Introduction to Cell & Molecular Biology (BIOL121) - Dr. S.G. Saupe (ssaupe@csbsju.edu); Biology Department, College of St. Benedict/St. John's University, Collegeville, MN 56321

Biological Polymers: Proteins, Carbohydrates, Lipids & Nucleic Acids

I.  Life shows molecular uniqueness
            We've already discussed the elemental uniqueness of life (i.e., C,H,O,N).  It shouldn't be too surprising that these atoms are used to construct a set of unique molecules (groups of atoms) and compounds (molecules with atoms of different elements) that characterize living systems.  Although chemists once thought that that carbon containing molecules (organic compounds) could only be made by organisms, an idea associated with vitalism that we now know is wrong; it is true that the presence of organic molecules in the environment is a sure sign of the activity of life.  Inorganic compounds are those that lack carbon.  Although there are non-biologically synthesized organic compounds, the role of these is minor in comparison.

II.  The chemistry of life is diverse
    Organisms are comprised of a diverse series of small and large (macromolecules) organic molecules. 

III. Life is polymeric
    Many macromolecules are polymers � large molecules made from two or more repeating units (called monomers).  As an analogy, a  polymer is like a freight train with many cars.  The individual cars would represent the monomers making up the polymer.  If two monomers are joined then the resulting molecule is a dimer, if three monomers are linked, it�s called a trimer, and so on� Thus, life is modular or has a modular construction.  The advantage of polymers is that: (1) an infinite diversity of structures can be produced with a limited number of starting materials (Xⁿ where X = number of different types of monomers, X = lenght of polymer); (2) a modular construction allows for ease in recycling the monomers; when a particular polymer is no longer needed its monomers can be used to build other polymers; and (3) transport - polymers are large and not easy/possible to move around.  Thus, monomers can be readily transported to the sites where the polymers are constructed.

IV. Organic molecules have recognizable collections of atoms - Functional Groups
    Functional groups are collections of atoms that have a particular set of chemical properties.  You should memorize the major functional groups and the names given to molecules that possess them (i.e., hydroxyl group - alcohol; carbonyl - ketone or aldehyde; carboxyl - organic or carboxylic acid, methyl, sulfhydryl, phosphate). 

VI. Polymers of life
     There are four major types of macromolecules in living systems.  These macromolecules and their monomeric building blocks (when appropriate) are:

1. Polysaccharides (also called complex carbohydrates) � monosaccharides (or simple sugars);

2. Proteins � amino acids;

3. Nucleic acids � nucleotides; and

4. Lipids � The lipids are a diverse group of molecules that are characterized by being water insoluble (hydrophobic).  This group doesn't neatly fit the polymer/monomer model.  However, the triglycerides can be considered to fit the model � these are of fatty acids and glycerol. 

VII.  Macromolecules (polymers) are synthesized by a condensation reaction and dissassembled by hydrolysis
    Monomers are joined by a condensation reaction (also called dehydration synthesis, because a unit of water is removed).  Hydrolysis (literally translated, water-splitting) is the process of breaking down polymers, dimers, etc. into simpler units (monomers).  Depending on the functional groups of the monomers that are being linked, a variety of different linkages can form, but the common feature to all is that water is removed.  As we�ll learn later, these reactions all require enzymes to proceed.

VIII.  Polysaccharides
    This group is also called the carbohydrates.  The basic building block of the larger polysaccharides (complex sugars) are the monosaccharides (or simple sugars) like  glucose, fructose and galactose.  See structures in book.

 A. Monosaccharides
    A monosaccharide is defined as a polyhydroxy aldehyde or ketone.  In other words they have two or more hydroxyl (-OH) functional groups and a carbonyl (C=O) functional group that can be terminal (as in an aldehyde, such as glucose and galactose) or in the middle of the molecule (as in a ketone, such as in fructose).

    Monosaccharides mostly occur in a ring form.  The position of the hydroxyl functional groups relative to the ring is important � it determines the chemical properties of the molecule.

    Monosaccharides, such as glucose, fructose, and galactose, can exist alone.  They are involved in many important cellular activities including energy metabolism and to build polymers via a condensation/dehydration synthesis reaction.

B.  Disaccharides
    These are made of two monosaccharides.  Important disaccharides include sucrose (table sugar) = glucose + fructose; maltose (malt sugar) = (1,4) glucose + glucose; trehalose = (1,1) glucose + glucose; lactose (milk sugar) = glucose + galactose.

C.  Oligosaccharides:  
    These are sugars made of from three to several (though usually not too many) monosaccharides.

D.  Polysaccharides:
    These polymers are made from many monosaccharides and are primarily for storage and or cellular building blocks.   Some examples include: 

1. Cellulose = beta 1,4 glucan (glucose polymer).  Straight chain polymer.  Many chains hydrogen bond with one another to form strands, like fibers in a thread.  Major component of plant cell walls.  The provide structural support for the cell;

2. Starch = alpha 1,4 glucan.  There are two types distinguished by the degree of branching (amylose, amylopectin).  Main form of carbohydrate storage in plants;

3. Glycogen = glucose polymer.  Highly branched.  Storage in animals.

4. Chitin

IX. Lipids
    These are the fats, oils, waxes.  A general term for water insoluble (hydrophobic) molecules.  This is a very diverse group.  There are several types of important lipids including triglycerides, phospholipids and steroids.

A.  Triglycerides
    Made from glycerol and three fatty acids.  A fatty acid has a carboxyl functional group (a molecule with a carboxyl functional group is termed an organic acid, because the carboxyl group ionizes to a small degree.)

B.  Phospholipids
    Similar to triglycerides, excepts that one of the fatty acids is replaced with a polar group (which is hydrophilic).  Thus these molecules have a hydrophobic end and a hydrophilic end.  They can be symbolized like this:  O=, where the "O" represents the hydrophilic polar head and the "=" represents the two fatty acid tails.  These molecules are called amphiphilic because they love both oil and water (hydrophobic/hydrophilic).  

    Mayonnaise demonstration.  Mix up oil, water, yolk of an egg, which contains lecithin, a phospholipids to make an emulsion.  (Check out Gink & Go)

    Phospholipids in water will form a bilayer, or sphere (liposome). 

C.  Steroids
    See book for structure.  Important in membranes, like cholesterol which helps keep the membrane fluid.  And in hormones.

 D.  Functions of lipids
    Lipids have a variety of functions including:  (1) energy storage, (2) membrane components, (3) insulation (blubber) , (4) cushioning, (5) protective coating around cells, (6) cell surface recognition; (7) hormones, vitamins, other metabolites.


X.  Proteins

A.  General
    Made from amino acids which have an amino and a carboxyl functional group.  There are approximately 20 different kinds of amino acids that occur in proteins.  These differ by the �R� or side groups.  Some amino acids are hydrophobic, others are hydrophilic. 

     The electrical charge on an amino acid is a function of pH.  At neutral pH, both the carboxyl and amino groups are ionized.  As the pH decreases, the carboxyl group gets protonated (grabs a hydrogen ion).  As the pH increases, the amino group looses a proton.

    Proteins are formed by a condensation reaction that joins the amino group of one amino acid with the carboxyl group of another.  The resulting bond is a type of covalent bond called a peptide bond.  Thus, proteins are also called polypeptides - because they contain oodles of peptide bonds. 

B. Protein structure

1. Primary structure -  Refers to the sequence of amino acids in the protein.  Once formed, the protein immediately folds and takes on a particular 3D configuration (see below).  The shape of the protein is determined by the sequence of amino acids (the primary structure).    Let�s use pop beads to model a protein.  Imagine a string of 300 pop beads linked together.  Each bead would represent one of the 20 different kinds of amino acids.  There are an infinite number of ways we could put together the 20 different kinds of popbeads.  This sequence of popbeads (amino acids) is unique for each protein.  
    

2. Secondary structure -  Regions of the protein with regularly occuring/predictable patterns like a helix or pleated sheet.  Collagen (tendons, ligaments) and keratin (hair, hooves), two structural proteins, are rich in secondary structure.  Fibrous proteins. 
    

3. Tertiary structure -  Regions of the protein that are more or less random appearing folding of the protein.  These are globular proteins like enzymes.
   

4. Quarternary structure  - Protein comprised of two or more polypeptide chains.  e.g., hemoglobin is made up of four chains, 2 of one kind and two of another.

C.  What determines the structure of a protein?  
    Answer - the kind and sequence of amino acids in the protein  (primary structure).  What determines the primary structure?  Answer - the genes (DNA).

D.  What holds proteins in a 3D shape?

1. hydrophobic/hydrophilic interactions between the amino acids in the polypeptide.

2. hydrogen bonds.

3. disulfide bonds (between two sulfur atoms).  These are easily broken by mercury.  No wonder the Mad Hatter was "mad or crazy" - mercury was a major ingredient in the felting process of hat making..  

4. Ionic bonds.  between negatively charged carboxyl groups and positively charged amino groups.

 E.  Functions of Proteins

1. Structural (e.g., connective tissue like collagen)

2. Contractile (e.g., muscle like actin and myosin)

3. Protective (e.g., antibodies, clotting)

4. Hormonal (e.g., insulin)

5. Storage (e.g., albumin in egg, casein in milk)

6. Transport (e.g., hemoglobin)

7. Toxins

8. Catalytic (ENZYMES!!)

9. Regulators of gene activity

XI.  Nucleic Acids 
    Examples include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).  These molecules are important for storing and transmitting the genetic instructions.  Nucleic acids are built from nucleotides.  More on these in genetics section.