Biology

Chapter 4.2

Proteins

Definitions:

  1. AMINO ACID – small group of organic compounds with an amino group (NH2 or NH3+), carboxyl group, (COOH or COO−), hydrogen atom (H), and one or more atoms called R groups, or side chains which in most cases are bonded covalently to the same carbon atom. Each amino acid contains a central carbon atom to which four other atoms or groups of atoms that are bonded covalently.  A single hydrogen bonds at one site, a carboxyl group (COOH) bond at a second site, and an amine group (NH2) at a third site.  At a fourth site an “R” group bonds which defines the type of amino acid it becomes.  When amino acids bond together, the amino group of one amino acid attaches to the carboxyl group of the next amino acid forming a polypeptide chain.  Thus at one end of any polypeptide chain is a free amino group, and at the other end is free carboxyl group.  Bonding occurs by a condensation reaction in which a hydrogen ion (H+) from an amine group of one amino acid and the carboxyl group of another amino acid.  The exact sequence of amino acids (also called the protein's primary structure) is determined by the nucleotide sequence of the accompanying nucleic acids and characterizes a certain, specifically acting protein molecule.  Amino acid sequences are written from N- to C-terminus, the direction in which protein synthesis proceeds. 
  2. POLYPEPTIDE CHAIN – three or more amino acids bonded together in the pattern:    −N−C−C−N−C−C−N−C−C−N−C−C−

      They are formed between the amino group (NH3+) of one amino acid and the carboxyl group 

      (COO−) of another amino acid.  Amino acid sequences are written from N- to C-terminus, 

      the direction in which protein synthesis proceeds.

  1. PEPTIDE BONDS – join amino acids one after another.  They are formed between the amino group (NH3+) of one amino acid and the carboxyl group (COO−) of another amino acid.
  2. DIPEPTIDE - two amino acids bonded together.  They are formed between the amino group (NH3+) of one amino acid and the carboxyl group (COO−) of another amino acid.
  3. ENZYMES - organic molecules that act as catalysts.  Most are proteins. Enzymes allow      substrates (substances) to come together or break apart. They act as a "key" unlocking chemical processes!  They are not broken down in reactions.   Changes in temperature, pH or other changes may hinder or stop enzymes from working.
  4. CATALYST – substances that speed up chemical reactions without being affected by the reactions themselves.  Catalysts lower the activation rate of a chemical reaction.
  5. SUBSTRATE - reactant (substance) being catalyzed (acted upon)
  6.  DENATURATION – the breaking down of the weak bonds that hold proteins together.  This changes the shape of the protein which in turn compromises the function of the protein.  A process of destruction of a protein’s higher order structure (i.e., secondary structure and above).
  7. PRIMARY STRUCTURE – first level of protein structure, DNA specified sequence or order of an amino acid along a peptide chain.  The primary structure dictates which parts of a chain will coil or bend, which in turn dictates a proteins function (enzyme, transporter, etc.)
  8. SECONDARY STRUCTURE – second level of protein structure having either sheet like regions and or coiled (helical) protein structures. Caused by hydrogen bonds.  These secondary structures are known as alpha helices and beta sheets.
  9. TERTIARY or THIRD LEVEL STRUCTURE – occurs when coils and sheets pack together in stable units called DOMAINS.
  10.  DOMAIN – a polypeptide chain or part of it that has become self-organized into structurally stable functional unit.
  11. QUATERNARY or FOURTH LEVEL STRUCTURE – a final protein consisting of two or more polypeptide chains joined together by hydrogen bonds.  The 3-dimensional structure of more than one polypeptide chain, which are intimately nestled together.
  12. GLYCOPROTEINS – proteins with attached carbohydrate groups
  13. LIPOPROTEINS - proteins with attached lipid groups
  14.  DENATURATION – the breaking down of the weak bonds that hold proteins together.  This changes the shape of the protein which in turn compromises the function of the protein.  A process of destruction of a protein’s higher order structure (i.e., secondary structure and above).
  15. N-Terminus – where the free amino group ends in a peptide chain
  16. C-Terminus – where the free carboxyl group ends in a peptide chain
  17.  AMINO GROUP – written −NH2  or structural formula     

                                                   H − N −        

                                                           |

                                                          H

       18.   Carboxyl Group – COOH or COO−

                                              −  C − OH

                                                   ||

                                                   O

AMINO ACIDS and PROTEINS

http://biology.clc.uc.edu/courses/bio104/protein.htm

http://biology.clc.uc.edu/courses/bio104/protein.htm

http://chemistry.about.com/library/weekly/blprotein.htm

PROTEIN TUTORIAL*****

http://www.mansfield.ohio-state.edu/~sabedon/biol1035.htm                              http://www.mansfield.ohio-state.edu/~sabedon/biol1035.htm - alpha_helix

Website of protein folding!

http://folding.stanford.edu/science.html

PROTEIN STRUCTURE WEB SITE:                        

http://www.chem4kids.com/files/bio_proteins.html