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Biological Molecules

Biology brings Chemistry to Life. Organic chemistry is the chemistry of carbon-based molecules. Part of the backbone or skeletal structure of Organic molecules is made of one or more carbon atoms. The application of chemical systems, structures, and processes to living systems is known as Biochemistry.

Some Useful Generalizations

Simple molecules linked together in various ways produce large molecules called MACROMOLECULES. In some cases, the formation of macromolecules consists of the production of long chains or POLYMERS; the simple molecules are the links of the chain or MONOMERS.

Fatty Acids and GlycerolSimple and Complex Lipids
Amino AcidsProteins
NucleotidesNucleic Acids

The PROCESS of joining simple molecules (monomers) into larger ones is called DEHYDRATION SYNTHESIS or CONDENSATION, whereby the equivalent of a water molecule is removed at each bonding site. In living organisms enzymes catalyze these reactions. The PROCESS of breaking MACROMOLECULES (polymers) into their constituent parts is known as HYDROLYSIS and takes place within the watery medium of the cytosol with the water supplying the H and OH molecules to the simple compounds. Once again, different enzymes catalyze these reactions in living systems.

Most organic molecules in living organisms have 4 broad functions
  1. some are essential to cellular and body structure
  2. some serve primarily as energy-rich fuels in cellular respiration
  3. some convey information controlling growth, differentiation, and biological specificity from one generation to another
  4. some operate primarily as catalytic agents in the cell's and body's chemical processes

Since there are hundreds of thousands of molecules in existence and there are only a hundred odd kinds of atoms from which they can be constructed, it follows that the uniqueness of the molecule must depend upon the:

number, type, and spatial arrangement of the atoms


Heterotrophic Metabolism involves both a catabolic (hydrolytic) phase and an anabolic (synthesis) phase. Reduced organic molecules are broken into smaller fragments and at the same time they are oxidized to obtain and ultimately store energy. In biosynthesis, small molecules are built up and atoms rearranged to make the monomeric units required by the cell (amino acids, fatty acids, nucleotides). Materials moving through a metabolic or biochemical pathway are called METABOLITES.

I.CARBOHYDRATES serve as structural components and energy reserves for the cell. They contain carbon, hydrogen, and oxygen. The hydrogen and oxygen are always in the same ratio as in water (2:1). The type of bond typical of carbohydrates is called a GLYCOSIDE BOND and is formed by removal of water at the bonding site. A bond formed by removal of water is called an ANHYDRO BOND. Thus GLYCOSIDE BONDS are ANHYDRO BONDS of carbohydrates. (Whenever you see the prefix GLYCO-, they are talking about sugars, e.g. glycoproteins refers to the addition of sugars to a protein)

  1. The basic building blocks of carbohydrates are the simple sugars or MONOSACCHARIDES. These monosaccharide monomers can be linked into two unit DISACCHARIDES or double sugars or into larger units known as POLYSACCHARIDES.

  2. The most important carbohydrate monomers are GLUCOSE, FRUCTOSE, and GALACTOSE. These have a common formula, C6H12O6, but different structural arrangements. The different structural arrangements cause the molecules to have different characteristics. When molecules have the same formula but are arranged differently they are called ISOMERS.

  3. Common disaccharides are SUCROSE which is table sugar, LACTOSE which is the sugar in milk, and MALTOSE which is used in brewing. Sucrose is made of glucose and fructose; Lactose is made of glucose and galactose, and Maltose is made of glucose plus glucose.

  4. Starch, glycogen, cellulose, chitin and agar are all examples of common polysaccharides. They differ primarily in the three-dimensional pattern is which the monomers are bonded to each other. They may be coiled or branched.

  5. Phosphorylation - Many sugars can react in biochemical processes, such as cellular respiration, only when phosphorylated -- that is, a phosphate group is added. (H2PO3) has replaced one or two of the -H in the sugar molecule).

II. LIPIDS include a variety of molecules that can serve as energy storage molecules or as building blocks of cells. They consist of hydrogen, carbon, and oxygen, are nonpolar molecules and thus are not soluble in water but are soluble in alcohol, benzene, or chloroform. They are usually solid in warm blooded animals and oils in cold blooded animals. The ANHYDRO BOND of lipids is known as an ESTER BOND.

    1. Each molecule contains a GLYCEROL molecule bonded to THREE (3) FATTY ACIDS (thus there are three bonding sites and the equivalent of three molecules of water are removed upon their bonding together)
    2. Because C-C and C-H bonds contain more energy than the C-O bonds common in carbohydrates, triglycerides have more bond energy than carbohydrates

  2. WAXES have long-chain fatty acids combined with long-chain alcohols rather than glycerol

  3. PHOSPHOLIPIDS are like lipids but have a phosphate group in place of one of the fatty acid chains, making the molecule hydrophilic. They are components of cell membranes

  4. STEROIDS are made of four interconnected rings of carbon atoms. They can pass through the hydrophobic molecules that make up cell membranes. Many are involved in the regulation of metabolism. They include such compounds as the MALE AND FEMALE SEX HORMONES (testosterone and estrogen), hormone groups from the outer portion (CORTEX) of the ADRENAL GLAND, CHOLESTEROL, and VITAMIN D. Cholesterol, while famous for clogging arteries, is essential for maintaining the integrity of animal cell membranes. It is converted by UV radiation into Vitamin D in our skin cells.
    (See also:( Lipid Derivatives of Biological Importance)

III. PROTEINS come in a wide variety of forms. Structural proteins contribute to the growth, repair, and replacement of cells and enzymes catalyze cellular chemical reactions. They consist of hydrogen, carbon, oxygen, nitrogen and sometimes sulfur.

  1. Proteins are long chains of AMINO ACID subunits (monomers) folded into characteristic three-dimensional shapes.
    1. There are about 20 amino acids commonly found in different types of eukaryotic cells although thousands of amino acids exist in nature. Some particularly unique ones are found in the prokaryotic bacteria and archaea.
    2. Amino acids are covalently joined by ANHYDRO BONDS KNOWN as PEPTIDE BONDS. An amino acid is an organic acid in which the amino group (-NH2) has been substituted for a -H attached to a carbon atom other than the one to which the carboxyl (organic acid) group (-COOH) is attached.Two amino acids join to form a DIPEPTIDE; long chains are called POLYPEPTIDES or PROTEINS. Proteins have sometimes been called "polypeptides with a purpose."

  2. Proteins have complex shapes based on four levels of structure.
    1. A protein's unique linear sequence of amino acids is its PRIMARY STRUCTURE. This sequence of amino acids is genetically determined. The substitution of one amino acid in a sequence results in an entirely different kind of protein. The classic example is SICKLE CELL ANEMIA where the substitution of GLUTAMIC ACID to VALINE is the difference between normal hemoglobin and sickle cell hemoglobin.
    2. A protein chain will assume a folding pattern, the SECONDARY STRUCTURE, that allows the maximum number of hydrogen bonds between amino acids.
      1. An ALPHA-HELIX occurs in proteins such as myoglobin.
      2. In BETA-PLEATED SHEETS, polypeptide chains lying side by side form accordion-like sheets.
    3. The TERTIARY STRUCTURE is determined by the interaction of the amino acid's side groups with their environment, generating the 3-dimensional shape of the protein molecule. The polypeptide continues to coil and fold over onto itself which provides a unique structure important in globular proteins such as enzymes and egg white (albumin). These folded areas may be held together by disulfide linkages. Sometimes other molecules or ions, known as chaperones, aid the protein in achieving its final structure.
      1. Antibodies and enzymes are important globular proteins. Egg white (albumin) is also globular.
      2. Collagen, actin, myosin, and keratin are examples of fibrous proteins.

    4. QUATERNARY STRUCTURE is based on two or more folded polypeptide chains that fit together. The most common example is hemoglobin.

The irreversible destruction of the primary level of protein organization, i.e. the breaking of the bonds joining the amino acids is known as DENATURATION. Removal of amino groups from an amino acid is called DEAMINATION.


Proteins fall into several major categories on the basis of functional activity. (See also: Classification Scheme of Proteins...)
Two of the most common are:

  1. Structural Proteins - used for growth, repair and replacement they are the major structural components of most living tissues; often they are found in combination with other molecules - such combinational proteins are known as CONJUGATED PROTEINS. Some examples include:
    1. nucleoproteins - proteins + nucleic acids
    2. glycoproteins - proteins + oligosaccharides
    3. lipoproteins - proteins + lipids
    4. chromoproteins - proteins + colored pigments

  2. Catalytic Proteins - primarily ENZYMES which serve as ORGANIC CATALYSTS affecting the rate of biochemical reactions without being used up in the process; they normally speed up reactions which are already thermo- dynamically possible and allow them to proceed at a rate which makes life, as we understand it, possible. ENZYMES normally operate by reducing the ACTIVATION ENERGY required to start reactions and thus reducing the thermal energy (high temperature) which would otherwise be needed but detrimental to living systems. In general enzymes function by providing a convenient surface for bringing together the reactants and then becoming separated from them.

    See Unit 4 for additional information about enzymes.

IV. NUCLEIC ACIDS are information-carrying molecules energy-carrying molecules. They are the largest of the biomolecules. An extensive look at the role of the nucleic acids as well as their history

  1. Nucleic acids are made of monomers called NUCLEOTIDES. Nucleotides consist of: a 5 carbon sugar, phosphoric acid (phosphate group), and one of 5 different nitrogenous bases. The phosphate is bonded to a sugar bonded to a Nitrogen base.

  2. DNA is a double stranded helix, RNA a single-stranded molecule.
    1. DNA contains deoxyribose sugar, phosphoric acid groups, and Adenine, Thymine, Guanine, & Cytosine. The strands of the double helix are COMPLEMENTARY to each other. Adenine is always bonded to Thymine and Guanine is always bonded to Cytosine. Thus the pairing of the nitrogen bases is key to the structure and the characteristics of the molecule.
    2. Specific segments of DNA represent coded information called GENES. Each gene codes for a type of protein (structural, catalytic, etc.). Each protein is responsible for certain characteristics of the organism. THUS THE SEQUENCE OF NITROGEN BASES IN THE DNA MOLECULE REPRESENTS THE CODE OF LIFE.
    3. DNA is capable of self-replication and thus is the root of reproduction at all levels. It is also capable of being mutated and thus represents a means for change in the genetic code and thus in the characteristics of an organism or the type of organism itself. Such mutations represent some of the raw material of evolution.
    4. RNA contains ribose sugar, phosphoric acid, and Adenine, Guanine, Cytosine or Uracil. Uracil replaces Thymine in RNA molecules.
    5. There are 3 types of RNA molecules. All are single stranded, although some are twisted or folded rather than straight. All 3 types are produced based on information provided in the structure of the DNA.
      1. mRNA - messenger RNA
      2. tRNA - transfer RNA
      3. rRNA - ribosomal RNA
    6. RNA's carry out the instructions set forth by the DNA molecules in the production of proteins. DNA provides, in the structure of RNA, instructions for production of ribosomes (the molecular workbenches upon which proteins are produced) as well as information on producing the primary structure of a protein. Thus, RNA is directly involved in protein synthesis.
    7. The enzymes used in the construction of nucleic acids are called POLYMERASES - DNA polymerase or RNA polymerase

  3. DNA and RNA are both composed of four different kinds of bases, so the number of symbols in the genetic code is four. Since the efficiency of a communication system is inversely proportional to the number of symbols used in the code, DNA and RNA represent a highly efficient means of communication.

  4. Nucleotides may function as (a) energy carriers, (b) coenzymes, or (c) components of genetic systems. ADENOSINE PHOSPHATES are not polymers. This class includes ATP and GTP, the universal energy molecules and cAMP, which carries chemical signals. ADP and NAD are also in this group.

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