Biochemistry: Aims to explain biological form and function in chemical terms. Mineral world
chemically simple, plant and animal worlds chemically complex, composed of compounds rich in
the elements carbon, oxygen, nitrogen, and phosphorus, which make up more than 99% of the
mass of most cells.
Biochemical Universality: Observed universality of chemical intermediates and
Biomolecules: Compounds of Carbon with a variety of functional groups.
Carbon: Chemistry of living organisms is organized around carbon, which accounts for more
than half the dry weight of cells.
Geometry of Carbon Bonding: Carbon atoms have a characteristic tetrahedral arrangement of
their four single bonds with bond angles of 109.5 degrees. C-C single bonds have free rotation,
while double bonds are shorter and do not allow free rotation.
Versatility of Carbon Bonding: Carbon can form single bonds with hydrogen atoms, and both
single and double bonds with oxygen and nitrogen atoms. Carbon can form very stable single
bonds with four other carbon atoms, and two carbon atoms can share two (or three) electron
pairs, thus forming double (or triple) bonds.
Common Functional Groups of Biomolecules: Gray for C (methyl, ethyl, phenyl), Red for O
(aldehyde carbonyl, ketone carbonyl, carboxyl, hydroxyl, enol, ether, ester, acetyl, anhydride),
Blue for N (amino, amido, imine, N-substituted imine, guanidinium, imidazole), Yellow for S
(sulfhydryl, disulfide, thioester), and Orange for P (phosphoryl, phosphoanhydride, mixed
Small Molecules: Act as building blocks for macromolecules and can include sugars, amino
acids, nucleotides, carboxylic acid derivatives.
Secondary Metabolites: Small molecules that play roles specific to plant life. These
metabolites include compounds that give plants their characteristic scents and colors, and
compounds such as morphine, quinine, nicotine, and caffeine that are valued for their
physiological effects on humans but used for other purposes by plants.
Metabolome: The entire collection of small molecules in a given cell under a specific set of
Metabolomics: The systematic characterization of the metabolome under very specific
conditions (such as following administration of a drug or a biological signal such as insulin). ~~~~~~
Macromolecules: Proteins (chains of amino acids), Polysaccharides (chains of simple sugars),
Nucleic Acids (chains of nucleotides), polymers with molecular weights above ~5,000 that are
assembled from relatively simple precursors. Proteins, polysaccharides, and nucleic acids are
macromolecules with molecular weights of 500 or less.
Oligomers: Shorter polymers.
Proteins: Long polymers of amino acids. Some proteins have catalytic activity and function as
enzymes; others serve as structural elements, signal receptors, or transporters that carry
specific substances into or out of cells.
Proteome: Sum of all the proteins functioning in a given cell.
Proteonomics: The systematic characterization of this protein complement under a specific set
Nucleic Acids: DNA and RNA, are polymers of nucleotides. They store and transmit genetic
information, and some RNA molecules have structural and catalytic roles in supramolecular
(def’n: consisting of more than one molecule) complexes.
Genome: The entire sequence of a cell’s DNA (or in the case of RNA viruses, its RNA).
Genomics: The characterization of the comparative structure, function, evolution, and mapping
Polysaccharides: Polymers of simple sugars such as glucose, which have three major
functions: as energy rich fuel stores, as rigid structural components of cell walls (in plants and
bacteria), and as extracellular recognition elements that binds to proteins on other cells.
Glycome: All of a cell’s carbohydrate-containing molecules.
Lipids: Water insoluble hydrocarbon (containing only hydrogen and carbon) derivatives, which
serve as structural components of membranes, energy rich fuel stores, pigments, and
Lipidome: All of a cell’s lipid containing molecules.
Informational Macromolecules: Proteins and Nucleic acids are often referred to as this given
their information-rich subunit sequences.
Stereoisomers: Molecules with the same chemical bonds, same chemical formulas, but different arrangements. Carbon containing compounds commonly exist as stereoisomers.
Cannot be interconverted without temporarily breaking one or more covalent bonds.
Chiral Center: Term given to alpha carbon, as for every common amino acid except glycine, the
alpha carbon is bonded to four different groups: a carboxyl group, an amino group, an R group,
and a hydrogen atom (in glycine, the R group is another H atom). Because of the tetrahedral
arrangement of the bonding orbitals around the alpha-carbon atom, the four different groups can
occupy two unique spatial arrangements, and thus amino acids have two possible
stereoisomers. All molecules with a chiral center are also optically active--that is, they rotate
plane polarized light.
Absolute Configuration: The spatial arrangement of atoms of a chiral molecular entity (or
group) and its stereochemical description. These are specified by the D, L system, based on the
absolute configuration of the three carbon sugar glyceraldehyde, a convention proposed by Emil
Fischer in 1891, since an aldehyde can be readily converted to a carboxyl group via a one-step
oxidation. When presented in a form where the terminal aldehyde or carboxyl carbon is on the
top with the R-group below the chiral carbon (carbons numbered 1 to 3), L-Glyceraldhyde has
an OH to the left of its chiral carbon atom while D-Glyceraldegyde has an OH to the right of its
chiral carbon atom. Similarly, in L-amino acids, the alpha amino group is on the left, while in D-
amino acids, the alpha amino group is on the right.
Configuration: The fixed spatial arrangement of atoms. Interactions between biomolecules are
invariably stereospecific, requiring specific configurations in the interacting molecules.
Configuration is conferred by:
1. Double bonds, around which there is little or no freedom of rotation.
2. Chiral centers, around which substituent groups are arranged in a specific orientation
Geometric Isomers: Also known as cis-trans isomers, are isomers that differ in the
arrangement of their substituent group with respect to the non-rotating double bond.
Enantiomers: Stereoisomers that are mirror images of each other. When four different
substituents are bonded to a tetrahedral carbon atom, they can be arranged in two different
ways in space, yielding tw