BASICS ABOUT PLASTICS

Natural vs Synthetic Polymers

Attributed to St. Lawrence's College

Proteins

• Protein Data Bank
  A worldwide repository on the 3D structures of large biological molecules (proteins, nucleic acids, etc.). Searchable for sequence, structure, and function from sets derived from X-ray crystallography, NMR, electron microscopy, and more.
• ExPASy Proteomics Server
  A collection of several protein sequence and structure databases, assembled by the Swiss Institute of Bioinformatics.
• Biological Macromolecule Crystallization Database
  The Biological Macromolecule Crystallization Database (BMCD) contains crystal data and the crystallization conditions, which have been compiled from literature. The current version of the BMCD includes 3547 crystal entries from 2526 biological macromolecules for which diffraction quality crystals have been obtained. These include proteins, protein:protein complexes, nucleic acid, nucleic acid:nucleic acid complexes, protein:nucleic acid complexes, and viruses.
• National Center for Biotechnology Information
  The premier center in the United States for molecular biology databases.
• European Bioinformatics Institute Services
  This site has a large collection of links to databases (most free on the Web) and software packages useful for nucleic acid and protein researchers.

A repository of nucleic acid crystal structure data, the NDB currently contains over 7100 structures.

A product of the Research Collaboratory for Structural Infomatics, the PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. The online PDB archive is a repository for the coordinates and related information for more than 97,000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques.

The PDB requires Java and JMol for structure viewing.

A macromolecule is any very large molecule, usually with a diameter ranging from about 1-1000 nanometers.

There are two types: Natural and synthetic. Plastic, resins and many synthetic fibres (e.g. nylon and cotton), rubbers and the biollogically important carbohydrates, proteins and nucleic acids, are among many substances that are made up of macromolecular units.

All of these macromolecules have significance in the modern world as their chemical structure significantly effects their properties and therefore uses/functions.

Above: Structure of rubber

Attributed to St. Lawrence's College

Organic molecules - contain Carbon atoms. They are found in all living things. The simplest organic molecules are Hydrocarbons - consist of only carbon and hydrogen.

	Prefix		       Suffix

Meth -     1 carbon atom     - ane    No double bonds
Eth -      2 carbon atoms									    
Prop -     3 carbon atoms    - ene    At least 1 double bond
But -      4 carbon atoms
Pent -     5 carbon atoms      
Hex -      6 carbon atoms

Isomers
Isomers are compounds with the same molecular formula, but different structural formulas.
a) Structural isomers - vary in the arrangement of their atoms
b) Geometric isomers - differ around the atoms in a double bond
c) Enantiomers - are molecules that are mirror-images of each other

Different isomers have different effects on the body eg Ibuprofen, Prozac, Thalidomide

Functional groups
Chemical properties of molecules depend on their functional groups (atoms on the outside of the molecule ).

Functional   Structure	  Example      Comments
  group  

Hydroxyl     - OH           Sugars       Dissolve in water
Carboxyl     - COOH         Fatty acids  Are acid
Amino        - NH2          Proteins     Are basic ( alkali)
Phosphate    - PO4          DNA          Dissolve  & are acid

Macromolecules : very large molecules, made of hundreds, or thousands, of atoms. Most are polymers : large molecules made of similar, small monomers joined together

Hydrolysis : a chemical reaction that breaks polymers into monomers eg digestion
Condensation synthesis : a chemical reaction that joins monomers together by removing water.

There are 4 types of macromolecule in living things : carbohydrates, lipids, proteins and nucleic acids.

1). Carbohydrates
Carbohydrates contain only C , H and O. They are made of simple sugars called monosaccharides such as glucose (C₆H₁₂O₆) and glyceraldehyde (C₃H₆O₃). Monosaccharides dissolve in water.

Disaccharides consist of 2 monosaccharides joined by condensation synthesis such as maltose or brewing sugar (2 glucose) and sucrose or table sugar (glucose + fructose . Monosaccharides and some disaccharides react with Benedicts reagent.

Polysaccharides are made of many monosaccharides, such as :

• starch (energy storage in plants).
  • glycogen (energy storage in animals).
    • cellulose (cell walls in plants).
      • chitin (hard outer layer of insects).
      2). Lipids
      Lipids contain C , H , and O. They do not dissolve in water. Lipids can be fats, phospholipids , waxes or steroids.
      
      A) Fats (triglycerides)
      They are made of glycerol and 3 fatty acids. Fats are used for energy storage and insulation.
      
      Saturated fats : no double bonds (only single bonds); straight molecules; solids; found in animals; eg butter.
      Eating a lot of saturated fat increases your risk of heart attack.
      
      Unsaturated fats : have 1 or more double bonds; bent molecules; liquids; in plants; eg corn oil.
      Unsaturated fats are more healthy for you than saturated.
      
      Some foods, like margarine, cookies and snack foods are hydrogenated (have hydrogen added to them) to make them more solid. This produces trans fat which is as bad for you as saturated fat. Since January 2006, food labels have been required to list any trans fat in the food.

      B) Phospholipids
      Phospholipids are made of glycerol, 2 fatty acids and phosphate. Part of the molecule is hydrophobic, part is hydrophilic.
      Phospholipids make up most of the cell membrane.
      
      C) Waxes
      Waxes consist of a fatty acid joined to an alcohol.They are used for waterproofing in plants (and some animals).
      
      D) Steroids
      Steroids are made of 4 rings of carbon. They form sex hormones eg estrogen, testosterone. Animals often need small amounts in their diet eg cholesterol. Drugs in world athletics. High levels of steroids can damage the brain.
      
      3). Proteins
      Proteins contain C , H , O and N. They are made of amino acids joined together with a peptide bond. There are 20 different amino acids (do not learn the names). The order of amino acids in a protein is important (see sickle cell anemia below).
      Primary structure : the order of amino acids
      Secondary structure : the protein folds, and is held by hydrogen bonds
      Tertiary structure : covalent or ionic bonds between different side chains of the protein.
      Sickle cell anemia : an often fatal genetic disease caused by one amino acid in the wrong place in the protein hemoglobin.
      
      Proteins are unusual because their shape is mainly affected by hydrogen bonds which are weak. This means that if a protein is heated it denatures : the shape changes. For example if you boil an egg (which contains lots of protein) it changes from a raw egg to a cooked egg because the proteins are denatured. This denaturing will usually kill a cell. Proteins are found in cell membranes, blood, hair, enzymes and muscles.
      
      4). Nucleic acids
      Nucleic acids contain C , H , O , N and P. They are made of nucleotides, (phosphate, sugar and base)
      
      DNA (Deoxyribonucleic acid) DNA has deoxyribose as the sugar. It has 4 bases :

       

      	Adenine		Thymine	
      	Guanine		Cytosine

      DNA bases pair up and join with hydrogen bonds to form a double helix. The code on DNA carries information the cell needs to make proteins (the primary structure).
      DNA can be used in vaccines. Closely related animals have similar DNA. Humans and primates.
      
      RNA (ribonucleic acid)
      RNA has ribose as the sugar. It also has 4 bases : with Uracil instead of Thymine.
      
      RNA is a single strand. RNA moves from the nucleus of the cell to the cytoplasm to allow the cell to make proteins (mRNA : messenger RNA). New RNA drugs could be very useful, for example to prevent blood clots, or treat cancer.
      
      Last edited August 2014, by David Byres, David.Byres@fscj.edu