The Nature of the Living State

Macromolecules of Living Systems

Cellular Life

Energy Flow in Living Systems

The Instruction Set of Life

Cell Division



Cellular Life

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Structure of the Nucleus
Nuclear Membrane
Nuclear Matrix
Endoplasmic Reticulum (ER)
Mitochondria and Chloroplasts
Vacuoles and Vesicles
Flagella and Cilia
Plant Cell Structure

All living cells can be divided into one of two different types either Prokaryotes or Eukaryotes.  Prokaryotes are believed to be the more primitive form and include bacteria and certain kinds of algae.  Eukaryotes are believed to be more advanced and include the cells of the higher plants and animals.  The main difference between the two types is whether or not a cell has internal compartments.  Prokaryotes do NOT have internal compartments while eukaryotes do.  

We will focus exclusively on eukaryotes in the following material.  All cells of eukaryotes have two main regions: a nucleus separated from the rest of the cell by a special kind of membrane and the rest of the cell called the cytoplasm.  

The important structures associated with the nucleus are as follows:
(1) the nuclear membrane
(2) chromosomes
(3) nucleolus
(4) nuclear matrix
(5) nucleoplasm  

(1) As above, the nucleus is set apart from the cytoplasm by a special membrane called the nuclear membrane.  It is the only double membrane in cells.  This means that there are two membranes side by side separated by a small space making up the nuclear membrane.  In addition, the nuclear membrane is unique because there are openings called nuclear pores all over its surface.  Inside the pores are special proteins which control what can and cannot move through the pores.  The openings plus the "guard" proteins together are called nuclear pore complexes.  

(2) Chromosomes contain the genetic information of living things in the form of DNA.  The DNA and special proteins called histones form a fiber from which chromosomes are made referred to as chromatin.  The chromatin coils at many levels forming the chromosome.  

Chromsomes are only sometimes seen in cells.  This is because of what is called the Cell Cycle.  Imagine a circle which represents a 24 hour day.  Only 1-2 hours are spent in the cell actually dividing to form two new cells.  This part of the cell cycle collectively is called M Phase.  The other 22-23 hours are spent in the cell preparing to divide again and is referred to as Interphase.  During Interphase, the cell duplicates or increases all of its components so there will be enough to form two new cells.  Interphase then is a time of intense synthesis. When a cell divides, there is practically no synthesis going on.  Because of this, the chromosomes uncoil during interphase so that the DNA information will be available to make new products.  The chromosomes are not seen during this time.  When the cell is finished making new products, the chromosomes re-coil becoming visible in the cell and the cell is ready to divide.  So, chromosomes are visible in M Phase only.  

Interphase is subdivided into three sub-phases:  G1, S, and G2.  G1 follows M phase and is a transition period between the division of M phase and the synthesis that will take place during S.  As such, G1 is a period of turning on of the cell's synthetic machinery.  After the intense synthesis that takes place during S, the cell enters G2 which is a period of the turning off of the cell's synthetic machinery.  Once completed, the cell is then ready to divide during the following M phase.  

(3) The nucleolus is a dense region of the nucleus where a special kind of RNA is made.  This RNA is called ribosomal RNA or abbreviated as rRNA.  Some cells have multiple nucleoli.  Because it is a place of synthesis, the nucleolus is only present during S phase of the cell cycle.  

(4) The nuclear matrix is a network of protein fibers attached to the inner nuclear membrane and to all of the above components of the nucleus.  As such it holds the other components of the nucleus in place.  

(5) The term nucleoplasm refers to all of the "filler" material found within the bounderies of the nucleus except for the structures mentioned above.  Since the cell makes different molecules during different phases of the cell cycle, the nucleoplasm is constantly changing.  

The Cytoplasm:  

The outer boundary of all cells is called the cell membrane or plasma membrane.  It is what is referred to as a selective, semipermeable membrane.  Selective means it can choose what can and cannot cross the membrane.  The semipermeable part means that of those molecules that can cross, they will cross at different rates.  These properties arise from the fact that in the center of all cell membranes is a phospholipid bilayer (see books for details).  

There is also a network of internal membranes within the cytoplasm.  Collectively, this network is known as the endoplasmic reticulum.  This divides the cell into a number of internal compartments in which certain special functions can be located.  

Certain sections of the endoplasmic reticulum (abbreviated as ER) appear rough while other areas appear smooth.  The rough ER appears rough because another component or organelle (functional part of cells) is attached in these areas.  These additional components are called ribosomes.  The rough ER produces proteins on the ribosomes while the smooth ER functions in lipid production.  

Ribosomes are made up of proteins and that special kind of RNA called rRNA from the nucleolus section above.  That consist mostly of two parts:  a large subunit and a small subunit with a groove formed between them.  This will become important in the second half of the semester.  


All higher plant and animal cells have special organelles called mitochondria.  In addition, plant cells have chloroplasts.  Both types of organelles are related.  

Mitochondria consist of two membranes: a smooth outer membrane and a highly folded inner membrane which increases its surface area.  Chloroplasts also have a smooth outer membrane but have many internal membranes.  

Mitochondria function as the primary site of energy production in cells.  Chloroplasts are the sites of photosynthesis in plant cells where sugars are made using carbon dioxide from the air and water from the ground in combination with energy in the form of light from the sun.  

Both of these organelles have their own source of genetic information in the form of a piece of circular DNA, their own form of small ribosomes and replicate independently from the rest of the cell.  As such they resemble prokaryotes.  Because of this, it is believed that they may have been free living organisms in the distant past which became permanent in the earliest eukaryotic cells where they remain up till today.  This is the basis for the endosymbiotic theory as to their origins.  

Although the books list numerous other organelles with different names, most are simply membrane bound portions of the cytoplasm usually with special functions.  For our purposes, we will just delineate two -- vacuoles and vesicles.  Both are membrane bound areas of the cell with the main difference being size -- vacuoles are large and vesicles are small.  Both can be used for storing things in the cell apart from the rest of the cell.  Most other organelles are simply variants of these two.  


There are two additional organelles specialized for movement of some cells: flagella and cilia.  Flagella are long whip like structures which push against the environment, usually water, and the cells move in the opposite direction.  Usually cells have only a few flagella.  In contrast, cilia are short hair like structures which work in the same way but usually there are thousands of cilia per cell.  Other forms of cell movement involve development of extensions of the cytoplasm termed pseudopodia in to which the rest of the cell flows.  Such movement is referred to as amoeboid motion and is seen mostly in a type of single cell organism called the amoeba.  

Finally, there are three structure that when present characterize plant cells.  When all three are absent, most probably a cell is of animal origin.  These three structure are:  (1) a cell wall made of cellulose, (2) the presence of chloroplasts, and (3) large central vacuoles.  The cell wall is actually found exterior to the plant cell and gives the cell its shape.  The chloroplast, as above, are the sites of photosynthesis.  The central vacuole is used to store materials such as in the potato cell where starch is stored.  

But what if only one or two of the three structures above are present??  Is a cell of plant or animal origin?  The answer is that it is of neither.  There is a third general class of organisms called protists which have both animal and plant characteristics.