BASIC CHEMISTRY 

I. Matter and Energy

A) Matter (anything that has mass and volume)

1) Three states of matter:

SOLIDS (definite shape, definite volume) Examples in the body include bones and teeth.

LIQUIDS (indefinite shape, definite volume) Examples in the body include blodd plasma, lymph and cerebrospinal fluid.

GASES (indefinite shape and indefinite volume) Examples in the body include air in our lungs.

B) Energy (has no mass, no volume)

1) Two classes of energy:

POTENTIAL ENERGY (stored energy or energy of position)

KINETIC ENERGY (energy of motion, initiated by a force)

2) Forms of potential and kinetic energy

Chemical Energy (a potential form of energy stored in the bonds of chemical substances) Examples in the body include storage of energy in sugar molecules, an storage of energy in ATP (adenosine triphosphate).

Mechanical Energy (a kinetic form of energy directly involved in moving matter and can be a form of energy converted from stored chemical energy) Examples in the body include the movement of our skeleton by our skeletal muscles.

Electrical Energy (a kinetic form of energy in the form of charged particles; the flow of electrons along household wiring.  Examples in the body include movement of charged particles called ions across a cell membrane.

Radiant Energy ( a kinetic form of energy also called electromagnetic energy and includes visible light, radio waves, ultraviolet waves, X rays, and gamma rays) Our body "responds" to different forms of radiant energy in our environment.  Ultraviolet light causes sunburn also stimulates our body to manufacture vitamin D. Light strikes the retina of our eyes to produce vision.  Radiant energy is also used in medical diagnosis.

II. Atoms and Molecules

A) Elements (unique substances that cannot be broken down into simpler substances by ordinary chemical means; includes 112 different elements arranged in the periodic table in Appendix D.

THE FOUR MOST COMMON ELEMENTS IN THE HUMAN BODY ARE OXYGEN, CARBON, HYDROGEN, AND NITROGEN (96.1% TABLE 2.1)

B) Atomic symbols (shorthand method for representing names of elements)

O (oxygen)   C (carbon)   H (hydrogen)    N (nitrogen)

Each "corner" of a symbol is a specified place to describe it's structure:

upper left: mass number;  lower left: atomic number;                                                     

lower right: number of atom; upper right: charge on the atom

C) Atoms (the smallest particle of an element, different for each element and gives each element their own set of physical and chemical properties.                                               1) made up of three particles: Protons (+ charged particles), Electrons (-charged particles), and Neutrons (particles with no charge).                                                         2) Planetary Model:                                                                                                    Protons and neutrons form the nucleus and form the center of atoms of atoms like the sum in our solar system.  The total number of protons and neutron is called the mass number.  The number of the protons alone is called the atomic number.

Electrons are moving negatively charged particles around the nucleus of atoms like planets around our sun (their number is equal to the number of protons in an atom giving the atom a net "zero" charge.  Chemical energy is stored within the orbits of the electrons in energy levels.

3) All elements are formed from two or more isotopes (atoms of the same element that differ in the number of neutrons).  The weighted averages of all the isotopes of each element is called the atomic weight.

4) Elements consisting of heavier isotopes are called radioisotopes.  There nuclei are unstable and they will release nuclear energy in the form of radioactivity.  Three forms of nuclear energy are releases: alpha particles (packets of two protons and two neutrons). beta particles (electron like particles), and gamma rays (high energy electromagnetic waves).  Disintegration of radioisotopes occur in time frame called a half life. 

III. Molecules and Mixtures

A) Atoms combine together to form molecules. Many molecules of the same type form a compound.  Compounds or molecules are expressed in the form of a molecular formula. The most abundant compound found in the human body is water.  The molecular formula for water is H₂O.  The atomic symbols H and O tell which elements are found in a molecule of water and the subscript ₂ gives the number  of hydrogen atoms in one atom.

B) Atoms are held together in a molecule by chemical bonds

1) Three major types of chemical bonds:

COVALENT BONDS: occurring only between nonmetals and involve a sharing of outer most valence electrons.

IONIC BONDS:  occurring between metals and nonmetals and involve a loss of valence electrons from the metal to the nonmetal resulting in the formation of a + ion (an anion), and - ions (cations).  Sodium chloride (NaCl) is an ionic compound.  When in aqueous solution Na and Cl dissociate to form Na⁺  and Cl^-  ions as do other ionic compounds. Most ionic compounds are called salts and in their dry state form crystals.

HYDROGEN BONDS: occurring between molecules containing a hydrogen atom such as water.  The water molecule is a polar molecule.  Polar molecules have one end with a slightly + charge and the other end with a slightly - charge .  In water the oxygen end (negatively charged) is attracted to the hydrogen end (positively charged) forming a hydrogen bond.  The principle behind surface tension.  All polar molecules are water soluble.  Nonpolar molecules are those which have no negative or positive ends to their molecules and are insoluble in water (oils and fats are examples).  Only covalent molecules are referred to as polar or nonpolar.  Ionic compounds are also soluble in water due to their ionic attractions to the water molecules 

C) Mixtures (composed of two or more compounds physically mixed together)

1) Three types of mixtures:

SOLUTIONS are mixtures formed between compounds in which all components of the mixture are the size of molecules (homogeneous).  The particles of a solution cannot be seen with the naked eye, do not settle out and will not scatter light.  A solution consists of a solute  (the compound in the least amount), and a solvent (a compound in the smallest amount).  The solute is said to be dissolved in the solvent.  Water is referred to as the universal solvent. 

COLLOIDS  or emulsions contain larger solute particles, but are not large enough to settle out of solution.  Particles mixed are of two different sizes (heterogeneous).  They appear milky, or translucent  and will scatter light.  They have a unique property of being able to change from a sol (fluid) state to a gel (solid) state reversably (sol-gel transformations).  Jello is a nonliving example and cytosol (the fluid within cells) is a living example.

SUSPENSIONS are heterogeneous mixtures with large visible solute which tend to settle out an scatter light more than colloids.  sand mixed in water is a nonliving example, blood is a living example in which the blood cells are suspended in plasma.

IV. Chemical Reactions

A Two types of changes can occur to matter: physical changes, and chemical changes.  Physical changes involve a change in matter in which no new substances is produced.  Chemical changes involve changes in matter in which a new substance is produced and is expressed using a chemical equation. 

B) Types of chemical equations:

1) synthesis or combination reactions (involve all anabolic activities in body cells):

A  +  B  d AB                        H + H d H₂

2) decomposition reactions (involve all catabolic activities in body cells):

A d A + B                                H₂ d H + H 

3) displacement reactions (involve both synthesis and decompostion)

Can be single displacement reactions:

AB + C d AC  +  B

or double displacement reactions:

AB + CD d AD + CB 

4) All chemical reactions result in a net absorption of energy (endergonic reactions) or a net release of energy (exergonic reactions).  Exergonic (exothermic) reactions release energy that can be harvested for other uses.

5) factors affecting the rate of chemical reactions (for chemical reactions to occur, molecules must collide with each other with enough force to overcome the repulsion of their valence electrons; any thing that will alter their force of collision will change their reaction rates):

TEMPERATURE: Increasing the temperature will speed up the movement of molecules thereby increasing the rate of chemical reactions because they are colliding with a greater force; decreasing the temperature will have just the opposite effect.

PARTICLE SIZE: The smaller the size of particles the faster the reaction rate, because smaller particles move faster than large ones.

CONCENTRATION: The greater the number of molecules in a given area, the greater the chance for a collision and an increase in reaction rate.

CATALYSTS: Chemical substances that speed up the rate of chemical reactions without being used up or being changed during the reaction.  Biological or organic catalysts are called enzymes.

V) Acids and Bases

A) Acids have a sour taste, corrode metals, and release hydrogen ions (H ⁺) when dissolved in water.  They are called proton donors, because a hydrogen ion is nothing but a proton.

example : HCl (hydrochloric acid)

                HCl d H⁺ + Cl^-

It is the concentration of protons that determine the acidity, not the anions.  A molecular formula for an acid will always have hydrogen written first.

C) Bases have a bitter taste, are slippery, and release hydroxyl ions (OH^-) in solution.  They are called proton acceptors, because they combine with hydrogen ions or protons.  

example: NaOH

 NaOH d Na⁺ + OH^- 

D) Both acids and bases are measured in units on the ph scale.  Measuring from 0 to 14, anything below a pH of 7 is an acid, anything above 7 is a base.  A pH of 7 is considered to be neutral.  The pH scale is a measurement of the relative concentration of hydrogen and hydroxide ions.

E) Neutralization reactions involve mixing an acid and a base.  The result is a neutral solution in which the same two products are always formed: salt and water.

example:     HCl + NaOH d NaCl   + H₂ O 

BIOCHEMISTRY

I) Organic compounds are classified as compounds containing carbon, and are the compounds that form living systems.  There are some exceptions.  Carbon dioxide for example contains carbon and is classified as an inorganic compound.

II) There are four groups of organic compounds that form living systems: CARBOHYDRATES, FATS, PROTEINS AND NUCLEIC ACIDS.

A) Carbohydrates:

1) include molecules commonly called sugars and starches.

2) represent 1 to 2% of a cell's mass

3) contain carbon, hydrogen, and oxygen atoms.  The hydrogen and oxygen atoms are always in the ratio of 2:1 as in water (the word carbohydrate means hydrated carbon)

example:

C₆H₁₂O₆ (glucose)    C₁₂H₂₂O₁₁ ( sucrose)

4) classified according to size and solubility:  monosaccharide (one sugar unit), disaccharide (two sugar units), and polysaccharide (3 or more sugar units). The larger the carbohydrate the less soluble in water.

a) Monosaccharides,

 are called simple sugars

contain from 3 to 5 carbon atoms arranged in a single chain or in a single ring. The carbon hydrogen and oxygen are in the ratio of 1:2:1.  Examples would include glucose (C₆ H₁₂ O₆ )  and ribose (C₅ H₁₀ O₅ ) The general formula for a monosaccharide would be C_n H_2n O_n . 

are classified according to the number of sugars they contain.  Examples include pentose (five carbon) and hexose (six carbon) sugars.  A pentose sugar deoxyribose is part of DNA, and glucose (a hexose) is blood sugar.

can be in the form of isomers which are molecules with the same molecular formula, but their atoms are arranged differently , giving them a different shape and chemical properties.  Galactose and fructose, for example are isomers of glucose. 

b) Disaccharides,

are formed when two monosaccharides are joined by a process called dehydration synthesis and become what is called are called double sugars.  An example would include the formation of sucrose (table sugar) formed from joining one glucose molecule with fructose:

2C₆ H₁₂ O₆  d   C₁₂ H₂₂ O₁₁  +  H₂ O

also include lactose (glucose + galactose) , found in milk, and maltose (glucose + glucose), also called malt sugar.

must be broken down into their single sugar units by a process called hydrolysis (digestion), by the addition of a water molecule (just the reverse of the above reaction)  They are two large to be absorbed into the bloodstream from the digestive tract as a disaccharide.

c) Polysaccharides,

are long chains of simple sugars linked together by dehydration synthesis.  Long chainlike molecules like this are called polymers.  The individual molecules forming a polymer are called monomers.

are used as storage molecules.  They are large, insoluble, and are not sweet to the taste as in the case of simple and double sugars.

include starch (a storage carbohydrate formed by plants), cellulose (a plant product forming the cell walls of plants), and glycogen ( a storage carbohydrate of animal tissues). All three are polymers of the mononer glucose and are different from each other because of the different number of glucose units forming each molecule.  We cannot digest cellulose, but it provides the bulk or fiber in out diet.  Starch must be digested by a process of hydrolysis for the body to absorb the glucose units forming them. Glycogen is stored in the skeletal muscle and in the liver in animals.

B) Lipids,

contain carbon, hydrogen and oxygen (proportion of oxygen is much lower than in carbohydrates.  Phosphorus is also an element found in more complex forms.

are insoluble in water, but are soluble in  other lipids, alcohol, and ether.

include the groups known as the neutral fats, phospholipids, steroids, and the eicosanoids. 

a) Neutral fats,

are commonly called fats (when solid at room temperature) and oils (when liquid at room temperature).

are made of two types of molecules, fatty acids (linear chains of carbon and hydrogen atoms with an organic acid group COOH, and glycerol (a sugar alcohol).

are called triglycerides because of the 3:1 ratio of fatty acids to glycerols formed together by the process of dehydration synthesis.  The three fatty acids are joined to the three alcohol groups on the glycerol molecule to form an "E" shaped molecule.

have the same glycerol molecule, but the types of fatty acids may differ producing different kinds of neutral fats.  Because of the length of the fatty acid chains, fat molecules have more hydrogen atoms than any other organic compound.  Energy is stored within the hydrogen atom, so fats contain more energy than carbohydrates, and proteins.  Fats are the body's most concentrated source of usable energy.

must be digested by the process called hydrolysis just like carbohydrates in order to be absorbed into the body from the digestive system.

can be in the form of saturated fats, in which only single bonds are found within the fatty acid chains.  The carbons are saturated or filled up with hydrogen atoms.  Saturated fats are solid at room temperature and are the least healthy type of fat in our diet.

can be in the form of unsaturated or polyunsaturated fats, in which there is one, or more double bonds in their fatty acid chains respectively.  They are liquid at room temperature and represent the more healthy types of fat in our diet.

b) Phospholipids,

are modified triglycerides with a phosphorus-containing group and two rather than three fatty acid chains.

are said to be amphipathic, because they contain a polar (water soluble) head.  Phospholipids are used by cells to form their cell membranes.

c) Steroids,

 are flat molecules made up of four interlocking hydrocarbon rings.

like neutral fats are fat soluble and contain little oxygen.

include one we know of as cholesterol which is actually a steroid alcohol more properly called a sterol.  The only source for cholesterol in our diet is animal products.  We do produce cholesterol naturally in our bodies in the liver.

It is essential for life since it helps form cell membranes, is the raw material for vitamin D, steroid hormones, and bile salts.  Too much of the "bad" cholesterol in the blood can lead to arteriosclerosis.

d) Eicosanoids,

are derived from a 20 carbon fatty acid called arachidonic acid found in all cell membranes. Most important are the prostaglandins used in blood clotting, inflammation, and labor contractions.

C) Proteins:

1) All contain carbon, oxygen, hydrogen, and nitrogen, and many also contain sulfur and phosphorus.

2) Proteins are polymers made up of smaller building blocks (monomers) called amino acids.  There are 20 different types of amino acids, and proteins can be constructed from any number and any sequence of the amino acids.  There is an infinite number of protein molecules that could exist.

3) Amino acids are joined together by a peptide bonds to form proteins in a process called dehydration synthesis like carbohydrates and fats.  Two amino acids joined together is called a dipepetide.  Three or more amino acids joined together is a called a tripeptide.  Ten or more amino acids joined together is called a polypeptide.  Polypeptides forming more than 50 amino acids are called a protein.  Proteins are broken down into amino acids by hydrolysis during digestion so that individual amino acids can be absorbed into the body. 

4) Proteins can be classified into four structural levels:

a) Primary structure is the linear sequence of amino acids forming the polypeptide chain.

b) Secondary structure occurs when amino acids twist or bend upon themselves due to the polarity or nonpolariity of their R groupings.  Two types of secondary structure include the alpha (a) helix resembling a slinky toy or the coils of a telephone cord, and the beta (b) pleated  sheet in which the primary polypeptide chains are linked side by side by hydrogen bonds to form a pleated ribbon like structure that resembles an accordion.  Polypeptide chains can fold back upon themselves and link with themselves or with different polypeptides, or both.

c) Tertiary structure is  superimposed upon the secondary structure, when alpha helical or beta pleated regions of a polypeptide chain fold upon one another to produce a compact ball-like or globular molecule.

d) Quaternary structure occurs when two or more polypeptide chains attach together to form an even more complex protein.  An example of this is hemoglobin.

5) Proteins can be classified according to their overall appearance and shape as either fibrous or globular proteins.

a) Fibrous proteins are the chief building materials of the body and are also called structural proteins.  They are strandlike, mostly exhibit secondary structure.  Collagen is the most abundant protein in the body and is a fibrous protein that exhibits quaternary structure.  Other fibrous proteins in the body include keratin, elastin and the contractile protein actin in muscle fibers.  They are all insoluble in water and very stable which are qualities they need to provide mechanical support and tensile strength to the body/s tissues

b) Globular proteins are spherical shaped proteins that have either tertiary or quaternary structure.  They are water soluble, and play crucial roles in all biological processes and are referred to as functional proteins, examples include antibodies which help provide immunity, protein based hormones which regulate growth and development, and others act as catalysts in chemical reactions and are called enzymes.  Globular proteins are very unstable as compared the the very stable fibrous proteins.  The properties of globular proteins can easily be destroyed by a process called denaturation, during which the specific three dimensional shape upon which the function of the protein is dependent  is unraveled by extreme changes in temperature, or pH.  Hydrogen bonds are very sensitive to changes in pH and temperature and  begins to break and the protein begins to unravel.  They can no longer perform their physiological roles, because their function depends upon a specific arrangement of atoms called active sites.  Active sites provide a particular shape that will fit into other molecules with which it interacts of opposite shape, or charge.  Hemoglobin becomes unable to bind and transport oxygen when the pH is too acidic because the shape of the binding site for oxygen (active site) has been destroyed.

6) Molecular chaperones or chaperonins 

a) prevent accidental, premature, or incorrect folding of polypeptide chains or their association with other polypeptides.

b) aides in the desired folding and association process and help proteins to achieve their functional three dimensional shape.

c) promote the breakdown of damaged or denatured proteins.                         

d) promote the breakdown of damaged or denatured proteins.

e) examples include heat shock proteins which accumulate in cells exposed to abnormally high temperatures and help protect cells from the destructive effects of heat.  They were later named stress proteins when they began to accumulate in response to the oxygen deprived cells of heart attack patients.  Metallochaperones aid in the transport of certain metal ions such as copper, iron, and zinc across the cell membrane helping to avoid an excess concentrations of these toxins in the extracellular fluids.  Once inside the cell they are delivered to appropriate protein receptors.

7) Enzymes,

a) are globular proteins that act as biological catalysts in that they speed up the rate of chemical reactions within living organisms (more than a millionfold), are not used up in the reaction (can be used over again), and are specific for the reaction that they catalyze.

b) can be completely protein, or consist of two parts: an apoenzyme (the protein portion), and a cofactor which in some cases is derived from a vitamin especially the B complex vitamins and is more precisely called a coenzyme, or a metallic element such as copper, or zinc.

c) are named after the type of reaction that they catalyze and end with the suffix ase.  Examples include hydrolases which add water during hydrolysis reactions, oxidases  which add oxygen.

d) can be produced in an inactive form and an active form. Digestive enzymes are a good example.  Pancreatic enzymes are produced as an inactive form in the pancreas and are not activated until they reach the small intestine (or they would digest the pancreas). Some are inactivated after they have produced their catalytic function.  An example would be the enzymes involved in blood clotting.  Your blood vessels would be full of solid blood at the injury site instead of a single clot if inactivation did not occur.

e)  lower  the activation energy needed for a reaction to occur.  ;In order for reactions to occur the speed and therefore the energy of molecules must increase to a certain point before the reaction can occur (activation energy).  Temperature is an obvious method by which this can be done, but this would also denature enzymes.  Normal activation energy would be above normal body temperature.  Enzymes are able to lower the activation energy by which reactions occur and keep it within our normal body temperature.  It is not known how they accomplish this.

f) bind to substances called substrates to form an enzyme-substrate complex at the active site of the enzyme.  Substrates are the substances that will chemically change due to the binding enzyme.  Enzymes are classified according to the substrates that they cause a change in.  Proteases for example will break down proteins into amino acids.  Without the specific active site ( vitamin or the metallic ion), the enzyme would not be able to bind with the substrate and catalyze the reaction.  Each substrate has a complimentary shape which will allow the enzyme to bind only to that specific substrate.  After the reaction the substrate changes shape, but the enzyme doesn't change and can be used over again, that is why enzymes are needed in such small amounts.  an enzyme can catalyze millions of reactions per minute.

D) Nucleic Acids,

1) are composed of carbon, oxygen, hydrogen, and phosphorous and are the largest molecules in the body.

2) are polymers consisting of monomers called nucleotides which consist of three components: a nitrogen containing base, a pentose sugar, and a phosphate group.  A nucleotide is formed when only a base and the sugar attach and is named after the nitrogenous base it contains.  When the phosphate attached it is the completed nucleotide.

3) contain five major varieties of nitrogen bases: adenine (A), guanine (G), cytosine (C) thymine (T), and uracil (U),.  Adenine and guanine are large two ring bases called purines and cytosine, thymine, and uracil are smaller single ring bases called pyrimidines.      

4) contain two classes of molecules, deoxyribonucleic acid (DNA), and ribonucleic acid (RNA).

a) DNA is found in the nucleus (control center) of the cell where it constitutes the genetic material of the cell.  Here it replicates prior to cell division to assure that the genes are passed down from one generation to another.  DNA also initiates a process called protein synthesis because it contains all the information required to produce all the proteins in the body. DNA is a double stranded polymer n the shape of a double helix.  It's nucleotides contain the sugar deoxyribose and he bases A,T,C, and G.  The two nucleotide chains are held together by hydrogen bonding between the bases.  Bonding of the bases is very specific.  A always pairs with T, and C always pairs G and each pair are referred to as complimentary bases.

b) RNA molecules are single strands of nucleotides.  RNA bases include A, G, C, and U (U replaces T found in DNA).  The sugar ribose is present in RNA instead of deoxyribose which ;is found in DNA.  RNA is involved in protein synthesis and consist of three forms known as mRNA (messenger RNA),  tRNA (transfer RNA), and rRNA (ribosomal RNA). 

5) Adenosine Triphosphate (ATP),

a) is an adenine-containing RNA nucleotide to which two additional phosphate groups have been attached ( a total of three phosphates).

b) is a molecule that carries energy (released by the breakdown of glucose in the cell) to a place where work is needed to be done in the cell.  energy is carried within the bond of the last phosphate molecule, and is released by a process called phosphorylation during which the third phosphate is released along with energy, and ADP (adenosine diphosphate is produced).  ATP is resynthesized when ADP is converted back into ATP to be used again as an energy source for the cell.  Hydrolysis and dehydration synthesis are also involved in the "ATP cycle". 

BASIC CELLULAR BIOLOGY

I) The three major parts of the cell are the plasma (cell 

membrane), the cytoplasm and the nucleus.

A) The Plasma Membrane....

a) is the outer boundary of a cell separating the intracellular fluid (fluid within the cells) with the extracellular fluid (fluid outside and between cells).

b) is very thin, (7-8 nm) and composed of a double layer of lipid molecules with protein molecules many which literally float in the fluid lipid bilayer .  The lipid bilayer is composed of mostly phospholipids with smaller amounts of cholesterol, and glycolipids. The phospholipids have an outer polar head which is charged and hydrophilic (water loving), and lie on the outer and inner surfaces of the plasma membrane. An uncharged nonpolar tail made of two fatty acid chains that are hydrophobic (water hating) are found lining up in the center of the membrane.

c) has attached sugar groups instead of phosphate groups   to some of the fatty acid tails (10%).  These are called glycolipids and they too are polar.

d) also contains cholesterol which gives the plasma membrane stability due to the plate like rings they possess.

e) contains two distinct populations of membrane protein  integral and peripheral proteins. Protein makes up about one half of the mass of the cell membrane and is responsible for it's specialized functions.  Integral proteins are embedded into the lipid bilayer, some only are partially imbedded, but most pass all the way through the membrane and are called transmembrane proteins. Transmembrane proteins are involved in transport functions. They act as channels(several clustering together to form a pore in the plasma membrane for the transport of water soluble molecules or ions can move), or carriers (carrier molecules)  by which they bind with molecules and pull them through the membrane. The integral proteins that only face the external environment are receptors for hormones, or chemical messengers (involved in signal transduction---the relay of a message to the cell interior. Peripheral proteins attach to the integral proteins or directly to the lipid bilayer. They contain a network of fibers on the cytoplasmic side only to give support to the membrane. Other functions of peripheral proteins include: acting as enzymes, the changing of cell shape during cell division, muscle cell contraction, and linking cells together. The peripheral proteins attached to the lipid bilayer on the outer layer of the plasma membrane are called glycoproteins. Each has a  branching sugar molecule that attaches to them. All of the glycoproteins along with the glycolipids together form a sugar coating over our cells called the glycocalyx.  Each glycocalyx contains different types of sugars on different cells, and is a method that one cell is able to recognize another of it's own type. Examples include sperm recognizing an ovum, cell recognition involved in the immune system.

f) Cell membranes of adjacent cells (particularly epithelial cells) are held together by membrane junctions.

There are three different types of membrane junctions:

1) Tight Junctions occur when proteins in adjacent plasma membranes fuse together forming a junction which is impermeable  to molecules that might seep through the intracellular space. An example of tight junctions are the epithelial cells lining the digestive tract. They prevent enzymes and microorganisms from leaking into the bloodstream.  

2) Desmosomes are called anchoring junctions and have a very complicated structure acting like rivets holding two adjacent cells together.  Both cells have a thickened area on the cytoplasmic side of the cell called a plaque. Thin proteins called linker proteins (cadherins)  extend from the plaque into the intercellular space and interdigitate like the teeth of a zipper. The adjacent membranes do not actually touch and are separated by the linker proteins. Thicker proteins on the cytoplasmic side of the plaque which are part of the cytoskeleton attach to the plaque and stretch across the cell's width to anchor another plaque on the opposite side of the cell.  This arrangement distributes tension within tissue and prevents it from tearing when subjected to pulling forces. Desmosomes are found in tissues which are subjected to a lot of mechanical stretching such as the skin, heart muscle, and the neck of the uterus.

3) Gap Junctions or nexus allow chemical substances to pass between adjacent cells. Adjacent cells are connected by hollow cylinders called connexons composed of transmembrane protein. The channels are water filled and allow ions, sugars, and other small molecules to pass from one cell to the next.  Gap junctions are found in human embryo tissue and allows the passage of nutrients through the tissue until the circulatory system develops and also in the heart and smooth muscle for the passage of ions  from cell to cell to synchronize electrical activity and contraction.

g) The cell membrane is said to be a selectively or differentially permeable membrane in that it will only allow certain substances to pass into and out of the cell.  There are two processes by which this can be accomplished: passive processes (transport), and active processes (transport).

1) Passive processes do not require an expenditures of energy by the cell and  include...

a) Diffusion (the tendency of molecules to move from a region of greater to lesser concentration. The rate of diffusion  is influenced by size of the molecules, and by the environmental temperature. Free diffusion of molecules can occur to a point at which a state of equilibrium is reached (when all the molecules are evenly dispersed). The plasma membrane acts as a barrier for most freely diffusing molecules.  In order for molecules to diffuse passively through the plasma membrane they must be either lipid soluble, or  small enough to pass through the membrane channels. This type of diffusion is called simple diffusion. An example is osmosis is the diffusion of solvents (usually water ) through the channels.   Another type of diffusion is called facilitated diffusion , in which a  protein carrier molecule carries them through the plasma membrane into the cytoplasm. Glucose is transported into the cell by simple diffusion and by facilitated diffusion.  Simple diffusion  of glucose is too slow to supply the energy needs of an active cell.  Most glucose is transported by facilitated diffusion which is about  a million times faster than simple diffusion.   

b) Osmosis is a very special type of passive transport. It involves the passage of a solvent such as water through a selectively permeable membrane. Water can move directly through the lipid bilayer between the hydrophobic lipid tails. They are able to to do this probably because water molecules are so small and there are gaps between the phospholipid tails as they move about.  Water can also pass through pores in the membrane called aquaporins constructed by transmembrane proteins. Osmolarity is the measure of the total concentration of all solute particles in a solution.  Osmolarity depends upon the number (not the types)  of particles of solute and solvent (water in most cases ).  If we have a greater concentration of non diffusable solutes inside of the cell, then water will diffuse into the cell and we have an increase in osmotic pressure (the back pressure of the water against the membrane  which attempts to  resist any further water entry). Osmotic imbalances cause animal cells to either swell or shrink until the solute concentration is the same on both sides of the membrane. We say that equilibrium has been reached at this time  The ability of a solution to change the tone or shape of cells by altering their internal water environment is called tonicity.  Solutions with the same concentrations of nonpenetrating solutes  are said to be isotonic.  A cell immersed in an isotonic solution retain their original shape and experience not net loss or gain in water. Solutions with a higher concentration of nonpenetrating solutes are said to be hypertonic.  Cells immersed into hypertonic solutions   experience a net loss of water and shrink. Solutions with a lower concentration of nonpenetrating solutes are said to be hypotonic.  Cells immersed into hypotonic solutions experience a net gain of water and swell up.  Cells placed into distilled water (the most extreme example of hypotonicity) will eventually lyse or burst.

2) Active Processes require an expenditure of energy by the cell to move solutes across the plasma membrane against a concentration gradient (from a region of higher to lower concentration of solutes).  Many molecules cannot move by passive means because they are too large, incapable of dissolving  in the bilipid membrane, or unable to move with their concentration gradient. There are two examples of active membrane transport: active transport and vesicular transport.

a) Active transport like facilitated diffusion requires carrier molecules that combine specifically and reversably with the transported substance. Facilitated diffusion always occurs with the concentration gradient, because it's driving force is kinetic energy. There are two types of active transport primary active transport where the energy required is supplied directly by the hydrolysis of ATP, and secondary active transport, in which the energy supplied is stored within ionic gradients created by the primary active transport pumps.   

 In primary active transport active transport protein transporters (solute pumps) move solutes in the form of ions (Na⁺, K⁺,and Ca²⁺) against a concentration gradient and must have energy in the form of ATP to accomplish this. One such system is the sodium-potassium pump and the carrier molecule is an enzyme called Na⁺  -K⁺  ATPase. The concentration of K⁺ inside the cell must always be higher (about 10 to20 times higher) than the outside and the concentration of Na⁺  must be higher on the outside of the membrane. These concentrations are necessary for muscle and nerve cells to function properly and for all cells to maintain their normal fluid volume.  Sodium and potassium ions constantly "leak" through the cell membrane along their concentration gradients, so the sodium-potassium pump works constantly to pump sodium back out of the cell and to pump potassium back in to maintain  the higher concentrations of potassium on the inside and the sodium on the outside of the plasma membrane.  The energy from the ATP is used to change the shape of the protein carrier molecule. After three sodium ions are pumped out then the carrier molecule changes shape to move  two potassium molecules into the cell.    Another example of primary transport is the calcium pump.

In secondary active transport  as sodium is pumped out of the cell against it's concentration gradient, a form of potential energy is produced outside the membrane by the extra sodium ions. So as sodium moves back into the cell be facilitated diffusion it pulls other molecules back into the cells  with it such as some sugars, amino acids, and many ions are "cotransported" in this way into the cells lining the small intestines.   

b) Vesicular transport involves the movement of very large particles and macromolecules across the plasma membrane. This type of transport also requires energy from ATP. Two examples are exocytosis and endocytosis.

Exocytosis transports large particles or macromolecules       out of the cell. Examples include: hormone secretion, neurotransmitter release, mucus secretion, and ejection of wastes. These substances are first enclosed in a membraneous sac or vesicle. The vesicle moves to the plasma membrane, fuses with it and then ruptures spilling it's contents to the outside. The vesicle becomes part of the plasma membrane, and is returned to the interior of the cell by the reverse process called endocytosis.

Endocytosis transports large particles and macromolecules  into the cell by the formation of membraneous sacs or vesicles produced by either the outfolding, or the infolding of the plasma membrane. There are three types of endocytosis: phagocytosis, bulk-phase endocytosis, and receptor -mediated endocytosis.

In phagocytosis, cytoplasmic extensions called pseudopods(false feet)  extend out from the plasma membrane and flow around large or solid material such as bacteria or cell debris and the cell engulfs the particles.  A portion of the membrane pinches off inside the cell containing the engulfed particle(s), and forms a vesicle called a phagosome. The phagosome (in most cases) will fuse with another vesicle containing digestive enzymes called a lysosome , and the particles inside of the phagosome are digested. Examples of the cells in the body which feed like this are macrophages and certain of our white blood cells. These cells are also move about through our body by a process called amoeboid movement. 

In bulk-phase endocytosis (pinocytosis), there is an infolding of the plasma membrane and a liquid  containing dissolved materials enters into a vesicle that pinches off as it did in phagocytosis.  Bulk-phase endocytosis  unlike phagocytosis occurs in most of our cells. Cells that line the small intestine absorb nutrients "nonselectively" this way. 

Receptor-mediated endocytosis is the major method of uptake of large macromolecules by body cells and is a "selective" process. Substances taken into the cell by this process include hormones, enzymes (such as insulin), LDL cholesterol, and iron. Flu viruses and diphtheria toxin use this method to enter our cells.    This type of endocytosis also involves an infolding of the plasma membrane.  On the exterior or the plasma membrane are receptors which bind only with certain substances. Lining the inside of the plasma membrane is a bristlelike clathrin protein coating which acts to deform the membrane  to form a vesicle when arriving molecules have binded with the exterior receptors.  Once inside ,the vesicle loses it's fuzzy bristlelike appearance and and fuses with  another vesicle called an endosome. Within the endosome the ingested materials detach from the receptors.  The receptors and membrane components will be recycled back to the plasma membrane, the contents of the endosome may combine with a lysosome for degradation and release as in the case of iron and cholesterol, or the endosome can be transported completely across the cell and released by exocytosis, a process called transcytosis. Transcytosis is common in endothelial cells lining blood vessels, since it is a quick way to get materials from the blood to the interstitial fluid. 

B)  THE CYTOPLASM is the cellular material between the plasma and the nucleus. It consists of three major elements:  the ctyosol, orgnelles and inclusions. 

The cytosol is the liquid portion of the cytoplasm consisting  largely of water containing dissolved proteins, salts, sugars and other solutes. It also contains some substances which are suspended but do not settle out. The cytosol has both a colloid and a solution like consistency.

Inclusions are chemical substances that are present only in certain types of cells. Examples include glycosomes , glycogen bodies stored in liver and muscle cells, lipid droplets common in fat cells, pigment  (melanin) granules in cells of the skin and hair and also crystals of various types.  

Cytoplasmic organelles are "little organs" that perform a specific function to maintain the life of the cell. Some orgnelles are called nonmembraneous organelles, which lack membrane. Examples include: ribosomes, the cytoskeleton, centrioles, and ribosomes. Most organelles are bound by a membrane just like the plasma membrane (except for the glycocalyx). These include the mitochondria, peroxisomes, lysosomes, endoplasmic reticulum, and golgi apparatus.

The mitochondria are called the power plants of the cell, providing most of the cell with it's supply of ATP. Cells that require a lot of energy such as muscle, nerve, liver cells have a lot of mitochondria.  Others like lymphocytes have only a few. Mitochondria are enclosed by two membranes with the inner membrane folding inward forming shelf like membrane folds called cristae, which protrude into the matrix which is the gel-like substance within the mitochondria. Enzymes are found within the matrix and on the cristae. Within these structures a process known as the Citric Acid Cycle or Kreb's Cycle takes place.  Food enters the cell in the form of sugar molecules known as glucose. The glucose is broken down anerobically (without oxygen) by enzymes present in the cytosol of the cytoplasm. The products of glycolysis will then enter into the mitochondria where they are further broken down for energy aerobically (in the presence of oxygen) by the citric acid cycle. During this process total process called cellular respiration a total of 38 ATP have been produced with the release of water and carbon dioxide as waste products from the mitochondria.  Mitochondria have a single circular DNA molecule and are capable of dividing  when the energy needs of the the cell increases.

Ribosomes are small dark staining granules that are found throughout the cytoplasm. They are composed of proteins and a variety of RNA called ribosomal (r RNA) RNA. Ribosomes are involved in a process called protein synthesis.  Some   ribosomes float freely and are called free ribosomes which make soluble proteins that will function in the cytosol. Others are found attached to a membraneous structure in the cytoplasm called the endoplasmic reticulum (ER).  Portions of the endoplasmic reticulum which contain ribosomes are called rough ER. Rough ER produce proteins which are incorporated into cellular membranes, or are exported out of the cell. Ribosomes can attach and detach from the ER depending upon which type of protein that is needed at the time.

Endoplasmic reticulum is a system of interconnected membraneous tubes within the cytoplasm enclosing fluid filled cavities called cisternae.  The ER is continuous with the nuclear membrane. There are two types of ER: Rough ER and smooth ER as described above.The rough ER will produce all proteins secreted out of the cells. Rough ER will be abundant in cells that secrete substances. Examples include antibody-producing plasma cells,the blood protein producing cells of the liver, and the formation of extracellular enzymes required for digestion. The rough ER is responsible for making cellular membranes. The integral proteins and the phospholipids are made here. Smooth ER lacks ribosomes and is not involved in protein synthesis.  It does have enzymes (integral proteins forming part of it's membranes), that catalyze the following reactions:                                                    1) lipid metabolism and the synthesis of cholesterol                     2) the synthesis of steroid hormones such as sex hormones                                                                                             3)the absorption, synthesis and transport of fats (in intestinal cells)                                                                                                    4) the detoxification of drugs, certain pesticides and carcinogens  (in the liver and kidneys)                                         5) the breakdown of stored glycogen to form free glucose (especially in liver cells) 

The Golgi apparatus stores protein which has been made on the rough ER.  Proteins are produced by the rough ER and carried in transport vesicles to the receiving side (convex side or the cis face) of golgi bodies.  Here they fuse with the membrane of the golgi body. Once inside the golgi body the proteins are modified.  During modification sugar groups may be added or trimmed, and in some cases phosphate groups may also be added.  Once modified, the proteins leave the receiving  side of the golgi body (concave side or trans face), in three distinct vesicles.  Secretory vesicles or granules, migrate to the plasma membrane and discharge contents by exocytosis.    Another type of vesicle released contains lipids and transmembrane proteins  which moves to and becomes part of the plasma membrane, or other membranes within the cell. Hydrolytic (digestive) enzymes are packaged within structures called lysosomes that remain in the cell.

Lysosomes produced by golgi bodies are packages of digestive enzymes which are used inside the cell. They contain enzymes called acid hydrolases because they work best in acid conditions (pH of 5). The lysosome has a membrane which contains hydrogen ion pumps that pump in hydrogen ions from the cytosol to maintain an acid pH within the lysosome. The membrane of the lysosome also acts as a barrier to separate the cell's content from the dangerous enzymes while allowing and to release the products of digestion to be used be or excrete by the cell. Lysosomal rupture of the cell can occur and a self digestion of the cell can occur called autolysis.  This can result from a damaged cell, a cell deprived of oxygen, and when excessive vitamin A is present.  Autolysis can occur from autoimmune diseases such as rheumatoid arthritis. The many functions of the lysosome include:                                                                                   1)digestion of material taken in by endocytosis especially bacteria, viruses and toxins   2) digesting worn out or nonfuctional organelles                                                                   3) breaking down glycogen stored in muscle and liver cells      4) release of thyroid hormones from storage in thyroid cells    5) breaking down nonuseful tissue such as the webs between the fingers of a developing fetus, and the uterine lining during menstruation                                                                                     6) breaking down bone to release calcium ions into the blood.

Peroxisomes are membraneous sacs of enzymes known as oxidases  which act to detoxify poisons such as alcohol and formaldehyde.  They also act to neutralize free radicals which they convert to hydrogen peroxide. Hydrogen peroxide is also poisonous to cells, and is quickly broken down into oxygen and water by the enzyme catalase.  They are predominately found in liver and kidney tissue.  They appear to be small lysosomes but are not produced by lysosomes.  They are produced by the pinching off of other preexisting peroxisomes.

The cytoskeleton of the cell consists of three types of rods in the cytosol: microtubules, microfilaments, and intermediate filaments.                                                                             Microtubules arise from a structure above the nucleus called the centrosome.  They determine the shape of the cell, as well as the proper distribution of mitochondria, lysosomes and secretory graunles.  These organelles are attached to the microtubules by way of motor proteins which move the organelles along the microtubules within the cell. They are the largest rods of the cytoskeleton and aremade of tubular subunits called tubulins.                                          Microfilaments are the thinnest of the rods in the cytoskeleton and are made of a protein called actin.  They attach to the cytoplasmic side of the cell membrane and act to strengthen and brace the cell.They also function in cell motility(cilia and flagella)  and in changes in cell shape.They interact with another protein called myosin in muscle cells to produce a shortening or contraction of a muscle cell. The also are are the parts of the cytoskeleton whcih produces the cleavage furrow that pinches a cell into two new daughter cells during mitosis.                     Intermediate filaments  are the most stable and permanent rods of the cytoskeleton and act as internal "guy wires" that resists pulling forces on the cell and also help form the desmosomes .

The centrosome  consist of a pair of barrel shaped structures called centrioles.  Each centriole consists of none triplets of microtubules arranged to form a hollow tube.  They function in organizing the mitotic spindle in cell division  and also forming the bases of cilia and flagella.

Cilia are formed from basal bodies which are produced from dividing centrioles.  The basal bodies are identical to centrioles except for the pattern of microtubules. The basal bodies line up on the free surface of the plasma membrane and tiny microtubules "sprout" out of each of them thereby applying pressure to the plasma membrane producing tiny projections. The cilia function in moving materials across the surface of the cell in contrast to flagella whose movement causes the movement of an entire cell such as a sperm cell.

C) THE NUCLEUS

a) is the control center of the cell

b) functions in initiating the process of protein synthesis, as well as passing down genetic traits by way of genes present on it's chromosomes.

c) larger than any of the cytoplasmic organelles and easily seen using a compound light microscope.

d) is bound by an outer nuclear envelope, nuclear membrane which is a double membrane similar to the mitochondrial membrane, it is continuous with the ER, and also contains pores lined with lined with proteins referred to as the pore complex, which regulate the passage of large  molecules into and out of the nucleus.

e) contains a jellylike fluid called the nucleoplasm similar to the cytosol of the cytoplasm.

f) contains dark bodies called nucleoli within the nucleoplasm which are the site of ribosome production within the cell. Nucleoli usually are very large in growing cells that are making large amounts of proteins to build tissue.

g)  also contains a substance called chromatin which appears as light and dark areas of the nucleoplasm.  Chromatin appears like "bumpy threads" and contain equal amounts of DNA, and globular histone proteins. The histones are arranged in clusters of eight to form a structure called a nucleosome, the fundamental unit of chromatin. Each nucleosome is surrounded by a winding DNA molecule.  Each segment of the DNA that connects each of the nucleosomes is called linker DNA segments. The histones function in packing the DNA molecule and helping to maintain it's characteristic helical structure and are also involved in dictating gene regulation. The histones can change shape by the addition of a phosphate, or a methyl group to expose specific genes for protein synthesis. These active chromatin segments are referred to as extended chromatin and are the light areas within the chromatin material. Also called active DNA this is where the process of protein synthesis is occurring at a certain time. The darker areas of the condensed chromatin is the area where no protein synthesis is occurring at a given time. Most active body cell nuclei contain larger amounts of extended chromatin.  All of the chromatin material will condense together prior to cell division to form short, barlike bodies called chromosomes. 

II) CELL GROWTH AND REPRODUCTION

A) The Cell Cycle  

a) consists of two major periods: interphase and the mitotic stage (cell division).

b) Interphase refers to the time period or the life of the cell between phases. Formerly called the resting stage of cell division, the cell is in contrast very active during this stage. Interphase is actually broken down into three subphases: G₁  ,S, and the  G₂ phase. During the G₁ phase the cells are actively synthesizing proteins and the cell is growing larger. The G₁ phase can last for several minutes or for several hours or days, depending upon whether the cell is a cell that typically is  a fast or a slow dividing cell.   Cells that are not actively dividing are in the G₀ stage. Most of the cells in our body remain in  interphase in this stage all of our lives. Cells that enter into the S stage, the second stage of interphase are those that will enter into  mitotic cell division ( mitosis). Such cells are only in growing regions of our body such as in our skin and bones.  During the S (synthetic) phase, DNA replicates itself, assuring that the new cells formed will have identical genes.  The final phase of interphase known as the G₂ stage is very brief.  Enzymes and other proteins that are needed for the mitotic stage are being synthesized, and by the end of G₂ the centrioles have become replicated (a process which began in G₁) .

DNA replication which occurs during the S phase of interphase consists of the following steps:

1) The DNA unwinds from the necleosome                                 2) An enzyme begins to separate the two strands at each end of the DNA molecule breaking apart and exposing the hydrogen bonds between the complimentary bases on each side of the DNA molecule.                                                                                 3) An enzyme known as DNA poymerase will then link and position matching DNA nucleotides found within the nucleoplasm.                                                                                     4) After replication histones  arrive from being produced on the ribosomes, and complete the formation of the chromosomes and condense into the chromatids of a chromosome, attached in the middle by a structure called the centomere.

CELL DIVISION

1)  is essential for body growth and tissue repair.  Cells that continually wear out such as the cells of the skin and intestinal lining reproduce almost continuously, in contrast to other body cells which retain the ability to divide if the organ is damaged.  Cells of the nervous system, skeletal muscle, and heart muscle lose their ability to divide upon maturity and repairs are made with scar tissue (a fibrous type of connective tissue).

2) The M phase of mitosis (mitotic phase) of cell division involves two events: mitosis and cytokinesis.

Mitosis consists of four phases: prophase, metaphase, anaphase, and telophase. The stages or mitosis and their descriptions are found in figure 3.30 on page 100-101.

Cytokinesis is the division of the cytoplasm  that occurs during late anaphase and is completed at the end of telophase when two identical cells are produced.  Cytokinesis  occurs when the plasma membrane is drawn inward across the center of the cell to form a cleavage furrow by the activity of a contractile ring of actin and myosin proteins.

Control of cell division 

1) All cells have to divide as they continue to grow or they would die, because the volume of the cytoplasm increases at a greater rate than the surface area of the cell membrane. As a cell grows the plasma membrane cannot transport enough glucose to maintain the larger increase in cytoplasm, so before the cell dies it divides.  This explains why all cells are microscopic.

2) Cells touching one another resist cell division because of contact inhibition.  If a cell is injured next to a healthy cell, then the healthy cell will divide to replace the damaged cell, because it isn't in physical contact with a cell next to.

3) Enzymes are also present during cell division that seem to initiate cell division known as cyclins (regulatory proteins) and Cdks (cyclin-dependent kinases).

PROTEIN SYNTHESIS consists of the following steps:

1) Transcription occurs in which a small segment of DNA produces a small segment of mRNA (messenger RNA). Messenger RNA contains a group of nitrogeneous bases whose base pairs "spell out" a message for a particular protein to be made.  Every three letters on the mRNA is called a codon and is the "message" for one of the 20 amino acids that can join together to form a polypeptide chain. The mRNA will then leave the nucleus and make it's way to the ribosome.