PROTEINS

The third class of macromolecule.
 Composed of monomers called AMINO ACIDS
            Fig. 2.12
With only minor exceptions, all organism use the same 20 different amino  acids for their proteins, though organisms may be enriched or  impoverished in some.
  For example, cereals like maize tend to be low in lysine.

All 20 amino acids have the same molecular motif.  (Fig. fig. 2.12, diagram on p. 24).
 Carbon to which is attached a hydrogen, a carboxyl group, an amino group, and an ‘R’ group.
 R can be as simple as another hydrogen, as in glycine, but it’s usually some sort of carbon chain or ring.
  R groups can be polar, or hydrophilic. Or, they can by
   hydrophobic.

All 20 amino acids can be polymerized into POLYPEPTIDES .

The term polypeptide is often used interchangeably with the word protein.

During polymerization, a bond is made between the carboxyl group of one  amino acid and the amino group of another. This is called a PEPTIDE BOND.
 It results from another deydration reaction.

Two amino acids linked together is called a dipeptide.
 Aspartame, the artificial sweetener, is a dipeptide containing aspartic acid and phenylalanine.

The number of combinations of amino acids is incredible, since the average polypeptide contains about 100 of them.

But not all combinations occur. The proteins in an organism are encoded in it’s GENOME, i.e. by its genes.
 In other words, the order of amino acids in a protein is determined by genes. That’s how genes work, for the most part.

DNA, which comprises genes, is a master set of instructions for making specific proteins with specific functions.

There are 4 levels of protein structure.   (Fig. 2.13)
 1. Primary structure.
 2. Secondary structure
  The kinds of amino acids, and their sequence, cause the polypeptide to twist, coil, or form sheet-like structures.
        e.g. alpha helix
 3. Tertiary structure
  The R groups cause the polypeptide to further coil and fold up into complex, 3-D structures.
        GLOBULAR SHAPE.
   R groups from distant parts of the polypeptide can interact in this way.

   In particular, hydrophobic R groups interact, avoiding surrounding water molecules.
    That’s because water is charged, or polar, and these R groups aren’t.
   Also, other, polar R groups can interact. E.g. via  opposite charges on polar R groups.
       Or, 2 -SH groups of adjacent cysteines can interact to form a disulfide bond, -S-S-, that bridges adjacent parts of the folded polypeptide chain.

    If these bonds are disrupted, the 3-D structure is destroyed. Under what conditions can that happen?

The 3-D tertiary structure of polypeptides is VERY IMPORTANT.
 It determines ACTIVE SITES on enzymes, clefts or  pockets in which chemical reactions occur.
 These active sites recognize specific reacting  molecules, and bring them   in close proximity.
 Some house extra catalysts in the form of metals such  as iron, copper, zinc, molybdenum and magnesium.
    E.g. hemoglobin, chlorophyll.
 Enzymes are CATALYSTS that speed up chemical  reactions. (Fig. 2.14)

Life as we know it at commonly occurring temperatures would be impossible without enzymes, because many chemical reactions    
    would be too slow.
 Enzymes lower the temperature needed to bring reactants together.
 They do not make impossible reactions possible. They just speed up, or facilitate reactions that are energetically possible.
   E.g. nitrogenase, which fixes atmospheric nitrogen into  ammonia.  
    The industrial process for fixing nitrogen requires very high  temperatures and pressures, way beyond those in  which organisms can survive. Yet  the nitrogen fixing bacteria in the roots of legumes do the reaction just  fine, using energy from the sun supplied by their host plants in the form  of sugar, at moderate temperatures.

  4. Quaternary structure.
   Two or more polypeptides interact to form a complex.
     Also crucial in the function of many proteins.
    E.g. cytochrome oxidase.

Remember -- all these interactions are determined by the primary structure, or linear sequence of amino acids.
 This in turn is encoded by genes, or DNA.
  THOUGHT QUESTION: So, why are mutations often harmful?

Proteins have a number of functions:
 1. Structural proteins such as keratin, collagen.
 2. Enzymes -- globular proteins.
  Control virtually all of an organism’s metabolic  functions!!!

NUCLEIC ACIDS

Fourth major group of macromolecule.
 And, in the case of DNA, the largest/longest.

Monomers called NUCLEOTIDES.
 Each nucleotide is a TRIPARTITE molecule.  (Fig. 2.15)
  1. 5 carbon sugar, either ribose or deoxyribose
       -H instead of -OH at carbon 2.
  2. phosphate group.
  3. nitrogenous base.

   Five different kinds of bases.
    Adenine, A.
    Guanine, G.
    Uracil, U
    Thymine, T.
    Cytosine, C

    A and G are called PURINES.
     Double rings.
    C, T, U are called PYRIMIDINES.
     Single rings.

Both kinds of rings have nitrogen atoms

Two forms of nucleic acid.
 RNA, or ribonucleic acid -- sugar is ribose.
 DNA, or deoxyribonucleic acid -- sugar is deoxyribose.

In both cases, nucleotides polymerize by a dehydration  reaction.

ALMOST universally, DNA carries the master set of  genetic instructions.
RNA acts as an intermediate in the synthesis of proteins encoded by DNA.
 In some cases, RNA also acts as master instructions.
  Example:  HIV, influenza viruses

DNA is DOUBLE STRANDED. A twisted Double Helix.
 RNA is mostly single stranded.
  U substitutes for T in RNA.

DNA very large: Human genome has about 3 (MILLION/BILLION?) nucleotides (per single complete set of chromosomes).
          Remember: we have 46 chromosomes, in 23 PAIRS.
Each set of 23 constitutes a complete set of instructions for a human being. But, each of our cells has 2 such sets.

What do we mean by the terms 'genome' and gene? Which is larger, a genome or a gene?
    If you don't know, look it up!!