serves to interconnect and support the other solid structures in the cytoplasm. In other
   words, the cytoplasm is like a fence's main purpose is to hold together the organelles within
   the cytoplasm.


Study guide questions:
       1. Cytoplasm is located between the ________________ and the _______ within a cell.
                                              plasma membrane              nucleus
       2. What kind of cells live in a cytoskeleton?
                eukaryotic.
       3. What organelles would you find in the cytoplasm?
               Mitochondria, lysosomes, endoplasmic reticulum, centrioles, and Golgi bodies.
       4. What is the function of the cytoskeleton?
                It maintains the cell's shape, keeps organelles in place.
       5. Which of the following organelles doesn't belong in the list?: mitochondrion,
               chloroplast, ribosome, lysosome, or peroxisome.
                                 Answer: ribosome.

Literature Cited:
1.Cytoplasm, by Evan and Melanie http://sm.n.edu/qa9//biology/cens/cell
2. Campbell, Mitchell and Reece. Biology, Concepts & Connections Third Edition.
                                                                                                 7

ORGANELLES of SYNTHESIS
     Nucleus
     Nucleolus
     Ribosomes
     Endoplasmic Reticulum

          These organelles are involved in the process of making new molecules.
          Growth and maintenance of organisms.
          Flow of genetic information from DNA in chromosomes to RNA to protein.
          Synthesis of proteins.
          Origin and distribution of membrane.


NUCLEUS
          It contains and protects the majority of the cell's DNA in the form of chromosomes.
          DNA also occurs in the mitochondria and chloroplasts.
          The nucleus occupies about 10% of volume of cell and typically averages 5 microns in
          diameter.
          Surrounded by nuclear envelope with pores.
          Nuclear pores regulate the passage of materials between the nucleus and the cytoplasm.
          Double membrane has an inner and outer membrane separated by a space.
          Outer membrane is continuous with the membrane of the rough endoplasmic reticulum (RER)
          and has ribosomes attached to its surface.
          Nucleoplasm (gel) contains the chromatin (chromosomes) and a nucleolus (plural nucleoli).



✎    Nucleus (shows extension to RER)




          The nucleus is present only when the cell is not dividing.
          When the cell is not dividing, the nucleus and nucleolus are visible under the light
          microscope--but the chromosomes cannot be seen.




✎     Nondividing Cell                         Dividing Cell
                                                                                                 8



NUCLEUS
(contributions by James Ransom)

          While DNA is found in the chloroplast and mitochondria of eukaryotic cells, the majority of the
DNA is located and protected within the cell’s nucleus. The nucleus is the largest organelle and is most
visible in slides. It occupies about 10% of volume of cell and typically averages 5 microns (5 ) in
diameter.

        During the first part of a cell’s life cycle (growth phase 1), the DNA molecules exist as long
threads surrounded by proteins. In this state the DNA lengths are called chromatin. Were you to
view a slide of a cell during this stage, you would not be able to see the DNA as discrete units. The
nucleus would simply appear as a dark nut or kernel thus the organelle’s name nucleus (=kernel).
During the synthesis stage (second part of the cell growth phase), the chromatin threads replicate in
preparation for mitosis or meiosis I. The original chromatin length and its copy are called chromatids
and are temporarily joined together at a point called a centromere. It is not until the first phase of
mitosis or meiosis I (prophase) that the DNA lengths condense into the shorter, thicker and finally visible
chromosomes. It is important to realize that a DNA molecule, a length of chromatin, a chromatid and a
chromosome are all the same unit.

        The DNA material takes up most of the volume of the nucleus. Surrounding it and protecting it is
a nucleoplasm, much like the cytosol found in the rest of the cell. The nucleoplasm is rich in
nucleotides to make nucleic acids and amino acids to make proteins. Two types of organelles exist inside
the nucleus: ribosomes and one or more nucleoli (singular nucleolus).

          The nucleus is part of the endomembrane system. A double layer of semipermeable (porous)
membranes (nuclear envelope) surrounds it. The nuclear envelope is a bilayer of lipids and proteins.
The two layers are separated by a space of about 20-40 nm. The outer membrane is studded with
ribosomes and is continuous with the membranes of the rough endoplasmic reticulum (ER). The space
between the two layers of nuclear membranes is also continuous with the space of the rough ER.
This space in between the nuclear membranes and the space in the ER can fill with proteins and proteins
can pass between the two organelles. True of all the membranes of the endomembrane system, the
nuclear envelope is strengthened by a mesh of protein filaments. Both the endoplasmic reticulum and
nucleus membranes are connected via membranous extensions to the plasma membrane and Golgi
apparatus. The nuclear pores regulate the passage of materials between the nucleus and the cytoplasm.
Lining the inside of the inner membrane is a layer of intermediate protein filaments 30-100 nm thick
(nuclear lamina), which is hypothesized to add strength and shape to the nucleus, to control the
assembly and disassembly of the nuclear membrane during prophase. After the proteins making up
these laminas are phosphorylated, the nuclear membrane begins breaking up into vesicles that appear to
disappear during nuclear division. During telophase these proteins lose the phosphate group
(dephosphorylation) and the proteins reassemble forming the nuclear membrane.
It is clear that laminas control this process because when antibodies to laminas are injected into a cell,
the nucleus cannot reform during telophase.

What happens inside the nucleus:
  Genes “turn on” (gene expression) and a complimentary strand of RNA is made of a particular
  gene. It is important to realize that in gene expression, that the entire chromosome is not copied
  and the copy made is not complimentary DNA but instead is RNA. Prior to exiting the nucleus RNA is
  called primary or nuclear RNA, but after it exits the nucleus it is called messenger RNA.
  The RNA can carry its DNA blueprint code for the synthesis of a particular protein to a ribosome
  within the nucleus, or, after further processing, can exit the nucleus through a nuclear pore and
                                                                                             9

travel to a cluster of ribosomes (polyribosomes) floating in the cytoplasm or to one attached to the
rough ER
Chromosomes are replicated (DNA replication) in preparation for nuclear division (mitosis or meiosis
I). I used the word chromosome even though the DNA lengths are still in their chromatin state
simply because people think, in general terms, of DNA as chromosomes
The number of chromosomes differs in various species, but all members of a particular species have
the same number. Humans (Homo sapiens) have 46 chromosomes (two sets or a pair of twenty-
three different chromosomes) in autosomal or body cells, and one set or one of each of the 23 types
of chromosomes in gametes~sperm or egg cells. The number of sets of chromosomes is called the
“ploid” number. Body cells are diploid they have two sets, while gametes are haploid having one set.

Nuclear Pores: pores about 100 nm in diameter perforate the nuclear envelope.
Occur in areas of the nuclear envelope, where the inner and outer membranes are joined. At the lip
of each pore, the inner and outer membranes are fused. An intricate structure of proteins, called a
“pore complex” lines each pore and regulates the entry and exit of certain large macromolecules and
particles. The pore is formed by a ring of eight spokes that point to the center of the pore. Each
spoke is a subunit 15 – 20 nm in diameter. At the center is a diaphragm or plug. The pore itself acts
as a water-filled channel 10 nm in diameter. Molecules of 5,000 MW are freely diffusable, while
those of 60,000 MW cannot enter by diffusion. This means that mature ribosomes with both subunits
attached together are too large to reenter the nucleus. So this means that the translation of mRNA
occurs outside the nucleus. The pore can be caused to dilate open up to 26 nm when the pore
recognizes certain peptide sequences rich in lysine, arginine and proline. These proteins control the
direction molecules can actively be transported (active transport requires an expenditure of ATP
energy, so it costs the cell) through the pore. In tests, gold-labeled tRNA or 5S RNA could exit
through the pore, but not enter. Transport of RNA is inhibited by alteration of the 3' end or the 5'
cap structure. The protein signal is so refined and specific, that if the sequence is altered by even
one amino acid the peptide no longer passes through the pore. While proteins can bind to the
surface of the nuclear membrane, they can only enter the pore in the presence of ATP.

The nuclear lamina, a netlike array of protein filaments gives the nucleus its shape. This
lamina lines the inner surface of the membrane.
                                                                                            10

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ORGANELLES INSIDE THE NUCLEUS – Note they are not part of the
endomembrane system. Why not?
     Nucleolus
     Ribosomes
     These organelles are not part of the endomembrane system—they are not surrounded by
     membranes nor are they extensions of the plasma membrane or associated membranous
     organelles.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Nucleolus:
           makes the ribosomal subunits.
           Nonmembrane-bound cloudlike mass composed of rRNA and proteins that are combined to
           form ribosome subunits.
           These subunits leave the nucleolus cloud and exit the nucleus through its pores.
           There is a region of the nucleolus that is called the "nucleolus organizer".
           Certain genes of chromosomes that are located here make many identical copies of the same
           rRNA gene. Humans have five pairs of chromosomes (13, 14, 15, 21 and 22) each that have
           a nucleolar organizer located at a constriction near one end of the chromosome (this is a
           second constriction, not the centromere). All of the copies of the rRNA are expressed within
           the same short period of time resulting in a large number of rRNA molecules, which bond
           with proteins forming large and small ribosome subunits.
           Nuclear Organizer of an elongated chromosome singlet and a condensed chromosome
           singlet.



✎      Elongated chromosome singlet                    Condensed chromosome singlet




NUCLEOLUS (plural nucleoli)
  synthesizes ribosomal RNA
  assembles the ribosomal subunits into a complete, mature, functional ribosome

This is a spherical organelle within the nucleus. The nucleolus contains histones, enzymes,
nucleotides, amino acids and RNA. Ribosomes are aggregates of copies of RNA (called
ribosomal RNA) aggregate with certain proteins into three-dimensional bodies called “subunits”.
Two subunits join together to form a mature ribosome that then becomes a site for reading
messenger RNA. There are certain blocks of genes (on chromosomes 13, 14, 15, 21 and 22 in
humans) that code for the production of these particular proteins and for this type of rRNA.
Those chromosomes, that contain these genes, aggregate in the area making up the nucleolus.
These blocks of active genes act as “nucleolar organizers”. These genes are veritable copy
machines continually “turning on” (gene expression), making sufficient copies of RNA to produce
the proteins necessary for the production of ribosomes, which then become the site of further
protein synthesis. An average, healthy cell reportedly can produce up to 10,000 ribosomes per
minute (http://www.stemnet.nf.ca/-dpower/cell/ncleolus.htm).
                                                                                                 11


The enzyme RNA polymerase I acts as a catalyst signaling genes to start transcription. The
resulting copies of rRNA join with proteins to make fibers 5-10 nm in length called the pars
fibrosa (PF). Endonuclease enzymes then convert various pre-ribosomal particles into an
aggregate of RNA and histone and non-histone proteins that make up a ribosomal subunit.
These fibers are linked to ribonucleoproteins to form the ribosomal subunits. These maturing
subunits are called pars granulosa , due to their granular appearance under an electron
microscope. These granules are 15-20 nm.
There are two types of ribosomal units, a large and a small component; the final ribosome has
one of each. Once these subunits are complete the do not join to each other, but exit the
nuclear pore separately. Once outside they are joined together by messenger RNA and become
the site where messenger RNA is read and polypeptides synthesized. The complete ribosomes
are too large to return into the nucleus. Once outside, always outside. The complete ribosomes
can float within the cytosol or attach to the rough endoplasmic reticulum, where they form a pore
that moves newly synthesized proteins into the endoplasmic reticulum’s cisterna.

It is a puzzle why the nucleolus contains heterochromatin, which is DNA that is not actively being
transcribed into RNA, and often involves highly repetitive sequences of satellite DNA usually
found in the centromere and telomere portions of a chromosome.

Any particular nucleus might have one or several nucleoli. The nucleoli are present while the cell
is in its “cell growth or interphase” portion of its life cycle, but disassemble during prophase and
reassemble during telophase.


There is a direct correlation between protein production and number of nucleoli contained within
a nucleus. Liver and muscle cells have great need for proteins, so they have great numbers of
ribosomes, consequently, the nucleus of such cells will contain a greater quantity of nucleoli. The
greater the quantity of proteins a cell manufactures, the greater the number of nucleoli that will
be found in that cell’s nucleus.


Organelles out in Cytoplasm:

    Cytosol = cytoplasm or cytoskeleton: (see information above on cytoplasm)
    Ribosomes
                                                                                                12

RIBOSOMES
(contributions by Chris Coetzee and Koren Kirby)
        float in the cytoplasm (of all cells, prokaryotic and eukaryotic alike)
        attach to the rough areas of the endoplasmic reticulum
        attach to nuclear envelope
        are in the nucleoli
        are in mitochondria
        are in chloroplasts

Ribosomes are composed of strands of ribosomal RNA (transcribed off of certain genes) and
complex proteins that bind the rRNA strands together. These ribonucleoprotein complexes form
two different sizes of units, one larger than the other. In order to be functional, a ribosome must
have one large and one small subunit attached together. These subunits are formed in the
nucleolus and exit the nucleus via pores in the nuclear envelope. Once, these subunits join
outside the nucleus they are too large to reenter the pores. Because proteins are synthesized in
the nucleus as well as outside, we know that some ribosomes become complete and functional in
the nucleus, but they stay inside while the nuclear membrane is intact, while the majority of
ribosomes are not put together until the subunits are outside the nucleus. For more information
concerning the formation of rRNA refer to the section above concerning the nucleolus.
The messenger RNA molecule holds the two subunits of the ribosome together during
protein synthesis.

A ribosome has a mRNA binding site and three tRNA binding sites, known as the P, A and E
binding sites. All are located on the large subunit.

Function of rRNA in the ribosome: rRNA is the catalyst for formation of the peptide bond
(Science, June 5, 1992).
The P site holds the tRNA carrying the growing polypeptide chain. The A site holds the tRNA
carrying the next amino acid to be added to the peptide chain. Discharged tRNAs leave the
ribosome from the E site.
Interfunction: Ribosomes are not part of the endomembrane system in that they are not
membranous, but the ones attached to the rough endoplasmic reticulum and nuclear envelope
(bound ribosomes) interfunction with this system. Bound ribosomes make proteins that will be
included into membranes, packaged within certain organelles such as lysosomes or exported
from the cell. Free ribosomes, floating in the cytoplasm, have to do with the synthesis of
hormones.

The ribosomes bring together mRNA and tRNA.

Differences between the tRNA of prokaryotic and eukaryotic cells:
Predictably, eukaryotic and prokaryotic rRNAs are distinctly different but the rRNA inside
mitochondria and chloroplasts are more similar to that found in prokaryotic cells.
The length of rRNA varies between species from 4700 bases to about 120 bases.

Eukaryotes contain 28, 18, 5.8 and 5 S rRNAs, while prokaryotes contain 23, 16 and 5 S rRNAs.
The "S" symbolizes a Svenberg unit (s), which measures the rate of sedimentation of molecules
and organelles during centrifugation. It is the sedimentation coefficient, and is a measure of
relative size.

Differences in life span of messenger, transfer and ribosomal RNA:
A study using Escherichia coli found that in at least that species, most of the cell’s RNA is ribosomal RNA,
only a small portion (3%) of the cell’s total RNA is made up of mRNA, but, that the cell uses almost 1/3
of its capacity for RNA synthesis to the production of mRNA. In fact, this value may increase to about
                                                                                                13

60% when the cell is growing slowly and does not need to replace ribosomes and tRNA. This probably is
due to the fact that transfer and ribosomal RNA are very stable and do not need to be rebuilt, but the
messenger RNA lives no longer than three minutes and then needs to be replaced. The average half-life
of mRNA in eukaryotic cells is about 30 minutes.

 Differences between ribosomes in prokaryotic and eukaryotic cells:
The differences in rRNA (detailed above) correlate to differences in ribosomes between bacteria
and eukaryotic cells. The ribosomes found within mitochondria and chloroplasts distinctly more
similar to those in bacteria.
    Size:
         Eukaryotic ribosomes are large (80S), consisting of 40S and 60S subunits, while
         prokaryotic ribosomes are smaller (70S), consisting of 30S and 50S subunits.
    Antibiotics:
         Certain antibiotics including tetracycline, streptomycin and chloramphenicol, kill bacteria by
         binding to their ribosomes but do not affect the ribosomes of eukaryotes...possibly due to their
         larger size.
    Number:
         Eukaryotic cells contain far more ribosomes than do bacterial cells. A single human cell might
         contain several million ribosomes.

Function of Ribosome:
During protein synthesis, several ribosomes called polyribosomes (or polysomes) follow one another
down the same messenger RNA molecule making it possible for tRNAs to bring amino acids to the mRNA
and for the amino acids to bond forming a peptide chain.

Each ribosome "car" "reads" the same mRNA and assembles the same amino acids that will result in
molecules of the same protein being synthesized repeatedly.
Polyribosomes synthesize multiple copies of the same protein.
Cells needing to make proteins most frequently, such as pancreatic, liver and muscle cells have the
greatest number of ribosomes.

Ribosome
            Organelle composed of two pieces (one large one small subunit).
            Acts as the platform upon which amino acids are assembled to form proteins.
            Several million ribosomes in a human cell.
            During protein synthesis, several ribosomes called polyribosomes (or polysomes) follow
            one another down the same messenger RNA molecule.
            Each ribosome "car" "reads" the same mRNA and assembles the same amino acids that will
            result in molecules of the same protein being synthesized repeatedly.



✎        Polyribosomes synthesize multiple copies of the same protein
                                                                                             14

             Ribosomes are located in two places within the cytoplasm:
                 • free ribosomes are found
                      . Suspended in cytosol and synthesize proteins that will be used in the cell
                         (except for membrane proteins).
                • bound ribosomes are found:
                      . Attached to the outer surface of f the membranous endoplasmic reticulum.
                               The areas of the ER that have attached ribosomes are called rough ER.
                      . Nuclear envelope, which is an extension of the ER.
                      . Iinside mitochondria and chloroplasts

Ribosome
(Tracie Viles)

        Ribosomes, the cellular “factory” at which proteins are made, was discovered over 45 years ago.
Since then, this structure has kept its own scientific research community of some 1,000 people busy
around the world. Yet, in spite of all of the interest, no one has “seen” the ribosome with any clarity.
Ribosomes are cytoplasmic organelles found in prokaryotes and eukaryotes.




STRUCTURE:
     Ribosomes are not organelles since they are non-membraneous.
     They are spherical bodies composed of RNA and protein enzyemes.
     Ribosomes are made up of two subunits or parts. There are two types of ribosomes: free
     ribsomes, which are suspended in the cytosol, and bound ribosomes, which are attached
     to the outside of a membranous network called the endoplasmic reticulum. In both cases
     the ribosomes often occur in clusters called polysomes.
     Ribosomes are found in the nucleus, cytosol, and are attached to the endoplasmic
     reticulum (ER) constituting rough ER.

FUNC TIONS::
FUNC TIONS:
FUNC TIONS
             The function of a ribosome is to convert the genetic code into a sequence of
             amino acids that form a specific protein. Ribosomes are involved in protein
             synthesis. It creates protein for the cell. Ribosomes can occur freely in the
             cytosol and it boundes attached to the outer membrane (endoplasmic
             reticulum).
             Ribosomes function with one organelle, endoplasmic reticulum.

STU DY G UIDE Q UE STIO NS ::
STU DY G UID E Q UE ST IONS :
STU DY G UID QUE S       NS

        1.   Which organelle does ribosomes attach themselves to?
        2.   How many sub units are there?
        3.   Where do ribosomes travel freely?
        4.   Where are ribosomes found?
                                                                                         15



  Which of the following proteins listed below would be synthesized on free ribosomes and which would
  be made on bound ribosomes?

     Type of Protein                                 Location where Protein would be synthesized:
        enzymes that function in the cytosol         free ribosomes
        chromosome proteins                          free ribosomes
        plasma membrane proteins                     bound ribosomes
        hemoglobin                                   free ribosomes
        insulin                                      bound ribosomes
        ribosome proteins                            free ribosomes



  Prokaryotes have smaller ribosomes (70s) than are found in eukaryotes (80s).
  The "s" symbolizes a Svenberg unit (s) which measures the rate of sedimentation of molecules and
  organelles during centrifugation. Certain antibiotics including tetracycline, streptomycin and
  chloramphenicol, kill bacteria by binding to their ribosomes but do not affect the ribosomes of
  eukaryotes...possibly due to their larger size.




ENDOPLASMIC RETICULUM
         Is an interconnected canal of membranes. Half of the membranes within a typical animal cell
         are endoplasmic reticulum.
         It comprises the largest portion of the endomembrane system of membrane-bound
         organelles that interrelate or interfunction through the production and distribution of
         membranes.


     Canal system of ER is composed of two connected subdivisions:
            Rough ER (RER)
                      Consists of layers (cisternae) with attached ribosomes on outer surface.
            Smooth ER (SER)
                      Consists of a network of interconnecting tubules without ribosomes.




✎      Rough endoplasmic and smooth endoplasmic reticulum
                                                                                              16




       The Rough ER is continuous with the outer layer of the nuclear envelope.
          Attached ribosomes synthesize membrane and secretory proteins.
          Membrane proteins enter ER membrane and diffuse throughout the entire ER membrane
          system.
          Secretory proteins pass through RER membrane and enter the RER cavity (lumen).
          Enzymes within ER add short chains of sugar molecules to membrane and secretory proteins
          changing them into glycoproteins (protein + carbohydrate = glycoprotein).
          Secretory proteins are transported along the following route
              RER       transitional ER     transport vesicle      Golgi Apparatus  secretory
              vesicle      plasma membrane.

       Smooth Endoplasmic Reticulum:
         Is continuous with RER
         lacks ribosomes
         has a tubular appearance
         SER contains enzymes that male lipids including membrane phospholipids, cholesterols, sex
         hormones.
         Phospholipids and cholesterol are incorporated into SER membrane and diffuse throughout
         entire ER membrane.
         In certain specialized cells, the SER has unique functions:
             in liver, SER has enzymes that detoxify many poisons such as barbituates,
             amphetamines, morphine and some pesticides



       The ER is the site of membrane synthesis.
                  Both RER and SER cooperate in membrane synthesis.
                  RER adds membrane proteins
                  SER adds membrane lipids to the membrane of the ER.
                  These proteins and lipids intermingle as they diffuse through and enlarge the ER
                  membrane.
                  Pieces of the ER membrane bud off membrane-bound transport vesicles containing
                  proteins.
                  These transport vesicles move to the Golgi apparatus and fuse with its membranes.
                  Enzymes within the Golgi apparatus further modify these proteins that are
                  repackaged in vesicles budded from the Golgi apparatus.
                  Some of these vesicles, secretory vesicles, move to the plasma membrane and fuse
                  with it resulting in the secretion of glycoproteins and the incorporation of secretory
                  vesicle membrane with the plasma membrane.

ENDOPLASMIC RETICULUM
(Travis King and Lara Grow)
                                                                                                17

Throughout the eukaryotic cell, especially those responsible for the production of hormones and
other secretory products, is a vast amount of membrane called the endoplasmic reticulum, or ER
for short.

The ER membrane is a continuation of the outer nuclear membrane and its function suggests just
how complex and organized the eukaryotic cell really is. When viewed by electron microscopy,
some areas of the endoplasmic reticulum look “smooth” (smooth ER) and some appear “rough”
(rough ER).
The rough endoplasmic reticulum consists of a system of membranous sacs and tubules known
as cisternae. It derives its name from the fact that it is coated with numerous ribosomes, which
line the cytoplasmic surface of its membrane. This causes the surface of rough ER to appear
studded or “rough” under the electron microscope. AN electron microscope must be used to
view the rough ER due to its extremely small size; 0.005 um in diameter

The rough ER has two primary functions; make more membrane and convert polypeptide chains into a
variety of functional proteins. Information coded in DNA sequences in the nucleus is transcribed as
messenger RNA. Messenger RNA exits the nucleus through small pores to enter the cytoplasm. At the
ribosomes on the rough ER, the messenger RNA is translated into proteins. The proteins are then
delivered into the endoplasmic cisterns.

In most instances, polypeptide chains require a considerable amount of processing before they
are ready for shipment. Some are fitted with carbohydrate side-chains, that contain as many as
ten or more sugar molecules (glycosylation). The smooth endoplasmic reticulum is an extensive
membranous network, and like the rough ER, it is continuous with the outer nuclear membrane.

The smooth ER is a network of interconnected tubules that lack ribosomes. Much of its activity
results from enzymes embedded in its membrane. One of the most important functions of the
smooth ER is the synthesis of lipids, which includes fatty acids, phospholipids, and steroids. Each
of these products is made by particular kinds of cells. In mammals, for example, smooth ER in
cells of the ovaries and testes synthesizes the steroid sex hormones.

These proteins are then transferred to the golgi in transport vesicles where they are further
processed and packaged into lysosomes, peroxisomes, or secretory vesicles.

Our liver cells also have large amounts of smooth ER, with additional kinds of functions (Bio.
Concepts and Connections pg. 59). Certain enzymes in the smooth ER of liver help regulate the
amount of sugar released from liver cells into the bloodstream. While other liver enzymes help
break down drugs and other potentially harmful substances. They also are used as a destruction
of toxic substances in the liver cells. The drugs detoxified by these enzymes include sedatives
such as barbiturates, stimulants such as amphetamines, and certain antibiotics.

Another function of the smooth ER is the storage of calcium ions. In the muscle tissue, these are
necessary for contraction. When a nerve stimulates a muscle cell, calcium ions leak from the
smooth ER into cytoplasmic fluid, where they trigger contraction of a cell. These proteins are
then transferred to the golgi in transport vesicles where they are further processed and packaged
into lysosomes, peroxisomes, or secretory vesicles. Living cells manufacture all sorts of export
materials, which they assemble, process, package, and transport in a chain of interconnected,
membrane-limited organelles. Biologists refer to this cytoplasmic network as the endomembrane
system. The endoplasmic reticulum is only one of the many organelles in the system responsible
for the synthesis, storage, and export of important molecules.


Study Guide Questions
   The genetic code of all cells is in the form of:
                                                                                          18

        double stranded DNA
        triple stranded RNA
        single stranded ribosomes
        mitochondrion
Extensions (evaginations ) of cell membrane
        are called cilia if very long
        are called flagella if very short
        neither of the above statements is true
Site where amino acids are assembled to form proteins.
        mitochondrion
        golgi apparatus
        ribosome
        nucleolus
        microtubules
Which organelle(s) produce(s) a great amount of cellular energy. The cell “powerhouse”.
    • mitochondrion
    • golgi apparatus
        ribosome
        nucleolus
        microtubules
Which organelle looks like a stack of pancakes.
        mitochondrion
        golgi apparatus
        ribosome
        nucleolus
        microtubules
Alternate name for the cell membrane.
        lysosome
        centriole
        cytolemma
        vacuole
        chromatin




Contains potent destructive enzymes.
        lysosome
        centriole
        cytolemma
        vacuole
        chromatin
Packages materials for cell export.
        mitochondrion
        golgi apparatus
        ribosome
        nucleolus
        microtubules
Stores food, water, or waste products.
        lysosome
        centriole
        cytolemma
        vacuole
        chromatin
                                                                                               19


    Sources
    Campbell, Neil, A., Mitchell, Lawrence, G., and Jane B. Reece.
      Biology: Concepts and Connections. 2 nd ed. Menlo Park: Longman Inc., 1997.

    De Duve, Christian. A Guided Tour of the Living Cell. Volume 1. New York: Rockefeller UP,
           1984.

    Gennis, Robert, B.. Biomembranes: Molecular Structure and Function. Cantor, Charles, R.
            ed. New York: Springer-Verlag, 1989.


ENDOPLASMIC RETICULUM
(by Natalya Cherepakhin)
Both the rough and smooth endoplasmic reticulum, along with the Golgi apparatus, lysosomes, vacuoles,
nuclear envelope and plasma membrane are part of the endomembrane system. All are interconnected
by membranous canals (folds or extensions) or by the transfer of membrane segments as tiny vesicles
(membrane enclosed sacs).
Endo=within, plasmic=cytoplasm, reticulum=network… Latin for network within the cytoplasm.

    Is the most extensive cellular organelle. It accounts for more than half of the total membrane within
    an eukaryotic cell.
    It consists of cisternae that form a network of membranous tubules and sacs that separate the
    internal compartment (cisternal space or lumen) from the cytoplasm.
    Areas embedded with ribosomes are called rough endoplasmic reticulum and those areas lacking
    ribosomes are called smooth endoplasmic reticulum.

Function of Rough ER:
       The polyribosome (subunits of rRNA + proteins) is connected or held together by a molecule of
       messenger RNA, which runs between the two subunits. As the polypeptide chain grows it
       projects down from the large subunit and is inserted into the membrane of the endoplasmic
       reticulum and then into the internal cisterae of the RER. The membrane of the RER has a
       receptor site that binds the larger subunit of the polyribosome. Adjacent to this receptor site is
       the pore through which the polypeptide chain will pass into the cisternae of the ER.
       The membranous sacs of the rough endoplasmic reticulum connect with the rest of the
       endomembrane system, with the nuclear envelope, plasma membrane and golgi apparatus (etc.),
       and the proteins synthesized by the ribosomes on the surface of the RER are passed through
       membranous canals or channels to the rest of the cell.

        Function of the Smooth ER:
               1. Produces enzymes for synthesis of lipids.
                       phospholipids, steroids, hormones
                  Metabolism of carbohydrates.
                  In the hydrolysis of glycogen in liver cells, glucose phosphate (the first product of the
                  reaction) cannot leave the cell and enter the blood until an enzyme embedded in the
                  cell’s smooth ER remove the phosphate from the glucose.
                  Detoxification of drugs and proteins.
                  Smooth ER adds hydroxyl groups to drugs such as barbiturates or alcohol, making
                  them more soluble and easier to flush from the body. Drugs induce a proliferation of
                  smooth ER that leads to an increased tolerance of the drug that then requires higher
                  does and this causes further proliferation of the smooth ER.
                  Contraction of muscle cells.
                                                                                            20

                  ER membrane pumps calcium ions from the cytosol into the cisternal space. When a
                  nerve impulse stimulates a muscle cell, calcium rushes back across the ER and
                  triggers the contraction.




GOLGI APPARATUS
          Modifies, sorts and packages proteins into secretory vesicles and lysosomes.
          Is a stack of flattened membrane-bound sacs (cisternae) that look like a stack of pita bread.
          Some cells have one large stack, others have hundreds of small stacks.
          Transport vesicles carry proteins from the ER to the Golgi apparatus.

       Transport vesicles:
                 Contain proteins, made on bound ribosomes of the RER.
                 Transport vesicles bud off from the RER and are transported to the Golgi Apparatus,
                 where they fuse with the face of the GA.
                 Enzymes in the GA modify these proteins by adding short chains of sugars.
                 Many of the polysaccharides secreted by cells are produced by the GA
                 (i.e. hyaluronic acid that helps glue animal cells together).
                 The GA packages its molecules into either secretory vesicles or lysosomes that bud
                 from the exit face of the GA.

Structure- description
                                                                                              21

        Flattened no interconnected sacs that look like a stack of pita bread.

Number
     The amount of golgi bodies in a cell depends on the level activity.
     The more activity the greater number of golgi bodies.

Function
       The function of the Golgi apparatus involves interaction with other organelles, but is not
       connected by membrane with the other organelles. The function is to chemically modify
       the secretory proteins and lipids transported from the ER in a transport vesicle. The
       transport vesicle enters the golgi sac through the bottom, the receiving side. Each sac in
       the golgi apparatus body contains a different enzyme (remember enzymes have active
       sites that only accept specific molecules) therefore there are many different modifications
       taking place. The mature cells are then marked with a sequence of molecules and sorted
       into different batches for various destinations with in the cell including the lyosomal
       membrane, plasma membrane and many others. They are the excreted through the
       shipping side of the golgi apparatus, the top.

Study Questions
       1. What are in the transport vesicles?
       2. From where do the transport vesicles transport?
       3. What is the basic function of the Golgi apparatus?
       4. Just as a letter is taken to the post office to be mailed to another
       location by means of the address, a ______ ______ is taken to the ________
       _______ to be _____________ and sorted for final destination by mean of a
       ________ ___________.

           Answers
               1. Proteins and Lipids
               2. ER
               3. Import ->Modify -> Export
               4. transport vesicle
                    Golgi apparatus
                    marked
                    sequence molecule


Sources
   Campbell, Mitchell, Reece, 2000, Biology: concepts and connections 3rd edition, page 60

    Natural Toxins Research Center at Texas A&M University Kingsville
    http://ntri.tamuk.edu/cell/golgi.html

    University of Tasmania Faculty of Health Science, Lee Weller, February 22, 200
    http://www.healthsci.utas.edu.au/weller/+doocs/cellbio2.htm



GOLGI APPARATUS
(by Ryan O’Connor)

Structure:
       Series of cisternal membranes that overlay one another to form sacs, which are in turn
       linked at their edges by tubules to form a highly ordered ribbon-like structure. Each
                                                                                               22

        saccule forms a separate compartment. The bottom saccule forms the cis, entry, or
        forming face. The top saccule forms the trans, exit, or maturing face.

Function:
       • The Golgi apparatus is responsible for modifying proteins that were produced in the
          endoplasmic reticulum. It is here that export proteins and membrane proteins mature and
          where polysaccharides, to be exported, are synthesized.
       • The GA receives newly synthesized proteins from the ER and then modifies them chemically.
       • The GA collects, prepares, packages, and releases secretory materials to the surface of the
          cell in vesicles pinched off from the GA. After a secretory vesicle has ruptured and expelled
          its secretory materials form the cell; its membrane often becomes part of the plasma
          membrane. This is the last stage in the directional flow of membrane that exists in cells.
          It also produces lysosomes, vesicles that contain powerful hydrolytic enzymes for digesting
          particles taken into the cell during endocytosis.

Structural Connection to other Organelles:
           The GA is connected at points to the ER.
           The forming face lies near the nucleus and the maturing face and secretory vesicles lie near
           the cell membrane at the surface opposite to the one where the raw materials enter.
Interfunction with other Organelles:
   Transfer vesicles carry secretory proteins from the ER to the GA.
   The rER and GA maintain cell membranes.

The Golgi Apparatus is part of the endomembrane system.




LYSOSOMES
(by Kieu Nguyen)
           Lysosomes are membrane-bound sacs of hydrolytic enzymes, which the cell uses to digest
           macromolecules.
           Lysosomes come from the endomembrane system. The rough ER makes both the hydrolytic
           enzymes that are found in lysosomes as well as the membranes that form the lysosome to
           carry the enzymes. Both products that are made in the rER are then sent to the GA for
           further processing.

            The enzymes that are contained in the lysosomes have varying functions. Some hydrolyze
            proteins, polysaccharides, fats, and nucleic acids.
            Lysosomes provide a safe way for the cell to digest products without having to deal with the
            destructive possibilities of hydrolytic enzymes. Lysosomes not only digest food products, but
            they also aid in the recycling of materials from defective or dying cell parts. Lysosomes also
            work closely with food vacuoles, which basically hold food products waiting for enzymes from
            lysosomes to come and continue with the cellular digestion of food.
            Interestingly enough, when lysosomes have small breaks in their membrane, the neutral
            environment of the cytosol will make the enzymes that leak out less active, thus limiting their
            damage to the cell itself. Large leaks, however, do cause autodigestion of the cell.
                                                                                             23

            Can kill bacteria.


PEROXISOMES
(Kieu Nguyen)
    Unlike lysosomes, peroxisomes do not bud from the endomembrane system.
    They are semi-spherical in shape and often have a granular or crystalline core. The core is probably
    made up of a collection of enzymes.
    The enzymes that are found in peroxisomes take hydrogen from various substrates and bind it to
    oxygen, making the by-product hydrogen peroxide (H202).
    In other peroxisomes, oxygen is used to break fatty acids into smaller molecules. The broken acids
    are then transported to the mitochondria and used as that organelle’s source of fuel for cellular
    respiration.
    Peroxisomes play an important role in the liver, where they detoxify alcohol by removing hydrogen to
    form H202. Although, hydrogen peroxide is toxic, enzymes do exist in peroxisomes that convert it
    into water.




VACUOLES
(by Kieu Nguyen, Sandra Robles))
           Vacuoles are membranous sacs that belong to the endomembrane system.
           Vaculoes are found both all eukaryotic cells.
           Plant cells have a large central water-filled vacuole enclosed by a membranous extension of
           the endomembrane system.
           Vacuoles play many roles in the maintenance and functioning of the cell. Vacuoles are
           primarily storage bins that hold a variety of substances, which in turn determine their
           function. For example, food vacuole hold food (leucoplasts hold starch). A lysosome(s) will
           fuse with the vacuole and hydrolytic enzymes will then mix with the food digesting it.
           In plants, some vacuoles are mainly for storing organic compounds. Others hold and/or help
           with the disposal of metabolic by-products that could be harmful were they to be in the
           cytosol. The color of flowers is the result of the pigments being stored in the petals’
           vacuoles.
           Vacuoles vary widely in size, shape, content, and function, and are considered in
           most occurrences to be true organelles of the cytoplasm.
           The structure of vacuoles is very simple. They consist of a single membrane
           surrounding the liquid or solid contents.
           There are different kind of vacuole including plant cell central vacuole, food vacuole,
           autophagic vacuole, and contractile vacuole.
                                                                                               24

            A plant cel’s central vacuole is formed from the fusion of smaller vacuoles that occur
            universally in plants. Plant cells are characteristically large and may constitute the
            greater part of the total size of the cell. The central vacuole of the plant cell may
            occupy as much as 90% of the volume of the mature cell. The large central vacuole
            may contain many diverse substances including salts, sugars, organic acids, amino
            acids, proteins, and pigments.
            The colors of many flowers and some leaves are due to pigments contained in the
            central vacuole. Plant cells central vacuole can serve as a large lysosome. The central
            vacuole may also help the plant cell grow in size by absorbing water, and it can store
            vital chemicals or waste products of cell metabolism.
            Food vacuoles are common in most protozoan and some algae. They form where the
            surface of the cell contacts a particle of food. The plasma membrane at the surface
            forms an in-pocketing to engulf the food, which is then detached from the plasma
            membrane and becomes a vacuole in the cytoplasm. Lysosome fuses with the food
            vacuoles, exposing the nutrients to hydrolytic enzymes that digest them.
            Autophagic vacuoles in needed for cell to digest portions of itself. This often happens
            in response to starvation.
            Contractile vacuoles are common in protozoan and are found in some algae.
            From experiments with fresh water algae it has been shown that the contractile
            vacuoles is essential only for the removal of excess water from the cytoplasm.
            Contractile vacuole is vital in maintaining the cells internal environment.

Study Guide Questions
       Q: What substances do large central vacuoles contain?
              A: Substances large central vacuoles contain are salts, sugars, organic acids,
              amino acids, proteins, and pigments.

        Q: Are there more than one kind of vacuole; if so what are their name?
                A: There are food vacuoles, plant cell central vacuoles, autophagic vacuoles, and
                contractile vacuoles.

        Q: What impact does the pigment substance from a central vacuole have on a plant?
               A: Pigments gives off different colors to flowers and some leaves.
Energy Producing Organelles:
There are two energy-producing organelles.
            Mitochondrion (found in all eukaryotic cells)
            Chloroplast (found in photosynthetic eukaryotic cells)

        Both are similar because they produce energy. In plants, chloroplast uses energy from
        the sun to convert molecules of carbon dioxide and water to make sugars. This process
        is called photosynthesis because its byproduct is oxygen. In animal cells mitochondria
        are the second largest organelles.


MITOC HO NDRI ON (M t ochondr a )
MITOC HO NDRI ON (Miitochondriia)
Melissa Goncalves

Places where mitochondria are found:
Mitochondria are found in animal tissues.
       An example of this is heart and skeletal muscle, which require large amounts of energy for
       mechanical work, in the pancreas, where there is biosynthesis, and in the kidney where the
       process of excretion occurs. They are the cells power source.
                                                                                              25



                                Replication of Mitochondria
                                Mitochondria replicate similarly to bacterial cells, when they get
                                llarge, they undergo fission. This involves furrowing of the inner
                                and then the outer membrane as if someone was pinching the
                                mitochondrion. The two daughter cells of the mitochondria must
                                first replicate the DNA.

                                The origin of the Mitochondria
                                The mitochondria have certain similar features that resemble those of
                                prokaryotes, which are primitive cells that lack a nucleus. Some of the
                                same features that these two have are: circular DNA, and ribosomes.
                                Also, the mitochondria divide independently of the cell through binary
                                fission, which is the method of cell division prokaryotes commonly use.
                                These similarities lead scientists to support what is called the
                                Endosymbiosis hypothesis, which states that millions of years ago,
                                prokaryotes capable of aerobic respiration were engulfed by other, larger
                                prokaryotes but not digested; it may be because they were able to resist
                                digestive enzymes. The two cells then developed a symbiotic
                                relationship the made the host provided the nutrients to carry aerobic
                                respiration, which provided the host cell with ATP. The engulfed cells
                                evolved into mitochondria, which retain the DNA and ribosomes
                                characteristic of their prokaryotic ancestors.

                                  Recent Mitochondria Research:
                                  Scientists have been using DNA in mitochondria to track genetic
                                  diseases and trace ancestry of organisms that contain eukaryotic
                                  cells. Scientists have found that in mammals, the mitochondrial
                                  DNA (mtDNA) is 99.99% inherited from the mother. This
                                  research has also show that through mitochondrial mutations,
                                  many diseases can occur, some of these diseases are:
                                  Alzheimer’s, Parkinson’s, and complete or partial blindness.
                                  However, newly found mitochondrial medicine, leads to
                                  understand the role of mitochondrial DNA mutations in these
genetic diseases. Mitochondrial research has also taken samples of different genetic samples
from people of different races to compare them and try to construct a family tree that shows
when each group probably began evolving away from one another. Also, scientists are using
mitochondrial DNA analysis in forensic science. Scientists can use this DNA to find a criminal by
matching the DNA at the scene of the crime with DNA from the suspect.

Study Guide Questions:
   1. Name one advantage of recent mitochondrial research.
   2. Where did mitochondria originate form?
   3. Where are mitochondria found?


The Mitochondria
                                                                                               26




MITOC HO NDRI ON ::
MITOC HO NDRI ON
(Michelle Nguyen)

STRUCTURE
   Structure of the mitochondrion is long and slender, or even bean-shaped, or oval through an
   electron microscope. They are anywhere from 0.5 micrometer (0.000005 in) to 1 micrometer
   (0.0001 in) long. The mitochondria have two membranes protecting it on the outside. The
   outer most layer is smooth, and also contains transport proteins that passes materials in and
   out of the mitochondrion. The outer compartment, the area between the two membranes, is
   filled with liquid. The inner membrane is call cristae. It looks like folds and are the sites of
   ATP synthesis. The structure of cristae is very important. The folds allow more surface
   area for ATP synthesis to occur. Transport proteins are molecules also known as electron
   transport chains. The enzymes that synthesize ATP are in the folds of the cristae. Within
   the cristae is a liquid filled area known as the inner compartment, or matrix. In the inner
   compartment is where the enzymes that are used in aerobic respiration.

    Q) What is the importance of cristae in the mitochondria?
       A) It is where ATP synthesis occurs. Their folded structure increases the surface area
                where ATP synthesis occurs.

FUNCTION
   The main function of the mitochondria is to make energy for cellular activity by the process
   of aerobic respiration. During aerobic respiration glucose is broken down in the cell’s
   cytoplasm to make pyruvic acid, which is transported into the mitochondrion. A sequence of
   reactions, called Krebs cycle, the pyruvic acid reacts with water to make carbon dioxide and
   ten hydrogens. The hydrogen atoms are then tranported by coenzymes to the cristae.
   There they are given to the electron transport chain (ETC). ETC separates the electron and
   proton of the hydrogens. The electrons and protons are sent through the ETC to combine
   with oxygen to make water.

    Energy is released when electrons flow from the coenzymes to the electron transport chain to
    the oxygen atoms. This energy is trapped by the ETC. As the electrons travel from one
    component to another it releases protons from the inner compartment to the outer
    compartment. The protons can only return by the enzyme ATP synthetase, which is only
    found in the inner membrane. As protons go back into the inner membrane, ATP synthesis
    adds a phosphate group to a molecule from the inner membrane, adenosine diphosphate
    (ADP). Therefore, making it into ATP.
                                                                                                 27

    Q)        What is the main function of mitochondria?
         A)     The main function of the mitochondria is to make energy for cellular activity by
                the process of aerobic respiration.


MITOCHONDRION (plural mitochondria)
(contributions by Antonio Frye)
        Is not a part of the endomembrane system.
        Measures 1 – 10 in length.
        Is the site in the cell where ATP or energy is produced. It is the site of cellular respiration (Krebs
        cycle and electron transport chain) in eukaryotic cells. Convert different food products into ATP.
        Oxidative phosphorylation: converting food into ATP and heat.
        Initial degradation of protein, carbohydrate and fat occurs in cytoplasm and yields acetyl-CoA
        Acetyl-CoA + oxaloacetate yields citric acid
        Progressive dehydrogenation drives electron transport chain, establishing a proton gradient
        Proton gradient is used by APT synthetase to produce ATP, and by thermogenin to produce heat
        Sometimes, a cell might only have one mitochondrion, but cells, such as muscle cells, that require
        large amounts of energy have great numbers of mitochondria. Muscle cells might contain
        thousands of mitochondria.
        The membranes of the mitochondrion are made—not by the ribosomes on ER—but by the free
        ribosomes floating in the cytosol and by the ribosomes within the mitochondrion itself.




CHLOROPLAST
(by Melissa Emerson)
    Found in all algae cells and in photosynthetic cells of plants.
    Is the site of photosynthesis.
    Using solar energy chloroplasts form sugar from carbon dioxide and water.
    Is not part of the endomembrane system.
    Is a member of a family of organelles called “plastids”, which are storage vacuoles.
    Chloroplasts store chlorophyll on their thylakoid membranes.
    Are lens shaped organelles measuring 2 – 5 .
    Contents are partitioned from the cytosol by an envelope made of two membranes separated by a
    narrow intermembrane space. Inside the chloroplast is another membranous system arranged into
    flattened discs called thylakoids. The fluid outside the thylakoids is called the stroma. The thylaloid
                                                                                               28

    membrane divides the interior of the chloroplast into two compartments: the tylakoid space and the
    stroma.
    Chloroplasts are mobile and move around the cell with the mitochondria and other organelles along
    tracks of the cytoskeleton.
    Are not part of the endomembrane system.




Structures outside the cell (plasma) membrane:

CELL WALL
(by Nahid Shahjafari)
       Heterotrophic protistans and animal cells lack a cell wall.
       Prokaryotes, algae, fungi and plant cells have cell walls. [Does this give you any clues as to the
       evolution of organisms from protistan amcestry?]

    Function:
       Protects the cell
               Maintains the cell’s shape
               Prevents excessive uptake of water
                                                                                                 29

        On the level of the whole plant, the strong walls of specialized cells hold the plant up against the
        force of gravity.

        Differences in the cell wall between prokaryotes and eukaryotes:
            The cell wall in most bacteria contain an unique material called peptidoglycan which is a
            polymer of modified sugars cross-linked by short polypeptides.
            The cell wall in plants is formed from cellulose, which are fibers embedded in a
            polysaccharide-protein matrix. Plant cell walls are much thicker than the plasma membrane.
            The cell wall measures between 0.1 and several microns.

        Parts to the cell wall:
           A young plant cell has primary cell wall, which is thin and flexible.
           Between primary walls of adjacent cells is the middle lamella, a thin layer of polysaccharide
           (pectins). Middle lamella glues the cells together. When the cell matures and stops growing
           it strengthens its wall by adding hardening substances into the primary wall.
           Other plant cells add a secondary cell wall between the plasma membrane and the
           primary wall. The secondary wall is strong and more rigid protecting and supporting the cell.
           It is also the primary component of wood.

        The cell wall is not part of the endomembrane system.




PILI, CILIA, FLAGELLA
(by Kari Coler)

Pili(sing.-Pilus):
        Found on some prokaryote cells.
        These long string-like appendages are attached to the outer surface of the cell.
        They allow the cell to attach itself to other surfaces or other prokaryotic cells.
        Select pili are active during conjugation by keeping the cells together for DNA transfer.

Cilia(sing.-Cilium) &
Flagella(sing.-Flagellum)
            Similarities:
                                                                                      30

    Both of these structures are used by the cell in locomotion.
    Also, they may be used to circulate fluid over an area of tissue, such as the cilia
    found on the lining of the human windpipe. These cilia move debris trapped in
    mucus from the lungs in this manner.
    Cilia and flagella are both made up of a particular arrangement of microtubules
    encased in an outgrowth of the plasma membrane.
    The microtubules are set up in a circle of nine pairs of microtubules with two,
    singular microtubules in the center. This is true for most cilia and flagella found
    in eukaryotic cells. Radial spokes reach out from the area near the center pair of
    microtubules to each of the outer pairs. In addition to the radial spokes, the
    outer pairs of microtubules have a pair of arms in between each pairs. These
    arms enable the cilia and flagella to move in a bending motion. The movement
    is made possible by a large protein molecule known as dynein. ATP provides the
    energy required by the dynein. The basal body, which has the same composition
    and structure as the centrioles, is the anchoring structure of the flagella and cilia.
    Some basal bodies turn into centrioles, such as the sperm's flagellum once it has
    entered the egg in human gametes.

Differences:
    Cells usually contain a large amount of cilia, whereas cells usually only have one
    or a small number of flagella.
    Cilia, in diameter, are approximately 0.25 micrometers and 2-20micrometers
    long. Flagella have a similar diameter but may range from 10-200 micrometers
    long.
    Movement is also different in the flagella and cilia.
    Flagella undulate and propell the cell in the same direction of its axis.
    Cilia move the cell perpendicular to it's axis using a propelling stroke followed by
    a recovery stroke.
    Movement in prokaryotic cells is usually accomplished by flagella. These flagella
    are different from eukaryotic flagella in their set up and function.
    They do not have a motor, filaments, or a plasma membrane covering of the anchor.
    They are also much thinner than the eukaryotic flagella.

				
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