Physical Structure

Key concepts:
• all but one of the common amino acids have the same general structure.
• four different functional or reactive groups are attached to a central carbon atom.
• each amino acid has an amino group, a hydrogen atom, a carboxylic acid group and a variable side chain group, usually designated with a letter R.
• this R-group varies from one amino acids to the next; it can be as simple as a hydrogen atom (to give the amino acid glycine) or as complicated as a phenolic ring (to give the amino acid phenylalanine).
• some of these R-group side chains are hydrophilic, and some are hydrophobic.

Polypeptides and the Peptide bond

Key concepts:
• when joining two amino acids together cells carry out a chemical reaction between the amine group of one amino acid and the carboxylic acid group of the second amino acid.
• as the chemical reaction takes place the nitrogen atom of the amine group is covalently linked directly to the carbon atom of the carboxylic acid group.
• a molecule of water is eliminated during this reaction which is called a condensation reaction or a dehydration synthesis.
• the four atoms, nitrogen, hydrogen, carbon and oxygen that link the two amino acids together is called a peptide bond.
• two amino acids linked together in his way is called a dipeptide and a long chain of amino acids is called a polypeptide.

  Polypeptides and Amino acid sequences

  If there are 20 different common amino acids, and any one of them could appear in any position, then a small polypeptide with only 8 amino acids along its length could potentially have 20 x 20 x 20 x 20 x 20 x 20 x 20 x 20 different possible sequences. This is a very large number (20 x 20 x 20 x 20 x 20 is already 3.2 million!).
  
  Key concepts:
  • polypeptides are heteropolymers.
  • the number of possible sequences of amino acids in even the smallest polypeptide is very large.
  • for polypeptides of 200 - 500 amino acids in length (a common range for many proteins) the possible sequences are in the millions of millions.
  • not all of these possible sequences are used by cells (just like not all combinations of letters make words in a language), but the diversity of polypeptide sequences is an important factor in their role and properties within a cell.
  • human cells may contain as many as 40,000 to 60,000 different polypeptides, each with its own unique sequence.
  • it is vital to the functioning of these macromolecules that the sequence of amino acids be exactly correct. As little as one mistake (one amino acid in the wrong place) can be fatal for the cell and for the organism.

  Structure of Proteins

  When dissolved in water, polypeptides take up unique shapes. Several levels of structure can be observed in a completely folded protein.
  
  Key concepts:
  • the linear sequence of amino acids along the polypeptide chain is the primary structure
  • amino acid R-groups along polypeptide chains interact with one another to produce regular and predictable shapes; alpha helix (a coil), beta pleated sheet (a saw tooth, or zigzag pattern), and a random walk or coil (which has no repeating pattern). This regular folding patterns are called secondary structure.
  • parts of the polypeptide chains and their amino acid R-groups also interact with the surrounding water and environment. These forces bend and twist and shape the molecule into a more complex three dimensional shapes.
  • hydrophilic R-groups interact strongly with the surrounding water and help keep the protein soluble and in suspension in the liquid.
  • hydrophobic R-groups are most often found buried deep within the final protein where there is less chance of them coming in contact with water molecules and destabilizing the protein.
  • the final shape take up at this level is called the tertiary structure
  • some proteins are complexes of several subunits and additional non-protein additions; this is the quaternary level of structure.

  Role of Proteins

  Proteins are the most versatile class of biopolymers. They play an enormous variety of roles within cells and living organisms.
  
  Key concepts:
  • structural; in the membranes of cells and in the extracelluar proteins such as collagen, proteins play a major role in keeping an organism in shape.
  • poisonous; many organisms from common garden plants to exotic snakes produce protein cocktails that are deadly to other organisms. These poisons are used to disable and kill prey, or to defend and protect the producer.
  • protective; organisms such as humans produce classes of proteins which are used to protect themselves against invasion by viruses, bacteria or other harmful agents; these are antibodies.
  • messengers; hormones, which help get messages around the body and coordinate metabolic activities are often proteins.
  • specialists; specially built proteins carry out an amazing array of unique functions such as the ability of muscles to contract.
  • chemical regulators; enzymes are proteins that regulate the rate of chemical reactions.

  Nucleic Acids I: the Nucleotides

  Nucleic acid monomers are the most complex. Chains of these monomers, the polynucleotides function as information storage, distribution and transmission agents for almost all living things.
  
  Key concepts:
  • the nucleotide is the monomer for both major classes of polynucleotide.
  • a nucleotide consists of a 5-carbon sugar, a phosphate group and a nitrogenous base (a complicated chemical group of one or two linked rings of carbon and nitrogen)
  • two different sugars, ribose and deoxyribose, are used in the two major classes of nucleotide.
  • five common nitrogenous bases, adenine, guanine, cytosine, thymine and uracil are components of nucleotides.
  • in theory therefore there could be ten different nucleotides, but nature only uses eight of the possible ten.

  Nucleic Acids II: RNA

  Nucleotides are joined together by forming covalent bonds between the phosphate group on one nucleotide and the sugar molecule of the second nucleotide.
  
  Key concepts:
  • nucleotides built around the ribose sugar are used in this molecule.
  • this molecule is called ribonucleic acid or RNA.
  • the four nitrogenous bases used in RNA are, adenine, guanine, cytosine and uracil.
  • the RNA molecule is a single chain of linked ribonucleotide bases.

  Nucleic Acids III: DNA

  DNA molecules are amongst the largest of the macromolecules. Two polynucleotide chains twist around one another in a double helix. This molecule plays a vital role in information storage and use.
  
  Key concepts:
  • nucleotides built around the deoxyribose sugar are used in this molecule.
  • this molecule is called deoxyribonucleic acid or DNA.
  • the four nitrogenous bases used in DNA are, adenine, guanine, cytosine and thymine.
  • two parallel chains of linked deoxyribonucleic acids twist around one another in a double helix.
  • the nitrogenous bases extend into the center of the helix.
  • a base from one strand pairs with a base on the opposite strand.
  • an adenine base always pairs with a thymine base, and a guanine base always pairs with a cytosine base; often represented as A:T and G:C.

  Roles of the Nucleic Acids

  DNA and RNA molecules are involved in biological information storage and utilization in cells and living organisms. Genetic messages are stored as a linear sequences of bases in the DNA molecules which are then copied into equivalent sequences as RNA molecules. These RNA molecules then carry the information to the parts of a cell where the translation and interpretation of the message takes place. DNA is also the molecule which is inherited from one cell to the next and from one generation to the next.
  
  Key concepts:
  • genetic information is stored as a sequence of nucleotides (as their bases) along a length of a polynucleotide molecule.
  • in most organisms the information is stored in and on DNA molecules, but certain viruses, such as the HIV virus, use RNA for this purpose.
  • every generation these DNA molecules are accurately copied and copies of the information they contain are passed along to the next generation.
  • cells pass on information this way during cell division.
  • sexual reproduction involves the copying and transmitting of DNA molecules from two parents into the next generation.
  • when needed, information is copied from the DNA molecule into the form of an RNA molecule, which is then used for the next stage. DNA is never used directly for this purpose.
  • RNA molecules carry the messages from the DNA to the next stage in the translation and use of this information.

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  Test Yourself with Quick Check Number PS-3025
  Lecture Notes - Part 1	Lecture Notes - Part 2
  Physical Structure

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  Science at a Distance
  © 1997, 1998, 1999, 2000, Professor John Blamire